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Diffstat (limited to 'docs/dev/reference')
139 files changed, 6494 insertions, 7119 deletions
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href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ same dataset." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the AIC for a column of an mmkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/AIC.mmkin.R'><code>R/AIC.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/AIC.mmkin.R" class="external-link"><code>R/AIC.mmkin.R</code></a></small> <div class="hidden name"><code>AIC.mmkin.Rd</code></div> </div> @@ -149,102 +94,110 @@ same dataset." /> same dataset.</p> </div> - <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, k <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> - -<span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, containing only one -column.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - <tr> - <th>k</th> - <td><p>As in the generic method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>As in the generic method (a numeric value for single fits, or a -dataframe if there are several fits in the column).</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, k <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, containing only one +column.</p></dd> + +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> + + +<dt>k</dt> +<dd><p>As in the generic method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>As in the generic method (a numeric value for single fits, or a +dataframe if there are several fits in the column).</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># skip, as it takes > 10 s on winbuilder</span> - <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, - <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='co'># We get a warning because the FOMC model does not converge for the</span> - <span class='co'># FOCUS A dataset, as it is well described by SFO</span> - - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span> -</div><div class='output co'>#> [1] 55.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># or when extracting an mkinfit object</span> -</div><div class='output co'>#> [1] 55.28197</div><div class='input'> - <span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span> - <span class='co'># of parameters, the higher (worse) the AIC</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> SFO 3 55.28197 -#> FOMC 4 57.28222 -#> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span> -</div><div class='output co'>#> df AIC -#> SFO 3 49.28197 -#> FOMC 4 49.28222 -#> DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span> -</div><div class='output co'>#> df BIC -#> SFO 3 55.52030 -#> FOMC 4 57.59999 -#> DFOP 5 59.67918</div><div class='input'> - <span class='co'># For FOCUS C, the more complex models fit better</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> SFO 3 59.29336 -#> FOMC 4 44.68652 -#> DFOP 5 29.02372</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> df BIC -#> SFO 3 59.88504 -#> FOMC 4 45.47542 -#> DFOP 5 30.00984</div><div class='input'> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># skip, as it takes > 10 s on winbuilder</span></span></span> +<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span> +<span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span></span> +<span class="r-in"><span> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># We get a single number for a single fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 55.28197</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="co"># or when extracting an mkinfit object</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 55.28197</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For FOCUS A, the models fit almost equally well, so the higher the number</span></span></span> +<span class="r-in"><span> <span class="co"># of parameters, the higher (worse) the AIC</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28222</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.28197</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28222</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 49.28197</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df BIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59999</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.67918</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For FOCUS C, the more complex models fit better</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 59.29336</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 44.68652</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 29.02372</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df BIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 59.88504</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 45.47542</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 30.00984</span> +<span class="r-in"><span> </span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html index 47efd056..33ae3f74 100644 --- a/docs/dev/reference/CAKE_export.html +++ b/docs/dev/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><meta name="robots" content="noindex"><!-- mathjax --><scrip </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -45,19 +45,25 @@ specified as well."><meta name="robots" content="noindex"><!-- mathjax --><scrip <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html index 5cf7604c..14840260 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><meta name="robots" content="noinde </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -49,19 +49,25 @@ constrained by data protection regulations."><meta name="robots" content="noinde <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html index f41d8e9b..c6746fe7 100644 --- a/docs/dev/reference/DFOP.solution.html +++ b/docs/dev/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><meta name="robots" content="noindex"><!-- m </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ two exponential decline functions."><meta name="robots" content="noindex"><!-- m <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html index 8381337a..cd863616 100644 --- a/docs/dev/reference/Extract.mmkin.html +++ b/docs/dev/reference/Extract.mmkin.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Subsetting method for mmkin objects — [.mmkin • mkin</title> - - -<!-- jquery --> -<script 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collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Subsetting method for mmkin objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>Extract.mmkin.Rd</code></div> </div> @@ -147,122 +92,127 @@ <p>Subsetting method for mmkin objects</p> </div> - <pre class="usage"># S3 method for mmkin -[(x, i, j, ..., drop = FALSE)</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre><code># S3 method for mmkin +[(x, i, j, ..., drop = FALSE)</code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An <code><a href='mmkin.html'>mmkin</a> object</code></p></td> - </tr> - <tr> - <th>i</th> - <td><p>Row index selecting the fits for specific models</p></td> - </tr> - <tr> - <th>j</th> - <td><p>Column index selecting the fits to specific datasets</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used, only there to satisfy the generic method definition</p></td> - </tr> - <tr> - <th>drop</th> - <td><p>If FALSE, the method always returns an mmkin object, otherwise -either a list of mkinfit objects or a single mkinfit object.</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>i</dt> +<dd><p>Row index selecting the fits for specific models</p></dd> - <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +<dt>j</dt> +<dd><p>Column index selecting the fits to specific datasets</p></dd> + + +<dt>...</dt> +<dd><p>Not used, only there to satisfy the generic method definition</p></dd> + + +<dt>drop</dt> +<dd><p>If FALSE, the method always returns an mmkin object, otherwise +either a list of mkinfit objects or a single mkinfit object.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># Only use one core, to pass R CMD check --as-cran</span> - <span class='va'>fits</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, - cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B C -#> FOMC OK OK -#> -#> OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"B"</span><span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B -#> SFO OK -#> FOMC OK -#> -#> OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span><span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B -#> SFO OK -#> -#> OK: No warnings</div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span> - <span class='co'># This extracts an mkinfit object with lots of components</span> - <span class='va'>fits</span><span class='op'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span><span class='op'>]</span><span class='op'>]</span> - <span class='op'>)</span> -</div><div class='output co'>#> $par -#> parent_0 log_alpha log_beta sigma -#> 99.666192 2.549850 5.050586 1.890202 -#> -#> $objective -#> [1] 28.58291 -#> -#> $convergence -#> [1] 0 -#> -#> $iterations -#> [1] 21 -#> -#> $evaluations -#> function gradient -#> 25 78 -#> -#> $message -#> [1] "both X-convergence and relative convergence (5)" -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core, to pass R CMD check --as-cran</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B C </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="co"># This extracts an mkinfit object with lots of components</span></span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $par</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $objective</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $convergence</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $iterations</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 21</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $evaluations</span> +<span class="r-out co"><span class="r-pr">#></span> function gradient </span> +<span class="r-out co"><span class="r-pr">#></span> 25 78 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $message</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "both X-convergence and relative convergence (5)"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html index a188430d..8891567a 100644 --- a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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table with the fitted parameters and the resulting DT50 and DT90 values +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" 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Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> @@ -155,59 +100,73 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_DFOP_ref_A_to_B</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>f</code></dt><dd><p>The fitted f parameter</p></dd> - <dt><code>k1</code></dt><dd><p>The fitted k1 parameter</p></dd> - <dt><code>k2</code></dt><dd><p>The fitted k2 parameter</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>f</code></dt> +<dd><p>The fitted f parameter</p></dd> + + <dt><code>k1</code></dt> +<dd><p>The fitted k1 parameter</p></dd> + + <dt><code>k2</code></dt> +<dd><p>The fitted k2 parameter</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_DFOP_ref_A_to_B</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 0bee1c16..a725ada7 100644 --- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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-<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> -<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F"><meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> @@ -155,58 +100,70 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_FOMC_ref_A_to_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>alpha</code></dt><dd><p>The fitted alpha parameter</p></dd> - <dt><code>beta</code></dt><dd><p>The fitted beta parameter</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>alpha</code></dt> +<dd><p>The fitted alpha parameter</p></dd> + + <dt><code>beta</code></dt> +<dd><p>The fitted beta parameter</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_FOMC_ref_A_to_F</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html index 460fdf0d..d6758f62 100644 --- a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1> @@ -155,59 +100,73 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_HS_ref_A_to_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_HS_ref_A_to_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>tb</code></dt><dd><p>The fitted tb parameter</p></dd> - <dt><code>k1</code></dt><dd><p>The fitted k1 parameter</p></dd> - <dt><code>k2</code></dt><dd><p>The fitted k2 parameter</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>tb</code></dt> +<dd><p>The fitted tb parameter</p></dd> + + <dt><code>k1</code></dt> +<dd><p>The fitted k1 parameter</p></dd> + + <dt><code>k2</code></dt> +<dd><p>The fitted k2 parameter</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_HS_ref_A_to_F</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_HS_ref_A_to_F</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1> @@ -155,57 +100,67 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_SFO_ref_A_to_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>k</code></dt><dd><p>The fitted first-order degradation rate constant</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>k</code></dt> +<dd><p>The fitted first-order degradation rate constant</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_SFO_ref_A_to_F</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,44 +41,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1> @@ -147,68 +92,73 @@ <p>Data taken from FOCUS (2006), p. 258.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_A</span> - <span class='va'>FOCUS_2006_B</span> - <span class='va'>FOCUS_2006_C</span> - <span class='va'>FOCUS_2006_D</span> - <span class='va'>FOCUS_2006_E</span> - <span class='va'>FOCUS_2006_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_A</span></span> +<span> <span class="va">FOCUS_2006_B</span></span> +<span> <span class="va">FOCUS_2006_C</span></span> +<span> <span class="va">FOCUS_2006_D</span></span> +<span> <span class="va">FOCUS_2006_E</span></span> +<span> <span class="va">FOCUS_2006_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>6 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>a factor containing the name of the observed variable</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>time</code></dt> +<dd><p>a numeric vector containing time points</p></dd> - <p>6 datasets with observations on the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> - -</dl> + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>FOCUS_2006_C</span> -</div><div class='output co'>#> name time value -#> 1 parent 0 85.1 -#> 2 parent 1 57.9 -#> 3 parent 3 29.9 -#> 4 parent 7 14.6 -#> 5 parent 14 9.7 -#> 6 parent 28 6.6 -#> 7 parent 63 4.0 -#> 8 parent 91 3.9 -#> 9 parent 119 0.6</div></pre> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_2006_C</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> name time value</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent 0 85.1</span> +<span class="r-out co"><span class="r-pr">#></span> 2 parent 1 57.9</span> +<span class="r-out co"><span class="r-pr">#></span> 3 parent 3 29.9</span> +<span class="r-out co"><span class="r-pr">#></span> 4 parent 7 14.6</span> +<span class="r-out co"><span class="r-pr">#></span> 5 parent 14 9.7</span> +<span class="r-out co"><span class="r-pr">#></span> 6 parent 28 6.6</span> +<span class="r-out co"><span class="r-pr">#></span> 7 parent 63 4.0</span> +<span class="r-out co"><span class="r-pr">#></span> 8 parent 91 3.9</span> +<span class="r-out co"><span class="r-pr">#></span> 9 parent 119 0.6</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html index f64e759c..e1f19dc1 100644 --- a/docs/dev/reference/FOMC.solution.html +++ b/docs/dev/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><meta name="robots" content="noindex"><!-- mathjax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ a decreasing rate constant."><meta name="robots" content="noindex"><!-- mathjax <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html index 5fcef9c0..241d8d69 100644 --- a/docs/dev/reference/HS.solution.html +++ b/docs/dev/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><meta name="robots" content="noindex"><!-- mathjax --><script src </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ between them."><meta name="robots" content="noindex"><!-- mathjax --><script src <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html index 90eccde9..991fb566 100644 --- a/docs/dev/reference/IORE.solution.html +++ b/docs/dev/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><meta name="robots" content="noindex"> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - 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<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Example datasets from the NAFTA SOP published 2015</h1> @@ -147,97 +92,107 @@ <p>Data taken from US EPA (2015), p. 19 and 23.</p> </div> - <pre class="usage"><span class='va'>NAFTA_SOP_Appendix_B</span> - <span class='va'>NAFTA_SOP_Appendix_D</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Appendix_B</span></span> +<span> <span class="va">NAFTA_SOP_Appendix_D</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>2 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>a factor containing the name of the observed variable</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>time</code></dt> +<dd><p>a numeric vector containing time points</p></dd> - <p>2 datasets with observations on the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</p></dd> - -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>nafta_evaluation</span> <span class='op'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Appendix_D</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 1378.6832 615.7730 517.8836 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 -#> -#> Representative half-life: -#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> +<span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 717.4598</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 83.7558 1.80e-14 77.18268 90.3288</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0017 7.43e-05 0.00112 0.0026</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.7518 1.22e-05 5.64278 11.8608</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.69e+01 NA 8.88e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 6.68e+00 NA 4.19e+00 9.17e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.85e+00 NA 3.76e+00 7.94e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03</span> +<span class="r-out co"><span class="r-pr">#></span> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 407 1350 407</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 541 5190000 1560000</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 429 2380 841</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="NAFTA_SOP_2015-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" 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href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,44 +41,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Example datasets from Attachment 1 to the NAFTA SOP published 2015</h1> @@ -147,91 +92,96 @@ <p>Data taken from from Attachment 1 of the SOP.</p> </div> - <pre class="usage"><span class='va'>NAFTA_SOP_Attachment</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Attachment</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable - for the evaluation with <code><a href='nafta.html'>nafta</a></code></p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + for the evaluation with <code><a href="nafta.html">nafta</a></code></p> + </div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>nafta_att_p5a</span> <span class='op'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Attachment</span><span class='op'>[[</span><span class='st'>"p5a"</span><span class='op'>]</span><span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 465.21753 56.27506 32.06401 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 64.4304 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 95.8401 4.67e-21 92.245 99.4357 -#> k_parent 0.0102 3.92e-12 0.009 0.0117 -#> sigma 4.8230 3.81e-06 3.214 6.4318 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -#> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 -#> N_parent 2.57e+00 NA 2.25e+00 2.89e+00 -#> sigma 1.68e+00 NA 1.12e+00 2.24e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 -#> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.26e-12 5.00e-01 0.0000 Inf -#> g 6.47e-01 3.67e-06 0.6248 0.6677 -#> sigma 1.27e+00 8.91e-06 0.8395 1.6929 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 67.7 2.25e+02 6.77e+01 -#> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.59e+11 3.07e+11 -#> -#> Representative half-life: -#> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> -</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_att_p5a</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The half-life obtained from the IORE model may be used</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 465.21753 56.27506 32.06401 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 64.4304</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.8401 4.67e-21 92.245 99.4357</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0102 3.92e-12 0.009 0.0117</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.8230 3.81e-06 3.214 6.4318</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.68e+00 NA 1.12e+00 2.24e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> +<span class="r-out co"><span class="r-pr">#></span> k1 2.67e-02 5.05e-06 0.0243 0.0295</span> +<span class="r-out co"><span class="r-pr">#></span> k2 2.26e-12 5.00e-01 0.0000 Inf</span> +<span class="r-out co"><span class="r-pr">#></span> g 6.47e-01 3.67e-06 0.6248 0.6677</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 67.7 2.25e+02 6.77e+01</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 58.2 1.07e+03 3.22e+02</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 55.5 5.59e+11 3.07e+11</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 321.51</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="NAFTA_SOP_Attachment-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex b3448db0..17a35806 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png Binary files differindex cb419daa..76f25647 100644 --- a/docs/dev/reference/Rplot005.png +++ b/docs/dev/reference/Rplot005.png diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html index 970a62c5..a0bb999c 100644 --- a/docs/dev/reference/SFO.solution.html +++ b/docs/dev/reference/SFO.solution.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html index e3e43557..c14d3a32 100644 --- a/docs/dev/reference/SFORB.solution.html +++ b/docs/dev/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ and no substance in the bound fraction."><meta name="robots" content="noindex">< <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/add_err-1.png b/docs/dev/reference/add_err-1.png Binary files differindex 9ba106db..4a3b4062 100644 --- a/docs/dev/reference/add_err-1.png +++ b/docs/dev/reference/add_err-1.png diff --git a/docs/dev/reference/add_err-2.png b/docs/dev/reference/add_err-2.png Binary files differindex 3088c40e..5aec1744 100644 --- a/docs/dev/reference/add_err-2.png +++ b/docs/dev/reference/add_err-2.png diff --git a/docs/dev/reference/add_err-3.png b/docs/dev/reference/add_err-3.png Binary files differindex 493a761a..2e71f02f 100644 --- a/docs/dev/reference/add_err-3.png +++ b/docs/dev/reference/add_err-3.png diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html index b94cef29..c70d43a0 100644 --- a/docs/dev/reference/add_err.html +++ b/docs/dev/reference/add_err.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title> - - -<!-- jquery --> -<script 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The variance of the error -may depend on the predicted value and is specified as a standard deviation." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +may depend on the predicted value and is specified as a standard deviation."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ may depend on the predicted value and is specified as a standard deviation." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,195 +43,203 @@ may depend on the predicted value and is specified as a standard deviation." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Add normally distributed errors to simulated kinetic degradation data</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/add_err.R'><code>R/add_err.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/add_err.R" class="external-link"><code>R/add_err.R</code></a></small> <div class="hidden name"><code>add_err.Rd</code></div> </div> <div class="ref-description"> <p>Normally distributed errors are added to data predicted for a specific -degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error +degradation model using <code><a href="mkinpredict.html">mkinpredict</a></code>. The variance of the error may depend on the predicted value and is specified as a standard deviation.</p> </div> - <pre class="usage"><span class='fu'>add_err</span><span class='op'>(</span> - <span class='va'>prediction</span>, - <span class='va'>sdfunc</span>, - secondary <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - n <span class='op'>=</span> <span class='fl'>10</span>, - LOD <span class='op'>=</span> <span class='fl'>0.1</span>, - reps <span class='op'>=</span> <span class='fl'>2</span>, - digits <span class='op'>=</span> <span class='fl'>1</span>, - seed <span class='op'>=</span> <span class='cn'>NA</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>prediction</th> - <td><p>A prediction from a kinetic model as produced by -<code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> - </tr> - <tr> - <th>sdfunc</th> - <td><p>A function taking the predicted value as its only argument and + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span> +<span> <span class="va">prediction</span>,</span> +<span> <span class="va">sdfunc</span>,</span> +<span> secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> +<span> n <span class="op">=</span> <span class="fl">10</span>,</span> +<span> LOD <span class="op">=</span> <span class="fl">0.1</span>,</span> +<span> reps <span class="op">=</span> <span class="fl">2</span>,</span> +<span> digits <span class="op">=</span> <span class="fl">1</span>,</span> +<span> seed <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>prediction</dt> +<dd><p>A prediction from a kinetic model as produced by +<code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd> + + +<dt>sdfunc</dt> +<dd><p>A function taking the predicted value as its only argument and returning a standard deviation that should be used for generating the -random error terms for this value.</p></td> - </tr> - <tr> - <th>secondary</th> - <td><p>The names of state variables that should have an initial -value of zero</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of datasets to be generated.</p></td> - </tr> - <tr> - <th>LOD</th> - <td><p>The limit of detection (LOD). Values that are below the LOD after -adding the random error will be set to NA.</p></td> - </tr> - <tr> - <th>reps</th> - <td><p>The number of replicates to be generated within the datasets.</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>The number of digits to which the values will be rounded.</p></td> - </tr> - <tr> - <th>seed</th> - <td><p>The seed used for the generation of random numbers. If NA, the -seed is not set.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. the -components of the list are datasets compatible with <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +random error terms for this value.</p></dd> + + +<dt>secondary</dt> +<dd><p>The names of state variables that should have an initial +value of zero</p></dd> + + +<dt>n</dt> +<dd><p>The number of datasets to be generated.</p></dd> + + +<dt>LOD</dt> +<dd><p>The limit of detection (LOD). Values that are below the LOD after +adding the random error will be set to NA.</p></dd> + +<dt>reps</dt> +<dd><p>The number of replicates to be generated within the datasets.</p></dd> + + +<dt>digits</dt> +<dd><p>The number of digits to which the values will be rounded.</p></dd> + + +<dt>seed</dt> +<dd><p>The seed used for the generation of random numbers. If NA, the +seed is not set.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the +components of the list are datasets compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p> + </div> + <div id="references"> + <h2>References</h2> <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy https://jrwb.de/posters/piacenza_2015.pdf</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># The kinetic model</span> -<span class='va'>m_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># Generate a prediction for a specific set of parameters</span> -<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> - -<span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span> -<span class='co'># from 2015</span> -<span class='va'>d_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>, - k_M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>/</span><span class='fl'>1000</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='co'># Add an error term with a constant (independent of the value) standard deviation</span> -<span class='co'># of 10, and generate three datasets</span> -<span class='va'>d_SFO_SFO_err</span> <span class='op'><-</span> <span class='fu'>add_err</span><span class='op'>(</span><span class='va'>d_SFO_SFO</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fl'>10</span>, n <span class='op'>=</span> <span class='fl'>3</span>, seed <span class='op'>=</span> <span class='fl'>123456789</span> <span class='op'>)</span> - -<span class='co'># Name the datasets for nicer plotting</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_SFO_SFO_err</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span> - -<span class='co'># Name the model in the list of models (with only one member in this case) for</span> -<span class='co'># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span> -<span class='co'># checks</span> -<span class='co'># \dontrun{</span> -<span class='va'>f_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_SFO_SFO</span><span class='op'>)</span>, - <span class='va'>d_SFO_SFO_err</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, - quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>)</span> -</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># We would like to inspect the fit for dataset 3 more closely</span> -<span class='co'># Using double brackets makes the returned object an mkinfit object</span> -<span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span> -<span class='co'># and plot.mmkin is used</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The kinetic model</span></span></span> +<span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span> +<span class="r-in"><span><span class="co"># from 2015</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span></span> +<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span> +<span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span> +<span class="r-in"><span><span class="co"># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span></span></span> +<span class="r-in"><span><span class="co"># checks</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span> +<span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span> +<span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span> +<span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html index 2c109cc2..1689e436 100644 --- a/docs/dev/reference/anova.saem.mmkin.html +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -20,7 +20,7 @@ the model on the previous line."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -62,7 +62,10 @@ the model on the previous line."><meta name="robots" content="noindex"><!-- math <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index e552cc62..81b9b2e9 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -61,7 +61,10 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index 2237a539..16bd388b 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -1,74 +1,19 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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The alternative method 'profile' is based on the profile likelihood for each parameter. The 'profile' method uses two nested optimisations and can take a very long time, even if parallelized by specifying 'cores' on unixoid platforms. The speed of the method could likely be improved by using the -method of Venzon and Moolgavkar (1988)." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +method of Venzon and Moolgavkar (1988)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -79,23 +24,21 @@ method of Venzon and Moolgavkar (1988)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -105,48 +48,50 @@ method of Venzon and Moolgavkar (1988)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Confidence intervals for parameters of mkinfit objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/confint.mkinfit.R" class="external-link"><code>R/confint.mkinfit.R</code></a></small> <div class="hidden name"><code>confint.mkinfit.Rd</code></div> </div> @@ -161,279 +106,301 @@ platforms. The speed of the method could likely be improved by using the method of Venzon and Moolgavkar (1988).</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span> - <span class='va'>object</span>, - <span class='va'>parm</span>, - level <span class='op'>=</span> <span class='fl'>0.95</span>, - alpha <span class='op'>=</span> <span class='fl'>1</span> <span class='op'>-</span> <span class='va'>level</span>, - <span class='va'>cutoff</span>, - method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"quadratic"</span>, <span class='st'>"profile"</span><span class='op'>)</span>, - transformed <span class='op'>=</span> <span class='cn'>TRUE</span>, - backtransform <span class='op'>=</span> <span class='cn'>TRUE</span>, - cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, - rel_tol <span class='op'>=</span> <span class='fl'>0.01</span>, - quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td> - </tr> - <tr> - <th>parm</th> - <td><p>A vector of names of the parameters which are to be given -confidence intervals. If missing, all parameters are considered.</p></td> - </tr> - <tr> - <th>level</th> - <td><p>The confidence level required</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>The allowed error probability, overrides 'level' if specified.</p></td> - </tr> - <tr> - <th>cutoff</th> - <td><p>Possibility to specify an alternative cutoff for the difference + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> <span class="va">parm</span>,</span> +<span> level <span class="op">=</span> <span class="fl">0.95</span>,</span> +<span> alpha <span class="op">=</span> <span class="fl">1</span> <span class="op">-</span> <span class="va">level</span>,</span> +<span> <span class="va">cutoff</span>,</span> +<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"quadratic"</span>, <span class="st">"profile"</span><span class="op">)</span>,</span> +<span> transformed <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> backtransform <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> cores <span class="op">=</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> rel_tol <span class="op">=</span> <span class="fl">0.01</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> + + +<dt>parm</dt> +<dd><p>A vector of names of the parameters which are to be given +confidence intervals. If missing, all parameters are considered.</p></dd> + + +<dt>level</dt> +<dd><p>The confidence level required</p></dd> + + +<dt>alpha</dt> +<dd><p>The allowed error probability, overrides 'level' if specified.</p></dd> + + +<dt>cutoff</dt> +<dd><p>Possibility to specify an alternative cutoff for the difference in the log-likelihoods at the confidence boundary. Specifying an explicit -cutoff value overrides arguments 'level' and 'alpha'</p></td> - </tr> - <tr> - <th>method</th> - <td><p>The 'quadratic' method approximates the likelihood function at +cutoff value overrides arguments 'level' and 'alpha'</p></dd> + + +<dt>method</dt> +<dd><p>The 'quadratic' method approximates the likelihood function at the optimised parameters using the second term of the Taylor expansion, using a second derivative (hessian) contained in the object. The 'profile' method searches the parameter space for the -cutoff of the confidence intervals by means of a likelihood ratio test.</p></td> - </tr> - <tr> - <th>transformed</th> - <td><p>If the quadratic approximation is used, should it be -applied to the likelihood based on the transformed parameters?</p></td> - </tr> - <tr> - <th>backtransform</th> - <td><p>If we approximate the likelihood in terms of the +cutoff of the confidence intervals by means of a likelihood ratio test.</p></dd> + + +<dt>transformed</dt> +<dd><p>If the quadratic approximation is used, should it be +applied to the likelihood based on the transformed parameters?</p></dd> + + +<dt>backtransform</dt> +<dd><p>If we approximate the likelihood in terms of the transformed parameters, should we backtransform the parameters with -their confidence intervals?</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to be used for multicore processing. -On Windows machines, cores > 1 is currently not supported.</p></td> - </tr> - <tr> - <th>rel_tol</th> - <td><p>If the method is 'profile', what should be the accuracy +their confidence intervals?</p></dd> + + +<dt>cores</dt> +<dd><p>The number of cores to be used for multicore processing. +On Windows machines, cores > 1 is currently not supported.</p></dd> + + +<dt>rel_tol</dt> +<dd><p>If the method is 'profile', what should be the accuracy of the lower and upper bounds, relative to the estimate obtained from -the quadratic method?</p></td> - </tr> - <tr> - <th>quiet</th> - <td><p>Should we suppress the message "Profiling the likelihood"</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A matrix with columns giving lower and upper confidence limits for -each parameter.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +the quadratic method?</p></dd> + + +<dt>quiet</dt> +<dd><p>Should we suppress the message "Profiling the likelihood"</p></dd> + +<dt>...</dt> +<dd><p>Not used</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A matrix with columns giving lower and upper confidence limits for +each parameter.</p> + </div> + <div id="references"> + <h2>References</h2> <p>Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications</p> <p>Pawitan Y (2013) In all likelihood - Statistical modelling and inference using likelihood. Clarendon Press, Oxford.</p> <p>Venzon DJ and Moolgavkar SH (1988) A Method for Computing Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, 87–94.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 71.8242430 93.1600766 -#> k_parent 0.2109541 0.4440528 -#> sigma 1.9778868 7.3681380</div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f</span>, method <span class='op'>=</span> <span class='st'>"profile"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 73.0641834 92.1392181 -#> k_parent 0.2170293 0.4235348 -#> sigma 3.1307772 8.0628314</div><div class='input'> -<span class='co'># Set the number of cores for the profiling method for further examples</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"NOT_CRAN"</span><span class='op'>)</span>, <span class='st'>"true"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span> -<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span> - <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> -<span class='op'>}</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>!=</span> <span class='st'>""</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> - -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>SFO_SFO.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>f_d_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> user system elapsed -#> 4.295 1.008 3.959 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> -<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> -<span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span> -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> user system elapsed -#> 1.451 0.126 0.923 </div><div class='input'><span class='va'>ci_profile</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003640 1.027703e+02 -#> k_parent_sink 0.040762501 5.549764e-02 -#> k_parent_m1 0.046786482 5.500879e-02 -#> k_m1_sink 0.003892605 6.702778e-03 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -<span class='va'>ci_quadratic_transformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841640 1.027931e+02 -#> k_parent_sink 0.041033378 5.596269e-02 -#> k_parent_m1 0.046777902 5.511931e-02 -#> k_m1_sink 0.004012217 6.897547e-03 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -<span class='va'>ci_quadratic_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841645 102.79312449 -#> k_parent_sink 0.040485331 0.05535491 -#> k_parent_m1 0.046611582 0.05494364 -#> k_m1_sink 0.003835483 0.00668582 -#> sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> -<span class='co'># intervals based on the internal parameter transformation are less</span> -<span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> -<span class='co'># interval based on the untransformed fit for k_m1_sink</span> -<span class='va'>rel_diffs_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> -<span class='va'>rel_diffs_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> -<span class='va'>rel_diffs_transformed</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent_sink TRUE FALSE -#> k_parent_m1 TRUE FALSE -#> k_m1_sink FALSE FALSE -#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006650 0.008380 -#> k_parent_m1 0.000183 0.002010 -#> k_m1_sink 0.030700 0.029100 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006800 0.002570 -#> k_parent_m1 0.003740 0.001180 -#> k_m1_sink 0.014700 0.002530 -#> sigma 0.055000 0.032700</div><div class='input'> - -<span class='co'># Investigate a case with formation fractions</span> -<span class='va'>f_d_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>ci_profile_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='va'>ci_profile_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003640 1.027703e+02 -#> k_parent 0.090911032 1.071578e-01 -#> k_m1 0.003892606 6.702775e-03 -#> f_parent_to_m1 0.471328495 5.611550e-01 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -<span class='va'>ci_quadratic_transformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833578 102.79311649 -#> k_parent 0.090823771 0.10725430 -#> k_m1 0.004012219 0.00689755 -#> f_parent_to_m1 0.469118824 0.55959615 -#> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -<span class='va'>ci_quadratic_untransformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833583 1.027931e+02 -#> k_parent 0.090491913 1.069035e-01 -#> k_m1 0.003835485 6.685823e-03 -#> f_parent_to_m1 0.469113477 5.598387e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'>-</span> <span class='va'>ci_profile_ff</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile_ff</span><span class='op'>)</span> -<span class='va'>rel_diffs_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'>-</span> <span class='va'>ci_profile_ff</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile_ff</span><span class='op'>)</span> -<span class='co'># While the confidence interval for the parent rate constant is closer to</span> -<span class='co'># the profile based interval when using the internal parameter</span> -<span class='co'># transformation, the interval for the metabolite rate constant is 'better</span> -<span class='co'># without internal parameter transformation.</span> -<span class='va'>rel_diffs_transformed_ff</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent TRUE TRUE -#> k_m1 FALSE FALSE -#> f_parent_to_m1 TRUE FALSE -#> sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408690 0.0002217233 -#> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283041 0.0290588361 -#> f_parent_to_m1 0.0046881769 0.0027780063 -#> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217232 -#> k_parent 0.0046102156 0.0023732281 -#> k_m1 0.0146740690 0.0025291820 -#> f_parent_to_m1 0.0046995211 0.0023457712 -#> sigma 0.0550252516 0.0327066836</div><div class='input'> -<span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> -<span class='co'># therefore we use the quadratic approximation</span> -<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>DFOP_par_c</span> <span class='op'><-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span> -<span class='va'>f_tc_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>DFOP_par_c</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, - error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596039609 106.19954892 -#> k_M1 0.037605368 0.04490762 -#> k_M2 0.008568731 0.01087676 -#> f_parent_to_M1 0.021462489 0.62023882 -#> f_parent_to_M2 0.015165617 0.37975348 -#> k1 0.273897348 0.33388101 -#> k2 0.018614554 0.02250378 -#> g 0.671943411 0.73583305 -#> sigma_low 0.251283495 0.83992077 -#> rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 71.8242430 93.1600766</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.2109541 0.4440528</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.9778868 7.3681380</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"profile"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 73.0641834 92.1392181</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.2170293 0.4235348</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.1307772 8.0628314</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Set the number of cores for the profiling method for further examples</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"NOT_CRAN"</span><span class="op">)</span>, <span class="st">"true"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 3.811 0.004 3.815 </span> +<span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> +<span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> +<span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile_no_parent_0</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 2.313 0.004 2.318 </span> +<span class="r-in"><span><span class="va">ci_profile</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040762501 5.549764e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046786482 5.500879e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003892605 6.702778e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403841640 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.041033378 5.596269e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046777902 5.511931e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.004012217 6.897547e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403841645 102.79312449</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040485331 0.05535491</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046611582 0.05494364</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003835483 0.00668582</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> +<span class="r-in"><span><span class="co"># Against the expectation based on Bates and Watts (1988), the confidence</span></span></span> +<span class="r-in"><span><span class="co"># intervals based on the internal parameter transformation are less</span></span></span> +<span class="r-in"><span><span class="co"># congruent with the likelihood based intervals. Note the superiority of the</span></span></span> +<span class="r-in"><span><span class="co"># interval based on the untransformed fit for k_m1_sink</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink TRUE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 TRUE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> sigma FALSE FALSE</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_transformed</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.000541 0.000222</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006650 0.008380</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.000183 0.002010</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.030700 0.029100</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_untransformed</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.000541 0.000222</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006800 0.002570</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.003740 0.001180</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.014700 0.002530</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Investigate a case with formation fractions</span></span></span> +<span class="r-in"><span><span class="va">f_d_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_profile_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> +<span class="r-in"><span><span class="va">ci_profile_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090911032 1.071578e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.003892606 6.702775e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.471328495 5.611550e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># While the confidence interval for the parent rate constant is closer to</span></span></span> +<span class="r-in"><span><span class="co"># the profile based interval when using the internal parameter</span></span></span> +<span class="r-in"><span><span class="co"># transformation, the interval for the metabolite rate constant is 'better</span></span></span> +<span class="r-in"><span><span class="co"># without internal parameter transformation.</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent TRUE TRUE</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 TRUE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> sigma TRUE FALSE</span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span></span> +<span class="r-in"><span><span class="co"># therefore we use the quadratic approximation</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">f_tc_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">DFOP_par_c</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> +<span class="r-in"><span> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html index 5d5870fe..e2a42873 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -125,8 +131,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.401 1.000 0.401 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.654 1.631 0.654 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.458 1.000 0.458 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.713 1.557 0.713 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -139,8 +145,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.843 1.000 0.843 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.445 1.714 1.445 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.884 1.000 0.883 0.000 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.526 1.726 1.522 0.004 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/dev/reference/dimethenamid_2018-1.png b/docs/dev/reference/dimethenamid_2018-1.png Binary files differindex 4300b0c0..c8b05bf5 100644 --- a/docs/dev/reference/dimethenamid_2018-1.png +++ b/docs/dev/reference/dimethenamid_2018-1.png diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index 2454a609..96ec73c6 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><meta name="robots" content="noinde </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -49,19 +49,25 @@ constrained by data protection regulations."><meta name="robots" content="noinde <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -180,17 +186,15 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># influence of ill-defined rate constants that have</span></span></span> <span class="r-in"><span><span class="co"># extremely small values:</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># If we disregards ill-defined rate constants, the results</span></span></span> <span class="r-in"><span><span class="co"># look more plausible, but the truth is likely to be in</span></span></span> <span class="r-in"><span><span class="co"># between these variants</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># We can also specify a default value for the failing</span></span></span> <span class="r-in"><span><span class="co"># log parameters, to mimic FOCUS guidance</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> <span class="r-in"><span> default_log_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># As these attempts are not satisfying, we use nonlinear mixed-effects models</span></span></span> <span class="r-in"><span><span class="co"># f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)</span></span></span> <span class="r-in"><span><span class="co"># nlme reaches maxIter = 50 without convergence</span></span></span> @@ -200,11 +204,11 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># graphics device used)</span></span></span> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:07 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:05:16 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:05:16 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +221,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 797.539 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 819.725 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -235,69 +239,79 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 2276 2272 -1120</span> +<span class="r-out co"><span class="r-pr">#></span> 2276 2273 -1120</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.5943 84.3961 92.7925</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0466 -3.5609 -2.5322</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0684 -4.9340 -3.2029</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8628 -4.2627 -3.4628</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9803 -4.4804 -3.4801</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1304 -0.2186 0.4795</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1490 -0.2559 0.5540</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3192 83.8656 92.7729</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0530 -3.5686 -2.5373</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0620 -4.9202 -3.2038</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8633 -4.2668 -3.4598</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9731 -4.4763 -3.4699</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0309 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0231 -0.0031 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0381 -0.0048 0.0039 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0303 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0229 -0.0032 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0372 -0.0049 0.0041 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0245 -0.0032 0.0022 0.0815 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0415 -0.0433 0.0324 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0267 -0.0893 -0.0361 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1755 -0.0135 0.0423 0.0775 0.0377 -0.0066 0.0060 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.3651 -0.9649 7.6951</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6415 0.2774 1.0055</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0176 0.3809 1.6543</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4538 0.1522 0.7554</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5684 0.1905 0.9464</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9349 0.8409 1.029</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1344 0.1178 0.151</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.59431 84.396147 92.79246</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04752 0.028413 0.07948</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01710 0.007198 0.04064</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02101 0.014084 0.03134</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01868 0.011329 0.03080</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14498 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12056 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11015 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.31924 83.865625 92.77286</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04722 0.028196 0.07908</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01721 0.007298 0.04061</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02100 0.014027 0.03144</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01882 0.011375 0.03112</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14608 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12077 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11123 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1450</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1206</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1101</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6243</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1461</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1208</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1112</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6219</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.59 48.45</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.52 134.62</span> -<span class="r-out co"><span class="r-pr">#></span> M27 32.99 109.60</span> -<span class="r-out co"><span class="r-pr">#></span> M31 37.11 123.26</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.68 48.76</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.27 133.76</span> +<span class="r-out co"><span class="r-pr">#></span> M27 33.01 109.65</span> +<span class="r-out co"><span class="r-pr">#></span> M31 36.84 122.38</span> <span class="r-in"><span><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span></span> <span class="r-in"><span><span class="co"># includes zero, we could try an alternative model without</span></span></span> <span class="r-in"><span><span class="co"># such random effects</span></span></span> diff --git a/docs/dev/reference/ds_mixed-1.png b/docs/dev/reference/ds_mixed-1.png Binary files differnew file mode 100644 index 00000000..a7f5c395 --- /dev/null +++ b/docs/dev/reference/ds_mixed-1.png diff --git a/docs/dev/reference/ds_mixed.html b/docs/dev/reference/ds_mixed.html new file mode 100644 index 00000000..09a6cc8c --- /dev/null +++ b/docs/dev/reference/ds_mixed.html @@ -0,0 +1,240 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand 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class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ds_mixed.R" class="external-link"><code>R/ds_mixed.R</code></a></small> + <div class="hidden name"><code>ds_mixed.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The R code used to create this data object is installed with this package in +the 'dataset_generation' directory.</p> + </div> + + + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">sfo_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">sfo_saem</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">sfo_mmkin</span>, no_random_effect <span class="op">=</span> <span class="st">"parent_0"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sfo_saem</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="ds_mixed-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is the code used to generate the datasets</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">cat</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"dataset_generation/ds_mixed.R"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span><span class="op">)</span>, sep <span class="op">=</span> <span class="st">"\n"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> # Synthetic data for hierarchical kinetic models</span> +<span class="r-out co"><span class="r-pr">#></span> # Refactored version of the code previously in tests/testthat/setup_script.R</span> +<span class="r-out co"><span class="r-pr">#></span> # The number of datasets was 3 for FOMC, and 10 for HS in that script, now it</span> +<span class="r-out co"><span class="r-pr">#></span> # is always 15 for consistency</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> library(mkin) # We use mkinmod and mkinpredict</span> +<span class="r-out co"><span class="r-pr">#></span> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</span> +<span class="r-out co"><span class="r-pr">#></span> n <- 15</span> +<span class="r-out co"><span class="r-pr">#></span> log_sd <- 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> err_1 = list(const = 1, prop = 0.05)</span> +<span class="r-out co"><span class="r-pr">#></span> tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop)</span> +<span class="r-out co"><span class="r-pr">#></span> const <- function(value) 2</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> SFO <- mkinmod(parent = mkinsub("SFO"))</span> +<span class="r-out co"><span class="r-pr">#></span> sfo_pop <- list(parent_0 = 100, k_parent = 0.03)</span> +<span class="r-out co"><span class="r-pr">#></span> sfo_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent = rlnorm(n, log(sfo_pop$k_parent), log_sd)))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_sfo <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(SFO, sfo_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = sfo_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, tc, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_sfo, "pop") <- sfo_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_sfo, "parms") <- sfo_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC <- mkinmod(parent = mkinsub("FOMC"))</span> +<span class="r-out co"><span class="r-pr">#></span> fomc_pop <- list(parent_0 = 100, alpha = 2, beta = 8)</span> +<span class="r-out co"><span class="r-pr">#></span> fomc_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> alpha = rlnorm(n, log(fomc_pop$alpha), 0.4),</span> +<span class="r-out co"><span class="r-pr">#></span> beta = rlnorm(n, log(fomc_pop$beta), 0.2)))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_fomc <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(FOMC, fomc_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = fomc_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, tc, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_fomc, "pop") <- fomc_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_fomc, "parms") <- fomc_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP <- mkinmod(parent = mkinsub("DFOP"))</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4)</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = rlnorm(n, log(dfop_pop$k1), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> k2 = rlnorm(n, log(dfop_pop$k2), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd))))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_dfop <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(DFOP, dfop_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = dfop_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, tc, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop, "pop") <- dfop_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop, "parms") <- dfop_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> HS <- mkinmod(parent = mkinsub("HS"))</span> +<span class="r-out co"><span class="r-pr">#></span> hs_pop <- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15)</span> +<span class="r-out co"><span class="r-pr">#></span> hs_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = rlnorm(n, log(hs_pop$k1), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> k2 = rlnorm(n, log(hs_pop$k2), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> tb = rlnorm(n, log(hs_pop$tb), 0.1)))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_hs <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(HS, hs_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = hs_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, const, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_hs, "pop") <- hs_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_hs, "parms") <- hs_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP_SFO <- mkinmod(</span> +<span class="r-out co"><span class="r-pr">#></span> parent = mkinsub("DFOP", "m1"),</span> +<span class="r-out co"><span class="r-pr">#></span> m1 = mkinsub("SFO"),</span> +<span class="r-out co"><span class="r-pr">#></span> quiet = TRUE)</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_sfo_pop <- list(parent_0 = 100,</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 = 0.007, f_parent_to_m1 = 0.5,</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = 0.1, k2 = 0.02, g = 0.5)</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_sfo_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = rlnorm(n, log(dfop_sfo_pop$k1), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> k2 = rlnorm(n, log(dfop_sfo_pop$k2), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> g = plogis(rnorm(n, qlogis(dfop_sfo_pop$g), log_sd)),</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 = plogis(rnorm(n,</span> +<span class="r-out co"><span class="r-pr">#></span> qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)),</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 = rlnorm(n, log(dfop_sfo_pop$k_m1), log_sd)))</span> +<span class="r-out co"><span class="r-pr">#></span> ds_dfop_sfo_mean <- lapply(1:n,</span> +<span class="r-out co"><span class="r-pr">#></span> function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> mkinpredict(DFOP_SFO, dfop_sfo_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = dfop_sfo_pop$parent_0, m1 = 0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> }</span> +<span class="r-out co"><span class="r-pr">#></span> )</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_dfop_sfo <- lapply(ds_dfop_sfo_mean, function(ds) {</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds,</span> +<span class="r-out co"><span class="r-pr">#></span> sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),</span> +<span class="r-out co"><span class="r-pr">#></span> n = 1, secondary = "m1")[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop_sfo, "pop") <- dfop_sfo_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop_sfo, "parms") <- dfop_sfo_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)</span> +</code></pre></div> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index e8198521..f8064098 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -65,7 +65,10 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/example_analysis/dlls/sforb_sfo2.so b/docs/dev/reference/example_analysis/dlls/sforb_sfo2.so Binary files differnew file mode 100755 index 00000000..a692256d --- /dev/null +++ b/docs/dev/reference/example_analysis/dlls/sforb_sfo2.so diff --git a/docs/dev/reference/example_analysis/example_analysis.Rmd b/docs/dev/reference/example_analysis/example_analysis.Rmd new file mode 100644 index 00000000..38a6bd20 --- /dev/null +++ b/docs/dev/reference/example_analysis/example_analysis.Rmd @@ -0,0 +1,314 @@ +--- +title: "Hierarchical kinetic modelling of degradation data" +author: +date: +output: mkin::hierarchical_kinetics +geometry: margin=2cm +--- + +\clearpage + +# Setup + +```{r packages, cache = FALSE, message = FALSE} +library(mkin) +library(knitr) +library(saemix) +library(parallel) +library(readxl) +``` + +```{r n_cores, cache = FALSE} +n_cores <- detectCores() + +if (Sys.info()["sysname"] == "Windows") { + cl <- makePSOCKcluster(n_cores) +} else { + cl <- makeForkCluster(n_cores) +} +``` + +\clearpage + +# Introduction + +This report shows hierarchical kinetic modelling for ... +The data were obtained from ... + +```{r ds} +data_path <- system.file( + "testdata", "lambda-cyhalothrin_soil_efsa_2014.xlsx", + package = "mkin") +ds <- read_spreadsheet(data_path, valid_datasets = c(1:4, 7:13)) +covariates <- attr(ds, "covariates") +``` + +The covariate data are shown below. + +```{r results = "asis", dependson = "ds", echo = FALSE} +kable(covariates, caption = "Covariate data for all datasets") +``` + +\clearpage + +The datasets with the residue time series are shown in the tables below. Please +refer to the spreadsheet for details like data sources, treatment of values +below reporting limits and time step normalisation factors. + +```{r results = "asis", dependson = "ds", echo = FALSE} +for (ds_name in names(ds)) { + print( + kable(mkin_long_to_wide(ds[[ds_name]]), + caption = paste("Dataset", ds_name), + booktabs = TRUE, row.names = FALSE)) + cat("\n\\clearpage\n") +} +``` + +# Parent only evaluations + +The following code performs separate fits of the candidate degradation models +to all datasets using constant variance and the two-component error model. + +```{r parent-sep, dependson = "ds"} +parent_deg_mods <- c("SFO", "FOMC", "DFOP", "SFORB") +errmods <- c(const = "constant variance", tc = "two-component error") +parent_sep_const <- mmkin( + parent_deg_mods, ds, + error_model = "const", + cluster = cl, quiet = TRUE) +parent_sep_tc <- update(parent_sep_const, error_model = "tc") +``` + +To select the parent model, the corresponding hierarchical fits are performed below. + +```{r parent-mhmkin, dependson = "parent-sep"} +parent_mhmkin <- mhmkin(list(parent_sep_const, parent_sep_tc), cluster = cl) +status(parent_mhmkin) |> kable() +``` + +All fits terminate without errors (status OK). The check for ill-defined +parameters shows that not all random effect parameters can be robustly +quantified. + +```{r dependson = "parent_mhmkin"} +illparms(parent_mhmkin) |> kable() +``` + +Therefore, the fits are updated, excluding random effects that were +ill-defined according to the `illparms` function. The status of the fits +is checked. + +```{r parent-mhmkin-refined} +parent_mhmkin_refined <- update(parent_mhmkin, + no_random_effect = illparms(parent_mhmkin)) +status(parent_mhmkin_refined) |> kable() +``` + +Also, it is checked if the AIC values of the refined fits are actually smaller +than the AIC values of the original fits. + +```{r dependson = "parent-mhmkin-refined"} +(AIC(parent_mhmkin_refined) < AIC(parent_mhmkin)) |> kable() +``` + +From the refined fits, the most suitable model is selected using the AIC. + +```{r parent-best, dependson = "parent-mhmkin"} +aic_parent <- AIC(parent_mhmkin_refined) +min_aic <- which(aic_parent == min(aic_parent), arr.ind = TRUE) +best_degmod_parent <- rownames(aic_parent)[min_aic[1]] +best_errmod_parent <- colnames(aic_parent)[min_aic[2]] +anova(parent_mhmkin_refined) |> kable(digits = 1) +parent_best <- parent_mhmkin_refined[[best_degmod_parent, best_errmod_parent]] +``` + +Based on the AIC, the combination of the `r best_degmod_parent` degradation +model with the error model `r errmods[best_errmod_parent]` is identified to +be most suitable for the degradation of the parent. The check below +confirms that no ill-defined parameters remain for this combined model. + +```{r dependson = "parent-best"} +illparms(parent_best) +``` + +The corresponding fit is plotted below. + +```{r dependson = "parent-best"} +plot(parent_best) +``` +The fitted parameters, together with approximate confidence +intervals are listed below. + +```{r dependson = "parent-best"} +parms(parent_best, ci = TRUE) |> kable(digits = 3) +``` + +To investigate a potential covariate influence on degradation parameters, a +covariate model is added to the hierarchical model for each of the degradation +parameters with well-defined random effects. Also, a version with covariate +models for both of them is fitted. + +```{r parent-best-pH} +parent_best_pH_1 <- update(parent_best, covariates = covariates, + covariate_models = list(log_k_lambda_free ~ pH)) +parent_best_pH_2 <- update(parent_best, covariates = covariates, + covariate_models = list(log_k_lambda_bound_free ~ pH)) +parent_best_pH_3 <- update(parent_best, covariates = covariates, + covariate_models = list(log_k_lambda_free ~ pH, log_k_lambda_bound_free ~ pH)) +``` + +The resulting models are compared. + +```{r dependson = "parent-best-pH"} +anova(parent_best, parent_best_pH_1, parent_best_pH_2, parent_best_pH_3) |> + kable(digits = 1) +``` + +The model fit with the lowest AIC is the one with a pH correlation of the +desorption rate constant `k_lambda_bound_free`. Plot and parameter listing +of this fit are shown below. Also, it is confirmed that no ill-defined +variance parameters are found. + +```{r dependson = "parent-best-pH"} +plot(parent_best_pH_2) +``` + +```{r dependson = "parent-best-pH"} +illparms(parent_best_pH_2) +parms(parent_best_pH_2, ci = TRUE) |> kable(digits = 3) +``` + +\clearpage + +# Pathway fits + +As an example of a pathway fit, a model with SFORB for the parent compound and +parallel formation of two metabolites is set up. + +```{r path-1-degmod} +if (!dir.exists("dlls")) dir.create("dlls") + +m_sforb_sfo2 = mkinmod( + lambda = mkinsub("SFORB", to = c("c_V", "c_XV")), + c_V = mkinsub("SFO"), + c_XV = mkinsub("SFO"), + name = "sforb_sfo2", + dll_dir = "dlls", + overwrite = TRUE, quiet = TRUE +) +``` + +Separate evaluations of all datasets are performed with constant variance +and using two-component error. + +```{r path-1-sep, dependson = c("path-1-degmod", "ds")} +sforb_sep_const <- mmkin(list(sforb_path = m_sforb_sfo2), ds, + cluster = cl, quiet = TRUE) +sforb_sep_tc <- update(sforb_sep_const, error_model = "tc") +``` + +The separate fits with constant variance are plotted. + +```{r dependson = "path-1-sep", fig.height = 9} +plot(mixed(sforb_sep_const)) +``` + +The two corresponding hierarchical fits, with the random effects for the parent +degradation parameters excluded as discussed above, and including the covariate +model that was identified for the parent degradation, are attempted below. + +```{r path-1, dependson = "path-1-sep"} +path_1 <- mhmkin(list(sforb_sep_const, sforb_sep_tc), + no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound"), + covariates = covariates, covariate_models = list(log_k_lambda_bound_free ~ pH), + cluster = cl) +``` + +```{r dependson = "path-1"} +status(path_1) |> kable() +``` + +The status information shows that both fits were successfully completed. + +```{r dependson = "path-1"} +anova(path_1) |> kable(digits = 1) +``` +Model comparison shows that the two-component error model provides a much +better fit. + +```{r dependson = "path-1"} +illparms(path_1[["sforb_path", "tc"]]) +``` + +Two ill-defined variance components are found. Therefore, the fit is +repeated with the corresponding random effects removed. + +```{r path-1-refined, dependson = "path-1"} +path_1_refined <- update(path_1[["sforb_path", "tc"]], + no_random_effect = c("lambda_free_0", "log_k_lambda_free_bound", + "log_k_c_XV", "f_lambda_ilr_2")) +``` + +The empty output of the illparms function indicates that there are no +ill-defined parameters remaining in the refined fit. + +```{r dependson = "path-1-refined"} +illparms(path_1_refined) +``` + +Below, the refined fit is plotted and the fitted parameters are shown together +with their 95% confidence intervals. + +```{r dependson = "path-1-refined", fig.height = 9} +plot(path_1_refined) +``` + +```{r dependson = "path-1-refined", fig.height = 9} +parms(path_1_refined, ci = TRUE) |> kable(digits = 3) +``` + +\clearpage + +# Appendix + +## Listings of initial parent fits + +```{r listings-parent, results = "asis", echo = FALSE, dependson = "parent_mhmkin"} +for (deg_mod in parent_deg_mods) { + for (err_mod in c("const", "tc")) { + caption <- paste("Hierarchical", deg_mod, "fit with", errmods[err_mod]) + tex_listing(parent_mhmkin[[deg_mod, err_mod]], caption) + } +} +``` + +## Listings of refined parent fits + +```{r listings-parent-refined, results = "asis", echo = FALSE, dependson = "parent_mhmkin_refined"} +for (deg_mod in parent_deg_mods) { + for (err_mod in c("const", "tc")) { + caption <- paste("Refined hierarchical", deg_mod, "fit with", errmods[err_mod]) + tex_listing(parent_mhmkin_refined[[deg_mod, err_mod]], caption) + } +} +``` + +## Listings of pathway fits + +```{r listings-path-1, results = "asis", echo = FALSE, dependson = "path-1-refined"} +tex_listing(path_1[["sforb_path", "const"]], + caption = "Hierarchical fit of SFORB-SFO2 with constant variance") +tex_listing(path_1[["sforb_path", "tc"]], + caption = "Hierarchical fit of SFORB-SFO2 with two-component error") +tex_listing(path_1_refined, + caption = "Refined hierarchical fit of SFORB-SFO2 with two-component error") +``` + +## Session info + +```{r echo = FALSE, cache = FALSE} +parallel::stopCluster(cl) +sessionInfo() +``` + diff --git a/docs/dev/reference/example_analysis/header.tex b/docs/dev/reference/example_analysis/header.tex new file mode 100644 index 00000000..a2b7ce83 --- /dev/null +++ b/docs/dev/reference/example_analysis/header.tex @@ -0,0 +1 @@ +\definecolor{shadecolor}{RGB}{248,248,248} diff --git a/docs/dev/reference/example_analysis/skeleton.pdf b/docs/dev/reference/example_analysis/skeleton.pdf Binary files differnew file mode 100644 index 00000000..53c5fb31 --- /dev/null +++ b/docs/dev/reference/example_analysis/skeleton.pdf diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf Binary files differnew file mode 100644 index 00000000..ab685d92 --- /dev/null +++ b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-11-1.pdf diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf Binary files differnew file mode 100644 index 00000000..5d88063b --- /dev/null +++ b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-16-1.pdf diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf Binary files differnew file mode 100644 index 00000000..5e0d7b6f --- /dev/null +++ b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-6-1.pdf diff --git a/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf Binary files differnew file mode 100644 index 00000000..eecd06a8 --- /dev/null +++ b/docs/dev/reference/example_analysis/skeleton_files/figure-latex/unnamed-chunk-9-1.pdf diff --git a/docs/dev/reference/experimental_data_for_UBA-1.png b/docs/dev/reference/experimental_data_for_UBA-1.png Binary files differindex 33946ded..b7b4d63b 100644 --- a/docs/dev/reference/experimental_data_for_UBA-1.png +++ b/docs/dev/reference/experimental_data_for_UBA-1.png diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html index 9904370f..a51ace27 100644 --- a/docs/dev/reference/experimental_data_for_UBA.html +++ b/docs/dev/reference/experimental_data_for_UBA.html @@ -1,46 +1,5 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some results are shown here do not imply a license to use them in the context of @@ -68,28 +27,14 @@ Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D the exception of the day three sampling of metabolite A2, which was set to one half of the LOD reported to be 1% AR. Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl - (United Kingdom, 2014, p. 81)." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> + (United Kingdom, 2014, p. 81)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -100,23 +45,21 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -126,44 +69,46 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Experimental datasets used for development and testing of error models</h1> @@ -203,30 +148,33 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).</p> </div> - <pre class="usage"><span class='va'>experimental_data_for_UBA_2019</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">experimental_data_for_UBA_2019</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>, + each containing, among others, the following components</p><dl><dt><code>title</code></dt> +<dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>data</code></dt> +<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd> - <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> <p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p> <p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> -<p>FOCUS (2014) “Generic guidance for Estimating Persistence and +<p>FOCUS (2014) “Generic guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <p>Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate and Behaviour</p> <p>Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the @@ -236,70 +184,75 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed Decision of the United Kingdom made to the European Commission under Regulation (EC) No. 1141/2010 for renewal of an active substance</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> - -<span class='co'># Model definitions</span> -<span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>sfo_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, - A2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>dfop_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, - A2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>d_1_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_1_2</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Soil"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>)</span> - - -<span class='va'>f_1_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo_sfo</span><span class='op'>)</span>, <span class='va'>d_1_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_1_2_tc</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span> -</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># }</span></div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Model definitions</span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">d_1_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_1_2</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Soil"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_1_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo_sfo</span><span class="op">)</span>, <span class="va">d_1_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_1_2_tc</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="experimental_data_for_UBA-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html index 852e00a0..b556df04 100644 --- a/docs/dev/reference/f_time_norm_focus.html +++ 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-73,23 +18,21 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Normalisation factors for aerobic soil degradation according to FOCUS guidance</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/f_time_norm_focus.R'><code>R/f_time_norm_focus.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/f_time_norm_focus.R" class="external-link"><code>R/f_time_norm_focus.R</code></a></small> <div class="hidden name"><code>f_time_norm_focus.Rd</code></div> </div> @@ -149,137 +94,138 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p> </div> - <pre class="usage"><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for numeric</span> -<span class='fu'>f_time_norm_focus</span><span class='op'>(</span> - <span class='va'>object</span>, - moisture <span class='op'>=</span> <span class='cn'>NA</span>, - field_moisture <span class='op'>=</span> <span class='cn'>NA</span>, - temperature <span class='op'>=</span> <span class='va'>object</span>, - Q10 <span class='op'>=</span> <span class='fl'>2.58</span>, - walker <span class='op'>=</span> <span class='fl'>0.7</span>, - f_na <span class='op'>=</span> <span class='cn'>NA</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='co'># S3 method for mkindsg</span> -<span class='fu'>f_time_norm_focus</span><span class='op'>(</span> - <span class='va'>object</span>, - study_moisture_ref_source <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"auto"</span>, <span class='st'>"meta"</span>, <span class='st'>"focus"</span><span class='op'>)</span>, - Q10 <span class='op'>=</span> <span class='fl'>2.58</span>, - walker <span class='op'>=</span> <span class='fl'>0.7</span>, - f_na <span class='op'>=</span> <span class='cn'>NA</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An object containing information used for the calculations</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Currently not used</p></td> - </tr> - <tr> - <th>moisture</th> - <td><p>Numeric vector of moisture contents in \% w/w</p></td> - </tr> - <tr> - <th>field_moisture</th> - <td><p>Numeric vector of moisture contents at field capacity -(pF2) in \% w/w</p></td> - </tr> - <tr> - <th>temperature</th> - <td><p>Numeric vector of temperatures in °C</p></td> - </tr> - <tr> - <th>Q10</th> - <td><p>The Q10 value used for temperature normalisation</p></td> - </tr> - <tr> - <th>walker</th> - <td><p>The Walker exponent used for moisture normalisation</p></td> - </tr> - <tr> - <th>f_na</th> - <td><p>The factor to use for NA values. If set to NA, only factors -for complete cases will be returned.</p></td> - </tr> - <tr> - <th>study_moisture_ref_source</th> - <td><p>Source for the reference value + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> field_moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> temperature <span class="op">=</span> <span class="va">object</span>,</span> +<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span> +<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkindsg</span></span> +<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> study_moisture_ref_source <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"meta"</span>, <span class="st">"focus"</span><span class="op">)</span>,</span> +<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span> +<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object containing information used for the calculations</p></dd> + + +<dt>...</dt> +<dd><p>Currently not used</p></dd> + + +<dt>moisture</dt> +<dd><p>Numeric vector of moisture contents in \% w/w</p></dd> + + +<dt>field_moisture</dt> +<dd><p>Numeric vector of moisture contents at field capacity +(pF2) in \% w/w</p></dd> + + +<dt>temperature</dt> +<dd><p>Numeric vector of temperatures in °C</p></dd> + + +<dt>Q10</dt> +<dd><p>The Q10 value used for temperature normalisation</p></dd> + + +<dt>walker</dt> +<dd><p>The Walker exponent used for moisture normalisation</p></dd> + + +<dt>f_na</dt> +<dd><p>The factor to use for NA values. If set to NA, only factors +for complete cases will be returned.</p></dd> + + +<dt>study_moisture_ref_source</dt> +<dd><p>Source for the reference value used to calculate the study moisture. If 'auto', preference is given to a reference moisture given in the meta information, otherwise -the focus soil moisture for the soil class is used</p></td> - </tr> - </table> +the focus soil moisture for the soil class is used</p></dd> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence +</dl></div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> -FOCUS (2014) “Generic guidance for Estimating Persistence +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> +FOCUS (2014) “Generic guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><a href='focus_soil_moisture.html'>focus_soil_moisture</a></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='fl'>25</span>, <span class='fl'>20</span>, <span class='fl'>25</span><span class='op'>)</span> <span class='co'># 1.37, compare FOCUS 2014 p. 184</span> -</div><div class='output co'>#> [1] 1.373956</div><div class='input'> -<span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>meta</span> -</div><div class='output co'>#> study usda_soil_type study_moisture_ref_type -#> Mississippi Cohen 1991 Silt loam <NA> -#> Fayette Liu and Adelfinskaya 2011 Silt loam pF1 -#> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1 -#> Site E1 Liu and Adelfinskaya 2011 Loam pF1 -#> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1 -#> rel_moisture temperature -#> Mississippi NA 25 -#> Fayette 0.5 20 -#> RefSol 03-G 0.5 20 -#> Site E1 0.5 20 -#> Site I2 0.5 20</div><div class='input'><span class='co'># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span> -<span class='co'># temperature only normalisation as in the EU evaluation</span> -<span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>D24_2014</span>, study_moisture_ref_source <span class='op'>=</span> <span class='st'>"focus"</span>, f_na <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> $time_norm was set to -#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre> +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="focus_soil_moisture.html">focus_soil_moisture</a></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1.373956</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span> +<span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span> +<span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span> +<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span> +<span class="r-out co"><span class="r-pr">#></span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span> +<span class="r-out co"><span class="r-pr">#></span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span> +<span class="r-out co"><span class="r-pr">#></span> rel_moisture temperature</span> +<span class="r-out co"><span class="r-pr">#></span> Mississippi NA 25</span> +<span class="r-out co"><span class="r-pr">#></span> Fayette 0.5 20</span> +<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span> +<span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span> +<span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span> +<span class="r-in"><span><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span></span> +<span class="r-in"><span><span class="co"># temperature only normalisation as in the EU evaluation</span></span></span> +<span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">D24_2014</span>, study_moisture_ref_source <span class="op">=</span> <span class="st">"focus"</span>, f_na <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> $f_time_norm was (re)set to normalised values</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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The table assumes field capacity +corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" 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href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/focus_soil_moisture.R'><code>R/focus_soil_moisture.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/focus_soil_moisture.R" class="external-link"><code>R/focus_soil_moisture.R</code></a></small> <div class="hidden name"><code>focus_soil_moisture.Rd</code></div> </div> @@ -149,58 +94,60 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.</p> </div> - <pre class="usage"><span class='va'>focus_soil_moisture</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">focus_soil_moisture</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A matrix with upper case USDA soil classes as row names, and water tension ('pF1', 'pF2', 'pF 2.5') as column names</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment -Version 2.2, May 2014 <a href='https://esdac.jrc.ec.europa.eu/projects/ground-water'>https://esdac.jrc.ec.europa.eu/projects/ground-water</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>focus_soil_moisture</span> -</div><div class='output co'>#> pF1 pF2 pF2.5 -#> Sand 24 12 7 -#> Loamy sand 24 14 9 -#> Sandy loam 27 19 15 -#> Sandy clay loam 28 22 18 -#> Clay loam 32 28 25 -#> Loam 31 25 21 -#> Silt loam 32 26 21 -#> Silty clay loam 34 30 27 -#> Silt 31 27 21 -#> Sandy clay 41 35 31 -#> Silty clay 44 40 36 -#> Clay 53 48 43</div></pre> +Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-water" class="external-link">https://esdac.jrc.ec.europa.eu/projects/ground-water</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">focus_soil_moisture</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> pF1 pF2 pF2.5</span> +<span class="r-out co"><span class="r-pr">#></span> Sand 24 12 7</span> +<span class="r-out co"><span class="r-pr">#></span> Loamy sand 24 14 9</span> +<span class="r-out co"><span class="r-pr">#></span> Sandy loam 27 19 15</span> +<span class="r-out co"><span class="r-pr">#></span> Sandy clay loam 28 22 18</span> +<span class="r-out co"><span class="r-pr">#></span> Clay loam 32 28 25</span> +<span class="r-out co"><span class="r-pr">#></span> Loam 31 25 21</span> +<span class="r-out co"><span class="r-pr">#></span> Silt loam 32 26 21</span> +<span class="r-out co"><span class="r-pr">#></span> Silty clay loam 34 30 27</span> +<span class="r-out co"><span class="r-pr">#></span> Silt 31 27 21</span> +<span class="r-out co"><span class="r-pr">#></span> Sandy clay 41 35 31</span> +<span class="r-out co"><span class="r-pr">#></span> Silty clay 44 40 36</span> +<span class="r-out co"><span class="r-pr">#></span> Clay 53 48 43</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes 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navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Retrieve a degradation function from the mmkin namespace</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> <div class="hidden name"><code>get_deg_func.Rd</code></div> </div> @@ -147,39 +92,39 @@ <p>Retrieve a degradation function from the mmkin namespace</p> </div> - <pre class="usage"><span class='fu'>get_deg_func</span><span class='op'>(</span><span class='op'>)</span></pre> - + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_deg_func</span><span class="op">(</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="value"> + <h2>Value</h2> + - <p>A function that was likely previously assigned from within +<p>A function that was likely previously assigned from within nlme.mmkin</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/hierarchical_kinetics.html b/docs/dev/reference/hierarchical_kinetics.html new file mode 100644 index 00000000..bedb8753 --- /dev/null +++ b/docs/dev/reference/hierarchical_kinetics.html @@ -0,0 +1,154 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Hierarchical kinetics template — hierarchical_kinetics • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Hierarchical kinetics template — hierarchical_kinetics"><meta property="og:description" content="R markdown format for setting up hierarchical kinetics based on a template +provided with the mkin package."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"><li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Hierarchical kinetics template</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/hierarchical_kinetics.R" class="external-link"><code>R/hierarchical_kinetics.R</code></a></small> + <div class="hidden name"><code>hierarchical_kinetics.Rd</code></div> + </div> + + <div class="ref-description"> + <p>R markdown format for setting up hierarchical kinetics based on a template +provided with the mkin package.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">hierarchical_kinetics</span><span class="op">(</span><span class="va">...</span>, keep_tex <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>...</dt> +<dd><p>Arguments to <code><a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a></code></p></dd> + + +<dt>keep_tex</dt> +<dd><p>Keep the intermediate tex file used in the conversion to PDF</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>R Markdown output format to pass to +<code><a href="https://pkgs.rstudio.com/rmarkdown/reference/render.html" class="external-link">render</a></code></p> + + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rstudio/rmarkdown" class="external-link">rmarkdown</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://pkgs.rstudio.com/rmarkdown/reference/draft.html" class="external-link">draft</a></span><span class="op">(</span><span class="st">"example_analysis.rmd"</span>, template <span class="op">=</span> <span class="st">"hierarchical_kinetics"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/illparms.html b/docs/dev/reference/illparms.html index c0de4115..9c498e1c 100644 --- a/docs/dev/reference/illparms.html +++ b/docs/dev/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ without parameter transformations is used."><meta name="robots" content="noindex <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -113,7 +116,14 @@ without parameter transformations is used.</p> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu">illparms</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> conf.level <span class="op">=</span> <span class="fl">0.95</span>,</span> +<span> random <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> errmod <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> slopes <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for illparms.saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> @@ -151,6 +161,12 @@ without parameter transformations is used.</p> <dd><p>For hierarchical fits, should error model parameters be tested?</p></dd> + +<dt>slopes</dt> +<dd><p>For hierarchical <a href="saem.html">saem</a> fits using saemix as backend, +should slope parameters in the covariate model(starting with 'beta_') be +tested?</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html index 452647d6..c1396303 100644 --- a/docs/dev/reference/ilr.html +++ b/docs/dev/reference/ilr.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Function to perform isometric log-ratio transformation — ilr • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" 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data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ transformations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ transformations." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to perform isometric log-ratio transformation</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/ilr.R'><code>R/ilr.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ilr.R" class="external-link"><code>R/ilr.R</code></a></small> <div class="hidden name"><code>ilr.Rd</code></div> </div> @@ -149,86 +94,100 @@ transformations." /> transformations.</p> </div> - <pre class="usage"><span class='fu'>ilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> - -<span class='fu'>invilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">invilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>A numeric vector. Naturally, the forward transformation is only -sensible for vectors with all elements being greater than zero.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>A numeric vector. Naturally, the forward transformation is only +sensible for vectors with all elements being greater than zero.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + - <p>The result of the forward or backward transformation. The returned +<p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Another implementation can be found in R package + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>René Lehmann and Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># Order matters</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> -<span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fl'>2.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> -<span class='fu'>invilr</span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> -<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>invilr</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>)</span> <span class='co'># Four elements</span> -</div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='fl'>1</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># Gives c(0.1, 0.3, 0.5)</span> -</div><div class='output co'>#> [1] 0.1 0.3 0.5</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Order matters</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">1</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] -1.628174 -2.820079</span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1.628174 2.820079</span> +<span class="r-in"><span><span class="co"># Equal entries give ilr transformations with zeros as elements</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0 0</span> +<span class="r-in"><span><span class="co"># Almost equal entries give small numbers</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.3</span>, <span class="fl">0.4</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] -0.2034219 0.1174457</span> +<span class="r-in"><span><span class="co"># Only the ratio between the numbers counts, not their sum</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fl">2.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> +<span class="r-in"><span><span class="co"># Inverse transformation of larger numbers gives unequal elements</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="op">-</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 7.213536e-07 9.999993e-01</span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 7.207415e-07 9.991507e-01 8.486044e-04</span> +<span class="r-in"><span><span class="co"># The sum of the elements of the inverse ilr is 1</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> +<span class="r-in"><span><span class="co"># This is why we do not need all elements of the inverse transformation to go back:</span></span></span> +<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">invilr</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span> <span class="co"># Four elements</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 4</span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="fl">1</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="co"># Gives c(0.1, 0.3, 0.5)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.1 0.3 0.5</span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 5a0ec596..b6d2db20 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -17,13 +17,13 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -34,6 +34,8 @@ <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -41,22 +43,29 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -64,6 +73,14 @@ <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -195,6 +212,10 @@ of an mmkin object</p></td> <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p> </th> </tr></tbody><tbody><tr><td> + <p><code><a href="hierarchical_kinetics.html">hierarchical_kinetics()</a></code> </p> + </td> + <td><p>Hierarchical kinetics template</p></td> + </tr><tr><td> <p><code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> </p> </td> <td><p>Read datasets and relevant meta information from a spreadsheet file</p></td> @@ -268,9 +289,9 @@ degradation models and one or more error models</p></td> <p class="section-desc"></p> </th> </tr></tbody><tbody><tr><td> - <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p> + <p><code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> </p> </td> - <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td> + <td><p>Synthetic data for hierarchical kinetic degradation models</p></td> </tr><tr><td> <p><code><a href="D24_2014.html">D24_2014</a></code> </p> </td> @@ -328,6 +349,10 @@ degradation models and one or more error models</p></td> </td> <td><p>Three experimental datasets from two water sediment systems and one soil</p></td> </tr><tr><td> + <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p> + </td> + <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td> + </tr><tr><td> <p><code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> </p> </td> <td><p>A dataset class for mkin</p></td> @@ -352,9 +377,9 @@ degradation models and one or more error models</p></td> <p class="section-desc"></p> </th> </tr></tbody><tbody><tr><td> - <p><code><a href="tex_listing.html">tex_listing()</a></code> </p> + <p><code><a href="summary_listing.html">summary_listing()</a></code> <code><a href="summary_listing.html">tex_listing()</a></code> <code><a href="summary_listing.html">html_listing()</a></code> </p> </td> - <td><p>Wrap the output of a summary function in tex listing environment</p></td> + <td><p>Display the output of a summary function according to the output format</p></td> </tr><tr><td> <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p> </td> @@ -489,7 +514,7 @@ kinetic models fitted with mkinfit</p></td> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> diff --git a/docs/dev/reference/intervals.saem.mmkin.html b/docs/dev/reference/intervals.saem.mmkin.html index ee714ad0..e67d8da0 100644 --- a/docs/dev/reference/intervals.saem.mmkin.html +++ b/docs/dev/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html index 314cb923..27e55455 100644 --- a/docs/dev/reference/llhist.html +++ b/docs/dev/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><meta name="robots" content="noin </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ original fit is shown as a red vertical line."><meta name="robots" content="noin <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png Binary files differindex d6006ecc..f1dc5fa7 100644 --- a/docs/dev/reference/loftest-1.png +++ b/docs/dev/reference/loftest-1.png diff --git a/docs/dev/reference/loftest-2.png b/docs/dev/reference/loftest-2.png Binary files differindex 4d0dc551..3f1015a9 100644 --- a/docs/dev/reference/loftest-2.png +++ b/docs/dev/reference/loftest-2.png diff --git a/docs/dev/reference/loftest-3.png b/docs/dev/reference/loftest-3.png Binary files differindex 6afd084b..d897c363 100644 --- 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It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test -lrtest.default from the lmtest package." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +lrtest.default from the lmtest package."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,48 +44,50 @@ lrtest.default from the lmtest package." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Lack-of-fit test for models fitted to data with replicates</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/loftest.R'><code>R/loftest.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/loftest.R" class="external-link"><code>R/loftest.R</code></a></small> <div class="hidden name"><code>loftest.Rd</code></div> </div> @@ -150,216 +95,231 @@ lrtest.default from the lmtest package." /> <p>This is a generic function with a method currently only defined for mkinfit objects. It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test -<code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code> from the lmtest package.</p> +<code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> from the lmtest package.</p> </div> - <pre class="usage"><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A model object with a defined loftest method</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A model object with a defined loftest method</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +<dt>...</dt> +<dd><p>Not used</p></dd> +</dl></div> + <div id="details"> + <h2>Details</h2> <p>The anova model is interpreted as the simplest form of an mkinfit model, assuming only a constant variance about the means, but not enforcing any structure of the means, so we have one model parameter for every mean of replicate samples.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>lrtest</p></div> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>lrtest</p></div> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>test_data</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span> -<span class='va'>sfo_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We see a clear pattern in the residuals</span> -</div><div class='img'><img src='loftest-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We have a clear lack of fit</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: SFO with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 10 -40.710 -#> 2 3 -63.954 -7 46.487 7.027e-08 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='co'># We try a different model (the one that was used to generate the data)</span> -<span class='va'>dfop_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># We don't see systematic deviations, but heteroscedastic residuals</span> -</div><div class='img'><img src='loftest-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># therefore we should consider adapting the error model, although we have</span> -<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># no lack of fit</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: DFOP with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 10 -40.710 -#> 2 5 -42.453 -5 3.485 0.6257</div><div class='input'><span class='co'>#</span> -<span class='co'># This is the anova model used internally for the comparison</span> -<span class='va'>test_data_anova</span> <span class='op'><-</span> <span class='va'>test_data</span> -<span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span> -<span class='va'>anova_fit</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='va'>time</span>, data <span class='op'>=</span> <span class='va'>test_data_anova</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> -</div><div class='output co'>#> -#> Call: -#> lm(formula = value ~ time, data = test_data_anova) -#> -#> Residuals: -#> Min 1Q Median 3Q Max -#> -6.1000 -0.5625 0.0000 0.5625 6.1000 -#> -#> Coefficients: -#> Estimate Std. Error t value Pr(>|t|) -#> (Intercept) 103.150 2.323 44.409 7.44e-12 *** -#> time1 -19.950 3.285 -6.073 0.000185 *** -#> time3 -50.800 3.285 -15.465 8.65e-08 *** -#> time7 -68.500 3.285 -20.854 6.28e-09 *** -#> time14 -79.750 3.285 -24.278 1.63e-09 *** -#> time28 -86.000 3.285 -26.181 8.35e-10 *** -#> time60 -94.900 3.285 -28.891 3.48e-10 *** -#> time90 -98.500 3.285 -29.986 2.49e-10 *** -#> time120 -100.450 3.285 -30.580 2.09e-10 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -#> -#> Residual standard error: 3.285 on 9 degrees of freedom -#> Multiple R-squared: 0.9953, Adjusted R-squared: 0.9912 -#> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09 -#> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> <span class='co'># We get the same likelihood and degrees of freedom</span> -</div><div class='output co'>#> 'log Lik.' -40.71015 (df=10)</div><div class='input'><span class='co'>#</span> -<span class='va'>test_data_2</span> <span class='op'><-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span> -<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_lin_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> <span class='co'># not a good model, we try parallel formation</span> -</div><div class='img'><img src='loftest-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 28 -93.606 -#> 2 7 -171.927 -21 156.64 < 2.2e-16 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='va'>m_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_par_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> <span class='co'># much better for metabolites</span> -</div><div class='img'><img src='loftest-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 28 -93.606 -#> 2 7 -156.331 -21 125.45 < 2.2e-16 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>dfop_par_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># No visual lack of fit</span> -</div><div class='img'><img src='loftest-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># no lack of fit found by the test</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 28 -93.606 -#> 2 9 -102.763 -19 18.313 0.5016</div><div class='input'><span class='co'>#</span> -<span class='co'># The anova model used for comparison in the case of transformation products</span> -<span class='va'>test_data_anova_2</span> <span class='op'><-</span> <span class='va'>dfop_par_fit</span><span class='op'>$</span><span class='va'>data</span> -<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span><span class='op'>)</span> -<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span> -<span class='va'>anova_fit_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>observed</span> <span class='op'>~</span> <span class='va'>time</span><span class='op'>:</span><span class='va'>variable</span> <span class='op'>-</span> <span class='fl'>1</span>, data <span class='op'>=</span> <span class='va'>test_data_anova_2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit_2</span><span class='op'>)</span> -</div><div class='output co'>#> -#> Call: -#> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2) -#> -#> Residuals: -#> Min 1Q Median 3Q Max -#> -6.1000 -0.5875 0.0000 0.5875 6.1000 -#> -#> Coefficients: (2 not defined because of singularities) -#> Estimate Std. Error t value Pr(>|t|) -#> time0:variableparent 103.150 1.573 65.562 < 2e-16 *** -#> time1:variableparent 83.200 1.573 52.882 < 2e-16 *** -#> time3:variableparent 52.350 1.573 33.274 < 2e-16 *** -#> time7:variableparent 34.650 1.573 22.024 < 2e-16 *** -#> time14:variableparent 23.400 1.573 14.873 6.35e-14 *** -#> time28:variableparent 17.150 1.573 10.901 5.47e-11 *** -#> time60:variableparent 8.250 1.573 5.244 1.99e-05 *** -#> time90:variableparent 4.650 1.573 2.956 0.006717 ** -#> time120:variableparent 2.700 1.573 1.716 0.098507 . -#> time0:variableM1 NA NA NA NA -#> time1:variableM1 11.850 1.573 7.532 6.93e-08 *** -#> time3:variableM1 22.700 1.573 14.428 1.26e-13 *** -#> time7:variableM1 33.050 1.573 21.007 < 2e-16 *** -#> time14:variableM1 31.250 1.573 19.863 < 2e-16 *** -#> time28:variableM1 18.900 1.573 12.013 7.02e-12 *** -#> time60:variableM1 7.550 1.573 4.799 6.28e-05 *** -#> time90:variableM1 3.850 1.573 2.447 0.021772 * -#> time120:variableM1 2.050 1.573 1.303 0.204454 -#> time0:variableM2 NA NA NA NA -#> time1:variableM2 6.700 1.573 4.259 0.000254 *** -#> time3:variableM2 16.750 1.573 10.646 8.93e-11 *** -#> time7:variableM2 25.800 1.573 16.399 6.89e-15 *** -#> time14:variableM2 28.600 1.573 18.178 6.35e-16 *** -#> time28:variableM2 25.400 1.573 16.144 9.85e-15 *** -#> time60:variableM2 21.600 1.573 13.729 3.81e-13 *** -#> time90:variableM2 17.800 1.573 11.314 2.51e-11 *** -#> time120:variableM2 14.100 1.573 8.962 2.79e-09 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -#> -#> Residual standard error: 2.225 on 25 degrees of freedom -#> Multiple R-squared: 0.9979, Adjusted R-squared: 0.9957 -#> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16 -#> </div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We see a clear pattern in the residuals</span></span></span> +<span class="r-plt img"><img src="loftest-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We have a clear lack of fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 10 -40.710 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -7 46.487 7.027e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># We try a different model (the one that was used to generate the data)</span></span></span> +<span class="r-in"><span><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># We don't see systematic deviations, but heteroscedastic residuals</span></span></span> +<span class="r-plt img"><img src="loftest-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># therefore we should consider adapting the error model, although we have</span></span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># no lack of fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> 1 10 -40.710 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -5 3.485 0.6257</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># This is the anova model used internally for the comparison</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova</span> <span class="op"><-</span> <span class="va">test_data</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">anova_fit</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="va">time</span>, data <span class="op">=</span> <span class="va">test_data_anova</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Call:</span> +<span class="r-out co"><span class="r-pr">#></span> lm(formula = value ~ time, data = test_data_anova)</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residuals:</span> +<span class="r-out co"><span class="r-pr">#></span> Min 1Q Median 3Q Max </span> +<span class="r-out co"><span class="r-pr">#></span> -6.1000 -0.5625 0.0000 0.5625 6.1000 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Coefficients:</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error t value Pr(>|t|) </span> +<span class="r-out co"><span class="r-pr">#></span> (Intercept) 103.150 2.323 44.409 7.44e-12 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time1 -19.950 3.285 -6.073 0.000185 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3 -50.800 3.285 -15.465 8.65e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7 -68.500 3.285 -20.854 6.28e-09 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14 -79.750 3.285 -24.278 1.63e-09 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28 -86.000 3.285 -26.181 8.35e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60 -94.900 3.285 -28.891 3.48e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90 -98.500 3.285 -29.986 2.49e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time120 -100.450 3.285 -30.580 2.09e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residual standard error: 3.285 on 9 degrees of freedom</span> +<span class="r-out co"><span class="r-pr">#></span> Multiple R-squared: 0.9953, Adjusted R-squared: 0.9912 </span> +<span class="r-out co"><span class="r-pr">#></span> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span> <span class="co"># We get the same likelihood and degrees of freedom</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 'log Lik.' -40.71015 (df=10)</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">test_data_2</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">sfo_lin_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span> <span class="co"># not a good model, we try parallel formation</span></span></span> +<span class="r-plt img"><img src="loftest-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 7 -171.927 -21 156.64 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">sfo_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span> <span class="co"># much better for metabolites</span></span></span> +<span class="r-plt img"><img src="loftest-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 7 -156.331 -21 125.45 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">dfop_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># No visual lack of fit</span></span></span> +<span class="r-plt img"><img src="loftest-5.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># no lack of fit found by the test</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 9 -102.763 -19 18.313 0.5016</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The anova model used for comparison in the case of transformation products</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span> <span class="op"><-</span> <span class="va">dfop_par_fit</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">anova_fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">observed</span> <span class="op">~</span> <span class="va">time</span><span class="op">:</span><span class="va">variable</span> <span class="op">-</span> <span class="fl">1</span>, data <span class="op">=</span> <span class="va">test_data_anova_2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Call:</span> +<span class="r-out co"><span class="r-pr">#></span> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2)</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residuals:</span> +<span class="r-out co"><span class="r-pr">#></span> Min 1Q Median 3Q Max </span> +<span class="r-out co"><span class="r-pr">#></span> -6.1000 -0.5875 0.0000 0.5875 6.1000 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Coefficients: (2 not defined because of singularities)</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error t value Pr(>|t|) </span> +<span class="r-out co"><span class="r-pr">#></span> time0:variableparent 103.150 1.573 65.562 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time1:variableparent 83.200 1.573 52.882 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3:variableparent 52.350 1.573 33.274 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7:variableparent 34.650 1.573 22.024 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14:variableparent 23.400 1.573 14.873 6.35e-14 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28:variableparent 17.150 1.573 10.901 5.47e-11 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60:variableparent 8.250 1.573 5.244 1.99e-05 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90:variableparent 4.650 1.573 2.956 0.006717 ** </span> +<span class="r-out co"><span class="r-pr">#></span> time120:variableparent 2.700 1.573 1.716 0.098507 . </span> +<span class="r-out co"><span class="r-pr">#></span> time0:variableM1 NA NA NA NA </span> +<span class="r-out co"><span class="r-pr">#></span> time1:variableM1 11.850 1.573 7.532 6.93e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3:variableM1 22.700 1.573 14.428 1.26e-13 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7:variableM1 33.050 1.573 21.007 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14:variableM1 31.250 1.573 19.863 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28:variableM1 18.900 1.573 12.013 7.02e-12 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60:variableM1 7.550 1.573 4.799 6.28e-05 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90:variableM1 3.850 1.573 2.447 0.021772 * </span> +<span class="r-out co"><span class="r-pr">#></span> time120:variableM1 2.050 1.573 1.303 0.204454 </span> +<span class="r-out co"><span class="r-pr">#></span> time0:variableM2 NA NA NA NA </span> +<span class="r-out co"><span class="r-pr">#></span> time1:variableM2 6.700 1.573 4.259 0.000254 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3:variableM2 16.750 1.573 10.646 8.93e-11 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7:variableM2 25.800 1.573 16.399 6.89e-15 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14:variableM2 28.600 1.573 18.178 6.35e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28:variableM2 25.400 1.573 16.144 9.85e-15 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60:variableM2 21.600 1.573 13.729 3.81e-13 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90:variableM2 17.800 1.573 11.314 2.51e-11 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time120:variableM2 14.100 1.573 8.962 2.79e-09 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residual standard error: 2.225 on 25 degrees of freedom</span> +<span class="r-out co"><span class="r-pr">#></span> Multiple R-squared: 0.9979, Adjusted R-squared: 0.9957 </span> +<span class="r-out co"><span class="r-pr">#></span> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index 3e9452c6..e77121d1 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - 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<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,136 +45,143 @@ the error model." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculated the log-likelihood of a fitted mkinfit object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/logLik.mkinfit.R'><code>R/logLik.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/logLik.mkinfit.R" class="external-link"><code>R/logLik.mkinfit.R</code></a></small> <div class="hidden name"><code>logLik.mkinfit.Rd</code></div> </div> <div class="ref-description"> <p>This function returns the product of the likelihood densities of each observed value, as calculated as part of the fitting procedure using -<code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution, and with the means +<code><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">dnorm</a></code>, i.e. assuming normal distribution, and with the means predicted by the degradation model, and the standard deviations predicted by the error model.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></code> with the number of estimated + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></code> with the number of estimated parameters (degradation model parameters plus variance model parameters) as attribute.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>The total number of estimated parameters returned with the value of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Compare the AIC of columns of <code><a href='mmkin.html'>mmkin</a></code> objects using -<code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Compare the AIC of columns of <code><a href="mmkin.html">mmkin</a></code> objects using +<code><a href="AIC.mmkin.html">AIC.mmkin</a></code>.</p></div> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># \dontrun{</span> - <span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span> - <span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> - <span class='va'>f_nw</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span> - <span class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> - <span class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> f_nw 5 204.4486 -#> f_obs 6 205.8727 -#> f_tc 6 141.9656</div><div class='input'> <span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">d_t</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nw</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">sfo_sfo</span>, <span class="va">d_t</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># no weighting (weights are unity)</span></span></span> +<span class="r-in"><span> <span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nw</span>, <span class="va">f_obs</span>, <span class="va">f_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_nw 5 204.4486</span> +<span class="r-out co"><span class="r-pr">#></span> f_obs 6 205.8727</span> +<span class="r-out co"><span class="r-pr">#></span> f_tc 6 141.9656</span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html index ebef3b10..fc06b36f 100644 --- a/docs/dev/reference/logLik.saem.mmkin.html +++ b/docs/dev/reference/logLik.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html index 1d1880fd..ac4961bc 100644 --- a/docs/dev/reference/logistic.solution.html +++ b/docs/dev/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><meta name=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ an increasing rate constant, supposedly caused by microbial growth"><meta name=" <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html index f2d8472e..a7198474 100644 --- a/docs/dev/reference/lrtest.mkinfit.html +++ b/docs/dev/reference/lrtest.mkinfit.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Likelihood ratio test for mkinfit models — lrtest.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - 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If two fitted +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Likelihood ratio test for mkinfit models — lrtest.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Likelihood ratio test for mkinfit models — lrtest.mkinfit"><meta property="og:description" content="Compare two mkinfit models based on their likelihood. If two fitted mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure that the models are nested, i.e. one of them has less degrees of freedom -and can be expressed by fixing the parameters of the other." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +and can be expressed by fixing the parameters of the other."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ and can be expressed by fixing the parameters of the other." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,48 +45,50 @@ and can be expressed by fixing the parameters of the other." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Likelihood ratio test for mkinfit models</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a></small> <div class="hidden name"><code>lrtest.mkinfit.Rd</code></div> </div> @@ -155,115 +100,117 @@ that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>object</span>, object_2 <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, object_2 <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object, or an <code><a href="mmkin.html">mmkin</a></code> column +object containing two fits to the same data.</p></dd> + -<span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> +<dt>object_2</dt> +<dd><p>Optionally, another mkinfit object fitted to the same data.</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object, or an <code><a href='mmkin.html'>mmkin</a></code> column -object containing two fits to the same data.</p></td> - </tr> - <tr> - <th>object_2</th> - <td><p>Optionally, another mkinfit object fitted to the same data.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Argument to <code><a href='mkinfit.html'>mkinfit</a></code>, passed to -<code><a href='update.mkinfit.html'>update.mkinfit</a></code> for creating the alternative fitted object.</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +<dt>...</dt> +<dd><p>Argument to <code><a href="mkinfit.html">mkinfit</a></code>, passed to +<code><a href="update.mkinfit.html">update.mkinfit</a></code> for creating the alternative fitted object.</p></dd> +</dl></div> + <div id="details"> + <h2>Details</h2> <p>Alternatively, an argument to mkinfit can be given which is then passed -to <code><a href='update.mkinfit.html'>update.mkinfit</a></code> to obtain the alternative model.</p> -<p>The comparison is then made by the <code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code> +to <code><a href="update.mkinfit.html">update.mkinfit</a></code> to obtain the alternative model.</p> +<p>The comparison is then made by the <code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> method from the lmtest package. The model with the higher number of fitted parameters (alternative hypothesis) is listed first, then the model with the lower number of fitted parameters (null hypothesis).</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>test_data</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span> -<span class='va'>sfo_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>dfop_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='va'>sfo_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model const -#> Model 2: SFO with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 5 -42.453 -#> 2 3 -63.954 -2 43.002 4.594e-10 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>sfo_fit</span>, <span class='va'>dfop_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model const -#> Model 2: SFO with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 5 -42.453 -#> 2 3 -63.954 -2 43.002 4.594e-10 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'> -<span class='co'># The following two examples are commented out as they fail during</span> -<span class='co'># generation of the static help pages by pkgdown</span> -<span class='co'>#lrtest(dfop_fit, error_model = "tc")</span> -<span class='co'>#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span> - -<span class='co'># However, this equivalent syntax also works for static help pages</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model tc -#> Model 2: DFOP with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 6 -34.587 -#> 2 5 -42.453 -1 15.731 7.302e-05 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, fixed_parms <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model const -#> Model 2: DFOP with error model const and fixed parameter(s) k2 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 5 -42.453 -#> 2 4 -57.340 -1 29.776 4.851e-08 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="va">sfo_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">sfo_fit</span>, <span class="va">dfop_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following two examples are commented out as they fail during</span></span></span> +<span class="r-in"><span><span class="co"># generation of the static help pages by pkgdown</span></span></span> +<span class="r-in"><span><span class="co">#lrtest(dfop_fit, error_model = "tc")</span></span></span> +<span class="r-in"><span><span class="co">#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># However, this equivalent syntax also works for static help pages</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model tc</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 6 -34.587 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -1 15.731 7.302e-05 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, fixed_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const and fixed parameter(s) k2</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 4 -57.340 -1 29.776 4.851e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div 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Currently, only calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models, using the analytical formulas given in the PEC -soil section of the FOCUS guidance." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +soil section of the FOCUS guidance."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -104,171 +47,176 @@ soil section of the FOCUS guidance." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/max_twa_parent.R'><code>R/max_twa_parent.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/max_twa_parent.R" class="external-link"><code>R/max_twa_parent.R</code></a></small> <div class="hidden name"><code>max_twa_parent.Rd</code></div> </div> <div class="ref-description"> <p>This function calculates maximum moving window time weighted average -concentrations (TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. +concentrations (TWAs) for kinetic models fitted with <code><a href="mkinfit.html">mkinfit</a></code>. Currently, only calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models, using the analytical formulas given in the PEC soil section of the FOCUS guidance.</p> </div> - <pre class="usage"><span class='fu'>max_twa_parent</span><span class='op'>(</span><span class='va'>fit</span>, <span class='va'>windows</span><span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="va">windows</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_sfo</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_fomc</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">alpha</span>, <span class="va">beta</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_dfop</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_hs</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span>, <span class="va">t</span><span class="op">)</span></span></code></pre></div> + </div> -<span class='fu'>max_twa_sfo</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k</span>, <span class='va'>t</span><span class='op'>)</span> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>fit</dt> +<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> -<span class='fu'>max_twa_fomc</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>alpha</span>, <span class='va'>beta</span>, <span class='va'>t</span><span class='op'>)</span> -<span class='fu'>max_twa_dfop</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>g</span>, <span class='va'>t</span><span class='op'>)</span> +<dt>windows</dt> +<dd><p>The width of the time windows for which the TWAs should be +calculated.</p></dd> -<span class='fu'>max_twa_hs</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>tb</span>, <span class='va'>t</span><span class='op'>)</span></pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>fit</th> - <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>windows</th> - <td><p>The width of the time windows for which the TWAs should be -calculated.</p></td> - </tr> - <tr> - <th>M0</th> - <td><p>The initial concentration for which the maximum time weighted +<dt>M0</dt> +<dd><p>The initial concentration for which the maximum time weighted average over the decline curve should be calculated. The default is to use a value of 1, which means that a relative maximum time weighted average -factor (f_twa) is calculated.</p></td> - </tr> - <tr> - <th>k</th> - <td><p>The rate constant in the case of SFO kinetics.</p></td> - </tr> - <tr> - <th>t</th> - <td><p>The width of the time window.</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>Parameter of the FOMC model.</p></td> - </tr> - <tr> - <th>beta</th> - <td><p>Parameter of the FOMC model.</p></td> - </tr> - <tr> - <th>k1</th> - <td><p>The first rate constant of the DFOP or the HS kinetics.</p></td> - </tr> - <tr> - <th>k2</th> - <td><p>The second rate constant of the DFOP or the HS kinetics.</p></td> - </tr> - <tr> - <th>g</th> - <td><p>Parameter of the DFOP model.</p></td> - </tr> - <tr> - <th>tb</th> - <td><p>Parameter of the HS model.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>For <code>max_twa_parent</code>, a numeric vector, named using the +factor (f_twa) is calculated.</p></dd> + + +<dt>k</dt> +<dd><p>The rate constant in the case of SFO kinetics.</p></dd> + + +<dt>t</dt> +<dd><p>The width of the time window.</p></dd> + + +<dt>alpha</dt> +<dd><p>Parameter of the FOMC model.</p></dd> + + +<dt>beta</dt> +<dd><p>Parameter of the FOMC model.</p></dd> + + +<dt>k1</dt> +<dd><p>The first rate constant of the DFOP or the HS kinetics.</p></dd> + + +<dt>k2</dt> +<dd><p>The second rate constant of the DFOP or the HS kinetics.</p></dd> + + +<dt>g</dt> +<dd><p>Parameter of the DFOP model.</p></dd> + + +<dt>tb</dt> +<dd><p>Parameter of the HS model.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>For <code>max_twa_parent</code>, a numeric vector, named using the <code>windows</code> argument. For the other functions, a numeric vector of length one (also known as 'a number').</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'>max_twa_parent</span><span class='op'>(</span><span class='va'>fit</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>7</span>, <span class='fl'>21</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> 7 21 -#> 34.71343 18.22124 </div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 7 21 </span> +<span class="r-out co"><span class="r-pr">#></span> 34.71343 18.22124 </span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,44 +43,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> @@ -151,120 +96,135 @@ extracts.</p> </div> - <pre class="usage"><span class='va'>mccall81_245T</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div> + </div> - <p>A dataframe containing the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as + <div id="format"> + <h2>Format</h2> + <p>A dataframe containing the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using - <code><a href='mkinmod.html'>mkinmod</a></code>.</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing sampling times in days after + <code><a href="mkinmod.html">mkinmod</a></code>.</p></dd> + + <dt><code>time</code></dt> +<dd><p>a numeric vector containing sampling times in days after treatment</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> - <dt><code>soil</code></dt><dd><p>a factor containing the name of the soil</p></dd> - -</dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> + + <dt><code>soil</code></dt> +<dd><p>a factor containing the name of the soil</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - doi: <a href='https://doi.org/10.1021/jf00103a026'>10.1021/jf00103a026</a></p> + <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>SFO_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, - phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span><span class='op'>)</span>, - anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span> - <span class='va'>fit.1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 -#> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02 -#> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05 -#> Lower Upper -#> T245_0 99.246061385 1.084640e+02 -#> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013879 7.525762e-01 -#> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559081 6.924813e-01 -#> f_phenol_to_anisole 0.000000000 1.000000e+00 -#> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 -#> -#> $distimes -#> DT50 DT90 -#> T245 15.982025 53.09114 -#> phenol 1.711229 5.68458 -#> anisole 103.784093 344.76329 -#> </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span> - <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span> - <span class='co'># the sink in the model generation</span> - <span class='va'>SFO_SFO_SFO_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, - phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO_2</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, - quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 -#> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587 -#> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637 -#> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 -#> Upper -#> T245_0 108.43904074 -#> k_T245 0.04743877 -#> k_phenol 0.75005585 -#> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212308 -#> sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 -#> -#> $distimes -#> DT50 DT90 -#> T245 15.982025 53.09114 -#> phenol 1.711229 5.68458 -#> anisole 103.784093 344.76329 -#> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit.1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span> +<span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061385 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559081 6.924813e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.706607296 3.322649e+00</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> +<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span></span> +<span class="r-in"><span> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span></span> +<span class="r-in"><span> <span class="co"># the sink in the model generation</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> +<span class="r-out co"><span class="r-pr">#></span> Upper</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904074</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005585</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212308</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> +<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mean_degparms.html b/docs/dev/reference/mean_degparms.html index 67db1868..feb37a1d 100644 --- a/docs/dev/reference/mean_degparms.html +++ b/docs/dev/reference/mean_degparms.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mhmkin-1.png b/docs/dev/reference/mhmkin-1.png Binary files differnew file mode 100644 index 00000000..2ecb6759 --- /dev/null +++ b/docs/dev/reference/mhmkin-1.png diff --git a/docs/dev/reference/mhmkin-2.png b/docs/dev/reference/mhmkin-2.png Binary files differnew file mode 100644 index 00000000..9bb43d35 --- /dev/null +++ b/docs/dev/reference/mhmkin-2.png diff --git a/docs/dev/reference/mhmkin.html b/docs/dev/reference/mhmkin.html index e87e20a1..1328aa48 100644 --- a/docs/dev/reference/mhmkin.html +++ b/docs/dev/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -64,7 +64,10 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -110,7 +113,6 @@ mhmkin( backend = "saemix", algorithm = "saem", no_random_effect = NULL, - auto_ranef_threshold = 3, ..., cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL @@ -147,16 +149,14 @@ supported</p></dd> <dt>no_random_effect</dt> -<dd><p>Default is NULL and will be passed to <a href="saem.html">saem</a>. If -you specify "auto", random effects are only included if the number -of datasets in which the parameter passed the t-test is at least 'auto_ranef_threshold'. -Beware that while this may make for convenient model reduction or even -numerical stability of the algorithm, it will likely lead to -underparameterised models.</p></dd> - - -<dt>auto_ranef_threshold</dt> -<dd><p>See 'no_random_effect.</p></dd> +<dd><p>Default is NULL and will be passed to <a href="saem.html">saem</a>. If a +character vector is supplied, it will be passed to all calls to <a href="saem.html">saem</a>, +which will exclude random effects for all matching parameters. Alternatively, +a list of character vectors or an object of class <a href="illparms.html">illparms.mhmkin</a> can be +specified. They have to have the same dimensions that the return object of +the current call will have, i.e. the number of rows must match the number +of degradation models in the mmkin object(s), and the number of columns must +match the number of error models used in the mmkin object(s).</p></dd> <dt>cores</dt> @@ -200,7 +200,7 @@ and the error model names for the second index (column index), with class attribute 'mhmkin'.</p> -<p>An object of class <code>mhmkin</code>.</p> +<p>An object inheriting from <code>mhmkin</code>.</p> </div> <div id="see-also"> <h2>See also</h2> @@ -211,6 +211,88 @@ attribute 'mhmkin'.</p> <p>Johannes Ranke</p> </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># We start with separate evaluations of all the first six datasets with two</span></span></span> +<span class="r-in"><span><span class="co"># degradation models and two error models</span></span></span> +<span class="r-in"><span><span class="va">f_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="va">ds_fomc</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">6</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># The mhmkin function sets up hierarchical degradation models aka</span></span></span> +<span class="r-in"><span><span class="co"># nonlinear mixed-effects models for all four combinations, specifying</span></span></span> +<span class="r-in"><span><span class="co"># uncorrelated random effects for all degradation parameters</span></span></span> +<span class="r-in"><span><span class="va">f_saem_1</span> <span class="op"><-</span> <span class="fu">mhmkin</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_sep_const</span>, <span class="va">f_sep_tc</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="status.html">status</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> error</span> +<span class="r-out co"><span class="r-pr">#></span> degradation const tc</span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: Fit terminated successfully</span> +<span class="r-in"><span><span class="co"># The 'illparms' function shows that in all hierarchical fits, at least</span></span></span> +<span class="r-in"><span><span class="co"># one random effect is ill-defined (the confidence interval for the</span></span></span> +<span class="r-in"><span><span class="co"># random effect expressed as standard deviation includes zero)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> error</span> +<span class="r-out co"><span class="r-pr">#></span> degradation const tc </span> +<span class="r-out co"><span class="r-pr">#></span> SFO sd(parent_0) sd(parent_0) </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC sd(log_beta) sd(parent_0), sd(log_beta)</span> +<span class="r-in"><span><span class="co"># Therefore we repeat the fits, excluding the ill-defined random effects</span></span></span> +<span class="r-in"><span><span class="va">f_saem_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_1</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="status.html">status</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> error</span> +<span class="r-out co"><span class="r-pr">#></span> degradation const tc</span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: Fit terminated successfully</span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> error</span> +<span class="r-out co"><span class="r-pr">#></span> degradation const tc</span> +<span class="r-out co"><span class="r-pr">#></span> SFO </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC </span> +<span class="r-in"><span><span class="co"># Model comparisons show that FOMC with two-component error is preferable,</span></span></span> +<span class="r-in"><span><span class="co"># and confirms our reduction of the default parameter model</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 95 observations of 1 variable(s) grouped in 6 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> SFO const 5 574.40 573.35 -282.20</span> +<span class="r-out co"><span class="r-pr">#></span> SFO tc 6 543.72 542.47 -265.86</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC const 7 489.67 488.22 -237.84</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC tc 8 406.11 404.44 -195.05</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 95 observations of 1 variable(s) grouped in 6 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> SFO const 4 572.22 571.39 -282.11</span> +<span class="r-out co"><span class="r-pr">#></span> SFO tc 5 541.63 540.59 -265.81</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC const 6 487.38 486.13 -237.69</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC tc 6 402.12 400.88 -195.06</span> +<span class="r-in"><span><span class="co"># The convergence plot for the selected model looks fine</span></span></span> +<span class="r-in"><span><span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mhmkin-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># The plot of predictions versus data shows that we have a pretty data-rich</span></span></span> +<span class="r-in"><span><span class="co"># situation with homogeneous distribution of residuals, because we used the</span></span></span> +<span class="r-in"><span><span class="co"># same degradation model, error model and parameter distribution model that</span></span></span> +<span class="r-in"><span><span class="co"># was used in the data generation.</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"tc"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mhmkin-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># We can specify the same parameter model reductions manually</span></span></span> +<span class="r-in"><span><span class="va">no_ranef</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"parent_0"</span>, <span class="st">"log_beta"</span>, <span class="st">"parent_0"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"parent_0"</span>, <span class="st">"log_beta"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="va">no_ranef</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_2m</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_1</span>, no_random_effect <span class="op">=</span> <span class="va">no_ranef</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2m</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 95 observations of 1 variable(s) grouped in 6 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> SFO const 4 572.22 571.39 -282.11</span> +<span class="r-out co"><span class="r-pr">#></span> SFO tc 5 541.63 540.59 -265.81</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC const 6 487.38 486.13 -237.69</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC tc 6 402.12 400.88 -195.06</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> diff --git a/docs/dev/reference/mixed-1.png b/docs/dev/reference/mixed-1.png Binary files differindex 54b81b70..dbba1b03 100644 --- a/docs/dev/reference/mixed-1.png +++ b/docs/dev/reference/mixed-1.png diff --git a/docs/dev/reference/mixed.html b/docs/dev/reference/mixed.html index b2b83312..01a0614b 100644 --- a/docs/dev/reference/mixed.html +++ b/docs/dev/reference/mixed.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -41,19 +41,28 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -84,73 +93,84 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mixed.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mixed.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object</p></dd> + + <dt>...</dt> <dd><p>Currently not used</p></dd> + + <dt>method</dt> <dd><p>The method to be used</p></dd> + + <dt>x</dt> <dd><p>A mixed.mmkin object to print</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to use for printing.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An object of class 'mixed.mmkin' which has the observed data in a + + +<p>An object of class 'mixed.mmkin' which has the observed data in a single dataframe which is convenient for plotting</p> </div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span> -<span class="r-in"><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span> -<span class="r-in"><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span> -<span class="r-in"><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> -<span class="r-in"> k1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span> -<span class="r-in"> k2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span> -<span class="r-in"> g <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> f_parent_to_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> k_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"> <span class="op">}</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456L</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span> -<span class="r-in"> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span> -<span class="r-in"> n <span class="op">=</span> <span class="fl">1</span>, secondary <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"><span class="op">}</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span></span> +<span class="r-in"><span><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span></span> +<span class="r-in"><span><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> k1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> k2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> g <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> f_parent_to_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> k_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456L</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span></span> +<span class="r-in"><span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> n <span class="op">=</span> <span class="fl">1</span>, secondary <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic model fitted by nonlinear regression to each dataset</span> <span class="r-out co"><span class="r-pr">#></span> Structural model:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -177,9 +197,9 @@ single dataframe which is convenient for plotting</p> <span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> <span class="r-out co"><span class="r-pr">#></span> -0.087392 </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -194,7 +214,7 @@ single dataframe which is convenient for plotting</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html index 6246fbe2..3e55885f 100644 --- a/docs/dev/reference/mkin_long_to_wide.html +++ b/docs/dev/reference/mkin_long_to_wide.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" 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href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide"><meta property="og:description" content="This function takes a dataframe in the long form, i.e. with a row for each observed value, and converts it into a dataframe with one independent -variable and several dependent variables as columns." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +variable and several dependent variables as columns."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ variable and several dependent variables as columns." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,48 +43,50 @@ variable and several dependent variables as columns." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Convert a dataframe from long to wide format</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkin_long_to_wide.R'><code>R/mkin_long_to_wide.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_long_to_wide.R" class="external-link"><code>R/mkin_long_to_wide.R</code></a></small> <div class="hidden name"><code>mkin_long_to_wide.Rd</code></div> </div> @@ -151,87 +96,89 @@ observed value, and converts it into a dataframe with one independent variable and several dependent variables as columns.</p> </div> - <pre class="usage"><span class='fu'>mkin_long_to_wide</span><span class='op'>(</span><span class='va'>long_data</span>, time <span class='op'>=</span> <span class='st'>"time"</span>, outtime <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">long_data</span>, time <span class="op">=</span> <span class="st">"time"</span>, outtime <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>long_data</th> - <td><p>The dataframe must contain one variable called "time" with + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>long_data</dt> +<dd><p>The dataframe must contain one variable called "time" with the time values specified by the <code>time</code> argument, one column called "name" with the grouping of the observed values, and finally one column of -observed values called "value".</p></td> - </tr> - <tr> - <th>time</th> - <td><p>The name of the time variable in the long input data.</p></td> - </tr> - <tr> - <th>outtime</th> - <td><p>The name of the time variable in the wide output data.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>Dataframe in wide format.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +observed values called "value".</p></dd> + + +<dt>time</dt> +<dd><p>The name of the time variable in the long input data.</p></dd> + + +<dt>outtime</dt> +<dd><p>The name of the time variable in the wide output data.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>Dataframe in wide format.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='fu'>mkin_long_to_wide</span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span><span class='op'>)</span> -</div><div class='output co'>#> time parent m1 -#> 1 0 99.46 0.00 -#> 2 0 102.04 0.00 -#> 3 1 93.50 4.84 -#> 4 1 92.50 5.64 -#> 5 3 63.23 12.91 -#> 6 3 68.99 12.96 -#> 7 7 52.32 22.97 -#> 8 7 55.13 24.47 -#> 9 14 27.27 41.69 -#> 10 14 26.64 33.21 -#> 11 21 11.50 44.37 -#> 12 21 11.64 46.44 -#> 13 35 2.85 41.22 -#> 14 35 2.91 37.95 -#> 15 50 0.69 41.19 -#> 16 50 0.63 40.01 -#> 17 75 0.05 40.09 -#> 18 75 0.06 33.85 -#> 19 100 NA 31.04 -#> 20 100 NA 33.13 -#> 21 120 NA 25.15 -#> 22 120 NA 33.31</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> time parent m1</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0 99.46 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0 102.04 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> 3 1 93.50 4.84</span> +<span class="r-out co"><span class="r-pr">#></span> 4 1 92.50 5.64</span> +<span class="r-out co"><span class="r-pr">#></span> 5 3 63.23 12.91</span> +<span class="r-out co"><span class="r-pr">#></span> 6 3 68.99 12.96</span> +<span class="r-out co"><span class="r-pr">#></span> 7 7 52.32 22.97</span> +<span class="r-out co"><span class="r-pr">#></span> 8 7 55.13 24.47</span> +<span class="r-out co"><span class="r-pr">#></span> 9 14 27.27 41.69</span> +<span class="r-out co"><span class="r-pr">#></span> 10 14 26.64 33.21</span> +<span class="r-out co"><span class="r-pr">#></span> 11 21 11.50 44.37</span> +<span class="r-out co"><span class="r-pr">#></span> 12 21 11.64 46.44</span> +<span class="r-out co"><span class="r-pr">#></span> 13 35 2.85 41.22</span> +<span class="r-out co"><span class="r-pr">#></span> 14 35 2.91 37.95</span> +<span class="r-out co"><span class="r-pr">#></span> 15 50 0.69 41.19</span> +<span class="r-out co"><span class="r-pr">#></span> 16 50 0.63 40.01</span> +<span class="r-out co"><span class="r-pr">#></span> 17 75 0.05 40.09</span> +<span class="r-out co"><span class="r-pr">#></span> 18 75 0.06 33.85</span> +<span class="r-out co"><span class="r-pr">#></span> 19 100 NA 31.04</span> +<span class="r-out co"><span class="r-pr">#></span> 20 100 NA 33.13</span> +<span class="r-out co"><span class="r-pr">#></span> 21 120 NA 25.15</span> +<span class="r-out co"><span class="r-pr">#></span> 22 120 NA 33.31</span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkin_wide_to_long.html b/docs/dev/reference/mkin_wide_to_long.html index f2bf00c1..fb23d3dc 100644 --- a/docs/dev/reference/mkin_wide_to_long.html +++ b/docs/dev/reference/mkin_wide_to_long.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title> - - -<!-- jquery --> -<script 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data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,118 +43,122 @@ mkinfit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Convert a dataframe with observations over time into long format</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkin_wide_to_long.R'><code>R/mkin_wide_to_long.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_wide_to_long.R" class="external-link"><code>R/mkin_wide_to_long.R</code></a></small> <div class="hidden name"><code>mkin_wide_to_long.Rd</code></div> </div> <div class="ref-description"> <p>This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by -<code><a href='mkinfit.html'>mkinfit</a></code>.</p> +<code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <pre class="usage"><span class='fu'>mkin_wide_to_long</span><span class='op'>(</span><span class='va'>wide_data</span>, time <span class='op'>=</span> <span class='st'>"t"</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide_data</span>, time <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>wide_data</th> - <td><p>The dataframe must contain one variable with the time + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>wide_data</dt> +<dd><p>The dataframe must contain one variable with the time values specified by the <code>time</code> argument and usually more than one -column of observed values.</p></td> - </tr> - <tr> - <th>time</th> - <td><p>The name of the time variable.</p></td> - </tr> - </table> +column of observed values.</p></dd> + - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>time</dt> +<dd><p>The name of the time variable.</p></dd> - <p>Dataframe in long format as needed for <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>Dataframe in long format as needed for <code><a href="mkinfit.html">mkinfit</a></code>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>wide</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>t <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span><span class='op'>)</span>, x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span><span class='op'>)</span>, y <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'>mkin_wide_to_long</span><span class='op'>(</span><span class='va'>wide</span><span class='op'>)</span> -</div><div class='output co'>#> name time value -#> 1 x 1 1 -#> 2 x 2 4 -#> 3 x 3 7 -#> 4 y 1 3 -#> 5 y 2 4 -#> 6 y 3 5</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">3</span><span class="op">)</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">4</span>,<span class="fl">7</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> name time value</span> +<span class="r-out co"><span class="r-pr">#></span> 1 x 1 1</span> +<span class="r-out co"><span class="r-pr">#></span> 2 x 2 4</span> +<span class="r-out co"><span class="r-pr">#></span> 3 x 3 7</span> +<span class="r-out co"><span class="r-pr">#></span> 4 y 1 3</span> +<span class="r-out co"><span class="r-pr">#></span> 5 y 2 4</span> +<span class="r-out co"><span class="r-pr">#></span> 6 y 3 5</span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinds.html b/docs/dev/reference/mkinds.html index b571e3a0..a7fb9916 100644 --- a/docs/dev/reference/mkinds.html +++ b/docs/dev/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><meta name="robot </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -47,19 +47,25 @@ provided by this package come as mkinds objects nevertheless."><meta name="robot <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html index d19a7a1d..cbf55fca 100644 --- a/docs/dev/reference/mkindsg.html +++ b/docs/dev/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><meta name="robots" content="noindex"><!-- mat </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -47,19 +47,25 @@ dataset if no data are supplied."><meta name="robots" content="noindex"><!-- mat <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html index 94c575cb..2c9f0b13 100644 --- a/docs/dev/reference/mkinerrmin.html +++ b/docs/dev/reference/mkinerrmin.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" 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src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the minimum error to assume in order to pass the variance test</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrmin.R'><code>R/mkinerrmin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrmin.R" class="external-link"><code>R/mkinerrmin.R</code></a></small> <div class="hidden name"><code>mkinerrmin.Rd</code></div> </div> @@ -149,89 +94,100 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> the chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </div> - <pre class="usage"><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit</span>, alpha <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>fit</th> - <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>The confidence level chosen for the chi-squared test.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A dataframe with the following components:</p> -<dt>err.min</dt><dd><p>The -relative error, expressed as a fraction.</p></dd> <dt>n.optim</dt><dd><p>The number of -optimised parameters attributed to the data series.</p></dd> <dt>df</dt><dd><p>The number of + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>fit</dt> +<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + +<dt>alpha</dt> +<dd><p>The confidence level chosen for the chi-squared test.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A dataframe with the following components:</p> +<dl><dt>err.min</dt> +<dd><p>The +relative error, expressed as a fraction.</p></dd> + <dt>n.optim</dt> +<dd><p>The number of +optimised parameters attributed to the data series.</p></dd> + <dt>df</dt> +<dd><p>The number of remaining degrees of freedom for the chi2 error level calculations. Note that mean values are used for the chi2 statistic and therefore every time -point with observed values in the series only counts one time.</p></dd> The +point with observed values in the series only counts one time.</p></dd> +</dl><p>The dataframe has one row for the total dataset and one further row for each -observed state variable in the model. - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence +observed state variable in the model.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>This function is used internally by <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>.</p> + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU -Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC +Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit_FOCUS_D</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_D</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.0640 4 15 -#> parent 0.0646 2 7 -#> m1 0.0469 2 8</div><div class='input'><span class='co'># \dontrun{</span> - <span class='va'>fit_FOCUS_E</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_E</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_E</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.1544 4 13 -#> parent 0.1659 2 7 -#> m1 0.1095 2 6</div><div class='input'><span class='co'># }</span> - -</div></pre> +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.0640 4 15</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.0646 2 7</span> +<span class="r-out co"><span class="r-pr">#></span> m1 0.0469 2 8</span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_FOCUS_E</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_E</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_E</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.1544 4 13</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.1659 2 7</span> +<span class="r-out co"><span class="r-pr">#></span> m1 0.1095 2 6</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model and this error model plot can be obtained with plot.mkinfit -using the argument show_errplot = TRUE." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +using the argument show_errplot = TRUE."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ using the argument show_errplot = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,48 +45,50 @@ using the argument show_errplot = TRUE." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot squared residuals and the error model for an mkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrplot.R" class="external-link"><code>R/mkinerrplot.R</code></a></small> <div class="hidden name"><code>mkinerrplot.Rd</code></div> </div> @@ -151,128 +96,133 @@ using the argument show_errplot = TRUE." /> <p>This function plots the squared residuals for the specified subset of the observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model -and this error model plot can be obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> +and this error model plot can be obtained with <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> using the argument <code>show_errplot = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinerrplot</span><span class='op'>(</span> - <span class='va'>object</span>, - obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, - xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>predicted</span><span class='op'>)</span><span class='op'>)</span>, - xlab <span class='op'>=</span> <span class='st'>"Predicted"</span>, - ylab <span class='op'>=</span> <span class='st'>"Squared residual"</span>, - maxy <span class='op'>=</span> <span class='st'>"auto"</span>, - legend <span class='op'>=</span> <span class='cn'>TRUE</span>, - lpos <span class='op'>=</span> <span class='st'>"topright"</span>, - col_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - frame <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td> - </tr> - <tr> - <th>obs_vars</th> - <td><p>A character vector of names of the observed variables for + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">predicted</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Predicted"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Squared residual"</span>,</span> +<span> maxy <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + + +<dt>obs_vars</dt> +<dd><p>A character vector of names of the observed variables for which residuals should be plotted. Defaults to all observed variables in -the model</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>plot range in x direction.</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>maxy</th> - <td><p>Maximum value of the residuals. This is used for the scaling of -the y axis and defaults to "auto".</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be plotted?</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>Where should the legend be placed? Default is "topright". Will -be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td> - </tr> - <tr> - <th>col_obs</th> - <td><p>Colors for the observed variables.</p></td> - </tr> - <tr> - <th>pch_obs</th> - <td><p>Symbols to be used for the observed variables.</p></td> - </tr> - <tr> - <th>frame</th> - <td><p>Should a frame be drawn around the plots?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>Nothing is returned by this function, as it is called for its side -effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> +the model</p></dd> - <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted -lines of the mkinfit object.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - <p>Johannes Ranke</p> +<dt>xlim</dt> +<dd><p>plot range in x direction.</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis.</p></dd> + + +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> + + +<dt>maxy</dt> +<dd><p>Maximum value of the residuals. This is used for the scaling of +the y axis and defaults to "auto".</p></dd> + + +<dt>legend</dt> +<dd><p>Should a legend be plotted?</p></dd> + + +<dt>lpos</dt> +<dd><p>Where should the legend be placed? Default is "topright". Will +be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd> + - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># \dontrun{</span> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +<dt>col_obs</dt> +<dd><p>Colors for the observed variables.</p></dd> -</div></pre> + +<dt>pch_obs</dt> +<dd><p>Symbols to be used for the observed variables.</p></dd> + + +<dt>frame</dt> +<dd><p>Should a frame be drawn around the plots?</p></dd> + + +<dt>...</dt> +<dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>Nothing is returned by this function, as it is called for its side +effect, namely to produce a plot.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted +lines of the mkinfit object.</p></div> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mkinerrplot-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 17da44cb..ee596e89 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -67,7 +67,10 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -381,17 +384,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:09:26 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:09:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:05:53 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:05:53 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.049 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.045 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -531,11 +534,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.559</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.556 0.870</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.603 1.455</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.616</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.505 0.927</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.455 1.512</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -562,10 +564,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:09:37 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:09:37 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:06:05 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:06:05 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -574,7 +576,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.43 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.81 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 5d362f76..145dee83 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -30,7 +30,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -45,19 +45,28 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -92,22 +101,22 @@ components.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinmod</span><span class="op">(</span> - <span class="va">...</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span>, - name <span class="op">=</span> <span class="cn">NULL</span>, - speclist <span class="op">=</span> <span class="cn">NULL</span>, - quiet <span class="op">=</span> <span class="cn">FALSE</span>, - verbose <span class="op">=</span> <span class="cn">FALSE</span>, - dll_dir <span class="op">=</span> <span class="cn">NULL</span>, - unload <span class="op">=</span> <span class="cn">FALSE</span>, - overwrite <span class="op">=</span> <span class="cn">FALSE</span> -<span class="op">)</span> - -<span class="co"># S3 method for mkinmod</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span> - -<span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinmod</span><span class="op">(</span></span> +<span> <span class="va">...</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span> +<span> name <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> speclist <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> dll_dir <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> unload <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinmod</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -123,76 +132,112 @@ the source compartment. Additionally, <code>mkinsub()</code> has an argument <code>to</code>, specifying names of variables to which a transfer is to be assumed in the model. If the argument <code>use_of_ff</code> is set to "min" -(default) and the model for the compartment is "SFO" or "SFORB", an +and the model for the compartment is "SFO" or "SFORB", an additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively fixing the flux to sink to zero. In print.mkinmod, this argument is currently not used.</p></dd> + + <dt>use_of_ff</dt> <dd><p>Specification of the use of formation fractions in the model equations and, if applicable, the coefficient matrix. If "max", formation fractions are always used (default). If "min", a minimum use of formation fractions is made, i.e. each first-order pathway to a metabolite has its own rate constant.</p></dd> + + <dt>name</dt> <dd><p>A name for the model. Should be a valid R object name.</p></dd> + + <dt>speclist</dt> <dd><p>The specification of the observed variables and their submodel types and pathways can be given as a single list using this argument. Default is NULL.</p></dd> + + <dt>quiet</dt> <dd><p>Should messages be suppressed?</p></dd> + + <dt>verbose</dt> <dd><p>If <code>TRUE</code>, passed to <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> if applicable to give detailed information about the C function being built.</p></dd> + + <dt>dll_dir</dt> <dd><p>Directory where an DLL object, if generated internally by <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved. The DLL will only be stored in a permanent location for use in future sessions, if 'dll_dir' and 'name' are specified.</p></dd> + + <dt>unload</dt> <dd><p>If a DLL from the target location in 'dll_dir' is already loaded, should that be unloaded first?</p></dd> + + <dt>overwrite</dt> <dd><p>If a file exists at the target DLL location in 'dll_dir', should this be overwritten?</p></dd> + + <dt>x</dt> <dd><p>An <code>mkinmod</code> object.</p></dd> + + <dt>submodel</dt> <dd><p>Character vector of length one to specify the submodel type. See <code>mkinmod</code> for the list of allowed submodel names.</p></dd> + + <dt>to</dt> <dd><p>Vector of the names of the state variable to which a transformation shall be included in the model.</p></dd> + + <dt>sink</dt> <dd><p>Should a pathway to sink be included in the model in addition to the pathways to other state variables?</p></dd> + + <dt>full_name</dt> <dd><p>An optional name to be used e.g. for plotting fits performed with the model. You can use non-ASCII characters here, but then your R code will not be portable, <em>i.e.</em> may produce unintended plot results on other operating systems or system configurations.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, + + +<p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, containing, among others,</p> <dl><dt>diffs</dt> <dd><p>A vector of string representations of differential equations, one for each modelling variable.</p></dd> + <dt>map</dt> <dd><p>A list containing named character vectors for each observed variable, specifying the modelling variables by which it is represented.</p></dd> + <dt>use_of_ff</dt> <dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> + <dt>deg_func</dt> <dd><p>If generated, a function containing the solution of the degradation model.</p></dd> + <dt>coefmat</dt> <dd><p>The coefficient matrix, if the system of differential equations can be represented by one.</p></dd> + <dt>cf</dt> <dd><p>If generated, a compiled function calculating the derivatives as returned by cfunction.</p></dd> + + </dl><p>A list for use with <code>mkinmod</code>.</p> </div> <div id="details"> @@ -202,7 +247,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <p>For kinetic models with more than one observed variable, a symbolic solution of the system of differential equations is included in the resulting mkinmod object in some cases, speeding up the solution.</p> -<p>If a C compiler is found by <code><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there +<p>If a C compiler is found by <code><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p> @@ -230,16 +275,16 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span> -<span class="r-in"><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order</span></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span> +<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span> <span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span> <span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span> @@ -252,30 +297,32 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> Differential equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span> -<span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span> -<span class="r-in"> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span> -<span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span> -<span class="r-in"> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span> -<span class="r-in"> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp6NiOcv/fileb89c01ace19ec.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> -<span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># Show details of creating the C function</span></span> -<span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span></span> +<span class="r-in"><span> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span></span> +<span class="r-in"><span> <span class="va">DLL_dir</span> <span class="op"><-</span> <span class="st">"~/.local/share/mkin"</span></span></span> +<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO.2</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpelWAOB/fileb43c31a25a86.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Program source:</span> <span class="r-out co"><span class="r-pr">#></span> 1: #include <R.h></span> <span class="r-out co"><span class="r-pr">#></span> 2: </span> @@ -297,10 +344,10 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];</span> <span class="r-out co"><span class="r-pr">#></span> 19: }</span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The symbolic solution which is available in this case is not</span></span> -<span class="r-in"><span class="co"># made for human reading but for speed of computation</span></span> -<span class="r-in"><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The symbolic solution which is available in this case is not</span></span></span> +<span class="r-in"><span><span class="co"># made for human reading but for speed of computation</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span></span> <span class="r-out co"><span class="r-pr">#></span> function (observed, odeini, odeparms) </span> <span class="r-out co"><span class="r-pr">#></span> {</span> <span class="r-out co"><span class="r-pr">#></span> predicted <- numeric(0)</span> @@ -316,21 +363,21 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555cd83c70></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> -<span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> -<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span> -<span class="r-in"> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f013820></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> +<span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit_DFOP_par_c</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +<span class="r-in"><span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -345,7 +392,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> 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parameters fitted using +mkinfit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,112 +42,119 @@ mkinfit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot the confidence intervals obtained using mkinfit</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinparplot.R'><code>R/mkinparplot.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinparplot.R" class="external-link"><code>R/mkinparplot.R</code></a></small> <div class="hidden name"><code>mkinparplot.Rd</code></div> </div> <div class="ref-description"> <p>This function plots the confidence intervals for the parameters fitted using -<code><a href='mkinfit.html'>mkinfit</a></code>.</p> +<code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <pre class="usage"><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + - <p>Nothing is returned by this function, as it is called for its side +<p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># \dontrun{</span> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - T245 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenol"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - phenol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>, - anisole <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> T245 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenol"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anisole"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> +<span class="r-in"><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" 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It now only calls the plot method -<code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> +<code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinplot</span><span class="op">(</span><span class="va">fit</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>mkinplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>fit</dt> +<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>fit</th> - <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>...</dt> +<dd><p>further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The function is called for its side effect.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 37930912..10d2c9a9 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -372,12 +372,11 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> <span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.2 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.2 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.8 0.204</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.4 0.022</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 41.0 0.205</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/dev/reference/mkinresplot-1.png b/docs/dev/reference/mkinresplot-1.png Binary files differindex ffd34f6f..97ccd762 100644 --- a/docs/dev/reference/mkinresplot-1.png +++ b/docs/dev/reference/mkinresplot-1.png diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html index 30377f2c..4d99f5be 100644 --- a/docs/dev/reference/mkinresplot.html +++ b/docs/dev/reference/mkinresplot.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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A combined plot of the fitted model and the residuals can be obtained using plot.mkinfit using the -argument show_residuals = TRUE." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +argument show_residuals = TRUE."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,23 +20,21 @@ argument show_residuals = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,181 +44,188 @@ argument show_residuals = TRUE." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot residuals stored in an mkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinresplot.R" class="external-link"><code>R/mkinresplot.R</code></a></small> <div class="hidden name"><code>mkinresplot.Rd</code></div> </div> <div class="ref-description"> <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted model and -the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the +the residuals can be obtained using <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> using the argument <code>show_residuals = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinresplot</span><span class='op'>(</span> - <span class='va'>object</span>, - obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, - xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span><span class='op'>)</span>, - standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, - xlab <span class='op'>=</span> <span class='st'>"Time"</span>, - ylab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span><span class='op'>)</span>, - maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, - legend <span class='op'>=</span> <span class='cn'>TRUE</span>, - lpos <span class='op'>=</span> <span class='st'>"topright"</span>, - col_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - frame <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td> - </tr> - <tr> - <th>obs_vars</th> - <td><p>A character vector of names of the observed variables for + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinresplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>,</span> +<span> maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + + +<dt>obs_vars</dt> +<dd><p>A character vector of names of the observed variables for which residuals should be plotted. Defaults to all observed variables in -the model</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>plot range in x direction.</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>Should the residuals be standardized by dividing by the -standard deviation given by the error model of the fit?</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>maxabs</th> - <td><p>Maximum absolute value of the residuals. This is used for the -scaling of the y axis and defaults to "auto".</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be plotted?</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>Where should the legend be placed? Default is "topright". Will -be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td> - </tr> - <tr> - <th>col_obs</th> - <td><p>Colors for the observed variables.</p></td> - </tr> - <tr> - <th>pch_obs</th> - <td><p>Symbols to be used for the observed variables.</p></td> - </tr> - <tr> - <th>frame</th> - <td><p>Should a frame be drawn around the plots?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>Nothing is returned by this function, as it is called for its side -effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> +the model</p></dd> - <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted -lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a></code> for a function -combining the plot of the fit and the residual plot.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +<dt>xlim</dt> +<dd><p>plot range in x direction.</p></dd> + + +<dt>standardized</dt> +<dd><p>Should the residuals be standardized by dividing by the +standard deviation given by the error model of the fit?</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis.</p></dd> + + +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> + + +<dt>maxabs</dt> +<dd><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></dd> + + +<dt>legend</dt> +<dd><p>Should a legend be plotted?</p></dd> + + +<dt>lpos</dt> +<dd><p>Where should the legend be placed? Default is "topright". Will +be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd> + + +<dt>col_obs</dt> +<dd><p>Colors for the observed variables.</p></dd> + + +<dt>pch_obs</dt> +<dd><p>Symbols to be used for the observed variables.</p></dd> + + +<dt>frame</dt> +<dd><p>Should a frame be drawn around the plots?</p></dd> + + +<dt>...</dt> +<dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>Nothing is returned by this function, as it is called for its side +effect, namely to produce a plot.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted +lines of the mkinfit object, and <code><a href="plot.mkinfit.html">plot_res</a></code> for a function +combining the plot of the fit and the residual plot.</p></div> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke and Katrin Lindenberger</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='st'>"m1"</span><span class='op'>)</span> -</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mmkin-1.png b/docs/dev/reference/mmkin-1.png Binary files differindex 701a6d6a..8ad9c11d 100644 --- a/docs/dev/reference/mmkin-1.png +++ b/docs/dev/reference/mmkin-1.png diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png Binary files differindex 5277b389..da2a48a8 100644 --- a/docs/dev/reference/mmkin-2.png +++ b/docs/dev/reference/mmkin-2.png diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png Binary files differindex 2659cd61..10d3f35b 100644 --- a/docs/dev/reference/mmkin-3.png +++ b/docs/dev/reference/mmkin-3.png diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png Binary files differindex ae16ee79..132380a8 100644 --- a/docs/dev/reference/mmkin-4.png +++ b/docs/dev/reference/mmkin-4.png diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png Binary files differindex 2b9dc831..4bfcc55e 100644 --- a/docs/dev/reference/mmkin-5.png +++ b/docs/dev/reference/mmkin-5.png diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index c385bbf6..5aa259f9 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,23 +20,21 @@ datasets specified in its first two arguments." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.5</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,213 +44,225 @@ datasets specified in its first two arguments." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>mmkin.Rd</code></div> </div> <div class="ref-description"> - <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and + <p>This function calls <code><a href="mkinfit.html">mkinfit</a></code> on all combinations of models and datasets specified in its first two arguments.</p> </div> - <pre class="usage"><span class='fu'>mmkin</span><span class='op'>(</span> - models <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, - <span class='va'>datasets</span>, - cores <span class='op'>=</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='fl'>1</span> <span class='kw'>else</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, - cluster <span class='op'>=</span> <span class='cn'>NULL</span>, - <span class='va'>...</span> -<span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mmkin</span><span class="op">(</span></span> +<span> models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> +<span> <span class="va">datasets</span>,</span> +<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> cluster <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>models</dt> +<dd><p>Either a character vector of shorthand names like +<code>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</code>, or an optionally named +list of <code><a href="mkinmod.html">mkinmod</a></code> objects.</p></dd> + -<span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> +<dt>datasets</dt> +<dd><p>An optionally named list of datasets suitable as observed +data for <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>models</th> - <td><p>Either a character vector of shorthand names like -<code><a href='https://rdrr.io/r/base/c.html'>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</a></code>, or an optionally named -list of <code><a href='mkinmod.html'>mkinmod</a></code> objects.</p></td> - </tr> - <tr> - <th>datasets</th> - <td><p>An optionally named list of datasets suitable as observed -data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to be used for multicore processing. This + +<dt>cores</dt> +<dd><p>The number of cores to be used for multicore processing. This is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, cores > 1 is not supported, you need to use the <code>cluster</code> argument to use multiple logical processors. Per default, all cores -detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used, except on Windows where -the default is 1.</p></td> - </tr> - <tr> - <th>cluster</th> - <td><p>A cluster as returned by <code>makeCluster</code> to be used -for parallel execution.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used.</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An mmkin object.</p></td> - </tr> - </table> +detected by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where +the default is 1.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A two-dimensional <code><a href='https://rdrr.io/r/base/array.html'>array</a></code> of <code><a href='mkinfit.html'>mkinfit</a></code> -objects and/or try-errors that can be indexed using the model names for the -first index (row index) and the dataset names for the second index (column -index).</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> +<dt>cluster</dt> +<dd><p>A cluster as returned by <code>makeCluster</code> to be used +for parallel execution.</p></dd> - <div class='dont-index'><p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for -plotting.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - <p>Johannes Ranke</p> +<dt>...</dt> +<dd><p>Not used.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># \dontrun{</span> -<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>m_synth_FOMC_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>models</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>SFO_lin <span class='op'>=</span> <span class='va'>m_synth_SFO_lin</span>, FOMC_lin <span class='op'>=</span> <span class='va'>m_synth_FOMC_lin</span><span class='op'>)</span> -<span class='va'>datasets</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>datasets</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span> -<span class='va'>time_default</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.0</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> -<span class='va'>time_1</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.4</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> +<dt>x</dt> +<dd><p>An mmkin object.</p></dd> -<span class='va'>time_default</span> -</div><div class='output co'>#> user system elapsed -#> 4.771 0.576 1.803 </div><div class='input'><span class='va'>time_1</span> -</div><div class='output co'>#> user system elapsed -#> 5.779 0.000 5.781 </div><div class='input'> -<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340481 0.2659519 0.7505683 0.2494317 -#> -#> $distimes -#> DT50 DT90 -#> parent 0.877769 2.915885 -#> M1 2.325744 7.725956 -#> M2 33.720100 112.015749 -#> </div><div class='input'> -<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span>, obs_var <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> -<span class='co'># by plot.mkinfit and can be plotted using plot_sep</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span>, show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> -<span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> -<span class='co'># allow to plot the observed variables separately</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># On Windows, we can use multiple cores by making a cluster using the parallel</span> -<span class='co'># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span> -<span class='va'>cl</span> <span class='op'><-</span> <span class='fu'>makePSOCKcluster</span><span class='op'>(</span><span class='fl'>12</span><span class='op'>)</span> -<span class='va'>f</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>A <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span>, D <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, - cluster <span class='op'>=</span> <span class='va'>cl</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model A B C D -#> SFO OK OK OK OK -#> FOMC OK OK OK OK -#> DFOP OK OK OK OK -#> -#> OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> -<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> -<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> -<span class='co'># }</span> +</dl></div> + <div id="value"> + <h2>Value</h2> + -</div></pre> +<p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code></p> + + +<p>objects and/or try-errors that can be indexed using the model names for the +first index (row index) and the dataset names for the second index (column +index).</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="Extract.mmkin.html">[.mmkin</a></code> for subsetting, <code><a href="plot.mmkin.html">plot.mmkin</a></code> for +plotting.</p></div> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_FOMC_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">models</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">datasets</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">datasets</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">time_default</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.0</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">time_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.4</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">time_default</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 7.113 0.837 2.580 </span> +<span class="r-in"><span><span class="va">time_1</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 5.617 0.008 5.626 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_M1 parent_sink M1_M2 M1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.7340481 0.2659519 0.7505683 0.2494317 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.877769 2.915885</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725956</span> +<span class="r-out co"><span class="r-pr">#></span> M2 33.720100 112.015749</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span></span> +<span class="r-in"><span><span class="co"># by plot.mkinfit and can be plotted using plot_sep</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span></span> +<span class="r-in"><span><span class="co"># allow to plot the observed variables separately</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span></span> +<span class="r-in"><span><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span></span> +<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">makePSOCKcluster</span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in makePSOCKcluster(12):</span> could not find function "makePSOCKcluster"</span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">FOCUS_2006_A</span>, B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in system.time({ if (is.null(cluster)) { results <- parallel::mclapply(as.list(1:n.fits), fit_function, mc.cores = cores, mc.preschedule = FALSE) } else { results <- parallel::parLapply(cluster, as.list(1:n.fits), fit_function) }}):</span> object 'cl' not found</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0.001</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in print(f):</span> object 'f' not found</span> +<span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span> +<span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span> +<span class="r-in"><span><span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in stopCluster(cl):</span> could not find function "stopCluster"</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png Binary files differindex 7fc24a04..dcd493c9 100644 --- a/docs/dev/reference/multistart-1.png +++ b/docs/dev/reference/multistart-1.png diff --git a/docs/dev/reference/multistart-2.png b/docs/dev/reference/multistart-2.png Binary files differindex 7553a51a..e1983f12 100644 --- a/docs/dev/reference/multistart-2.png +++ b/docs/dev/reference/multistart-2.png diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 3f5c4b35..0f2988bd 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noi </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -64,7 +64,10 @@ mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noi <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/nafta-1.png b/docs/dev/reference/nafta-1.png Binary files differindex 4f0d7833..5d2d434b 100644 --- a/docs/dev/reference/nafta-1.png +++ b/docs/dev/reference/nafta-1.png diff --git a/docs/dev/reference/nafta.html b/docs/dev/reference/nafta.html index 6fb797a5..eafbca7f 100644 --- a/docs/dev/reference/nafta.html +++ b/docs/dev/reference/nafta.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Evaluate parent kinetics using the NAFTA guidance — nafta • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script 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src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Evaluate parent kinetics using the NAFTA guidance — nafta"><meta property="og:description" content="The function fits the SFO, IORE and DFOP models using mmkin and returns an object of class nafta that has methods for printing and plotting. Print nafta objects. The results for the three models are printed in the -order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,188 +45,198 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Evaluate parent kinetics using the NAFTA guidance</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> <div class="hidden name"><code>nafta.Rd</code></div> </div> <div class="ref-description"> - <p>The function fits the SFO, IORE and DFOP models using <code><a href='mmkin.html'>mmkin</a></code> + <p>The function fits the SFO, IORE and DFOP models using <code><a href="mmkin.html">mmkin</a></code> and returns an object of class <code>nafta</code> that has methods for printing and plotting.</p> <p>Print nafta objects. The results for the three models are printed in the order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</p> </div> - <pre class="usage"><span class='fu'>nafta</span><span class='op'>(</span><span class='va'>ds</span>, title <span class='op'>=</span> <span class='cn'>NA</span>, quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, digits <span class='op'>=</span> <span class='fl'>3</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>ds</th> - <td><p>A dataframe that must contain one variable called "time" with the -time values specified by the <code>time</code> argument, one column called -"name" with the grouping of the observed values, and finally one column of -observed values called "value".</p></td> - </tr> - <tr> - <th>title</th> - <td><p>Optional title of the dataset</p></td> - </tr> - <tr> - <th>quiet</th> - <td><p>Should the evaluation text be shown?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='mmkin.html'>mmkin</a></code> (not for the -printing method).</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An <code>nafta</code> object.</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to be used for printing parameters and -dissipation times.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nafta</span><span class="op">(</span><span class="va">ds</span>, title <span class="op">=</span> <span class="cn">NA</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for nafta</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">3</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides -<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> +<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation -<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>ds</dt> +<dd><p>A dataframe that must contain one variable called "time" with the +time values specified by the <code>time</code> argument, one column called +"name" with the grouping of the observed values, and finally one column of +observed values called "value".</p></dd> + + +<dt>title</dt> +<dd><p>Optional title of the dataset</p></dd> + - <p>An list of class <code>nafta</code>. The list element named "mmkin" is the -<code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models. The +<dt>quiet</dt> +<dd><p>Should the evaluation text be shown?</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="mmkin.html">mmkin</a></code> (not for the +printing method).</p></dd> + + +<dt>x</dt> +<dd><p>An <code>nafta</code> object.</p></dd> + + +<dt>digits</dt> +<dd><p>Number of digits to be used for printing parameters and +dissipation times.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An list of class <code>nafta</code>. The list element named "mmkin" is the +<code><a href="mmkin.html">mmkin</a></code> object containing the fits of the three models. The list element named "title" contains the title of the dataset used. The list element "data" contains the dataset used in the fits.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='va'>nafta_evaluation</span> <span class='op'><-</span> <span class='fu'>nafta</span><span class='op'>(</span><span class='va'>NAFTA_SOP_Appendix_D</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 1378.6832 615.7730 517.8836 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 -#> -#> Representative half-life: -#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu">nafta</span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> +<span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 717.4598</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 83.7558 1.80e-14 77.18268 90.3288</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0017 7.43e-05 0.00112 0.0026</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.7518 1.22e-05 5.64278 11.8608</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.69e+01 NA 8.88e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 6.68e+00 NA 4.19e+00 9.17e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.85e+00 NA 3.76e+00 7.94e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03</span> +<span class="r-out co"><span class="r-pr">#></span> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 407 1350 407</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 541 5190000 1560000</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 429 2380 841</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="nafta-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png Binary files differindex 67cc7f3c..c4fc9d31 100644 --- a/docs/dev/reference/nlme-1.png +++ b/docs/dev/reference/nlme-1.png diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png Binary files differindex bb1e6f81..d9512f41 100644 --- a/docs/dev/reference/nlme-2.png +++ b/docs/dev/reference/nlme-2.png diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index e7844299..b8b36d56 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -29,7 +29,7 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -44,19 +44,28 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -90,20 +99,25 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span> - -<span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A function that can be used with nlme -A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> + + +<p>A function that can be used with nlme</p> + + +<p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> </div> <div id="see-also"> <h2>See also</h2> @@ -112,78 +126,78 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># These assignments are necessary for these objects to be</span></span> -<span class="r-in"><span class="co"># visible to nlme and augPred when evaluation is done by</span></span> -<span class="r-in"><span class="co"># pkgdown to generate the html docs.</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">m_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span> -<span class="r-in"> data <span class="op">=</span> <span class="va">grouped_data</span>,</span> -<span class="r-in"> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span> -<span class="r-in"> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span> -<span class="r-in"> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># These assignments are necessary for these objects to be</span></span></span> +<span class="r-in"><span><span class="co"># visible to nlme and augPred when evaluation is done by</span></span></span> +<span class="r-in"><span><span class="co"># pkgdown to generate the html docs.</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">m_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">grouped_data</span>,</span></span> +<span class="r-in"><span> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) </span> <span class="r-out co"><span class="r-pr">#></span> Data: grouped_data </span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 300.6824 310.2426 -145.3412</span> +<span class="r-out co"><span class="r-pr">#></span> 266.6428 275.8935 -128.3214</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)</span> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 1.697361 0.6801209 3.666073</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.000368491 0.7058039 3.065183</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> -<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.99378 1.3890416 46 72.70753 0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0</span> +<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07257 0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0</span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> prnt_0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.027 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.031 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> -<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> -<span class="r-out co"><span class="r-pr">#></span> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 </span> +<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> +<span class="r-out co"><span class="r-pr">#></span> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 50</span> +<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 47</span> <span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># augPred does not work on fits with more than one state</span></span> -<span class="r-in"><span class="co"># variable</span></span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span> -<span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># augPred does not work on fits with more than one state</span></span></span> +<span class="r-in"><span><span class="co"># variable</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span></span> +<span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></span> </code></pre></div> </div> @@ -199,7 +213,7 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index 2bbadb88..8c069470 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><meta name= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -46,19 +46,25 @@ have been obtained by fitting the same model to a list of datasets."><meta name= <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -97,7 +103,7 @@ have been obtained by fitting the same model to a list of datasets.</p> <span> data <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span></span> <span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,</span> -<span> random <span class="op">=</span> <span class="fu">pdDiag</span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,</span> +<span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,</span> <span> <span class="va">groups</span>,</span> <span> start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span> correlation <span class="op">=</span> <span class="cn">NULL</span>,</span> diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html index 0b6c963c..8c2d04f0 100644 --- a/docs/dev/reference/nobs.mkinfit.html +++ b/docs/dev/reference/nobs.mkinfit.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Number of observations on which an mkinfit object was fitted — nobs.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" 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data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Number of observations on which an mkinfit object was fitted</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nobs.mkinfit.R'><code>R/nobs.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nobs.mkinfit.R" class="external-link"><code>R/nobs.mkinfit.R</code></a></small> <div class="hidden name"><code>nobs.mkinfit.Rd</code></div> </div> @@ -147,51 +92,49 @@ <p>Number of observations on which an mkinfit object was fitted</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/nobs.html'>nobs</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/nobs.html" class="external-link">nobs</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An mkinfit object</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An mkinfit object</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> - <p>The number of rows in the data included in the mkinfit object</p> +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The number of rows in the data included in the mkinfit object</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 95db0593..b0385c8a 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><meta nam </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -61,7 +61,10 @@ without considering the error structure that was assumed for the fit."><meta nam <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index ffe93e6c..720c0b2a 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -61,7 +61,10 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -100,6 +103,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p> <span><span class="fu">parplot</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span> +<span> llquant <span class="op">=</span> <span class="cn">NA</span>,</span> <span> scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span> <span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span> <span> main <span class="op">=</span> <span class="st">""</span>,</span> @@ -121,8 +125,14 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p> <dd><p>The minimum likelihood of objects to be shown</p></dd> +<dt>llquant</dt> +<dd><p>Fractional value for selecting only the fits with higher +likelihoods. Overrides 'llmin'.</p></dd> + + <dt>scale</dt> -<dd><p>By default, scale parameters using the best available fit. +<dd><p>By default, scale parameters using the best +available fit. If 'median', parameters are scaled using the median parameters from all fits.</p></dd> @@ -134,6 +144,12 @@ If 'median', parameters are scaled using the median parameters from all fits.</p <dd><p>Title of the plot</p></dd> </dl></div> + <div id="details"> + <h2>Details</h2> + <p>Starting values of degradation model parameters and error model parameters +are shown as green circles. The results obtained in the original run +are shown as red circles.</p> + </div> <div id="references"> <h2>References</h2> <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index b1c62721..4bd170a1 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html index 764f0699..d125a606 100644 --- a/docs/dev/reference/plot.mkinfit.html +++ b/docs/dev/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><meta name="robot </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -46,19 +46,25 @@ observed data together with the solution of the fitted model."><meta name="robot <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png Binary files differindex 647dfb8a..235e33a7 100644 --- a/docs/dev/reference/plot.mmkin-1.png +++ b/docs/dev/reference/plot.mmkin-1.png diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png Binary files differindex 1bc1c9db..7af84edf 100644 --- a/docs/dev/reference/plot.mmkin-2.png +++ b/docs/dev/reference/plot.mmkin-2.png diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png Binary files differindex 50d6ffac..56bfac50 100644 --- a/docs/dev/reference/plot.mmkin-3.png +++ b/docs/dev/reference/plot.mmkin-3.png diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png Binary files differindex e049fa16..5da05f40 100644 --- a/docs/dev/reference/plot.mmkin-4.png +++ b/docs/dev/reference/plot.mmkin-4.png diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png Binary files differindex 2421995b..3ec224f4 100644 --- a/docs/dev/reference/plot.mmkin-5.png +++ b/docs/dev/reference/plot.mmkin-5.png diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html index 9ca0df94..09f311c5 100644 --- a/docs/dev/reference/plot.mmkin.html +++ b/docs/dev/reference/plot.mmkin.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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<ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,200 +45,210 @@ the fit of at least one model to the same dataset is shown." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mmkin.R" class="external-link"><code>R/plot.mmkin.R</code></a></small> <div class="hidden name"><code>plot.mmkin.Rd</code></div> </div> <div class="ref-description"> - <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the + <p>When x is a row selected from an mmkin object (<code><a href="Extract.mmkin.html">[.mmkin</a></code>), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.</p> </div> - <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> - <span class='va'>x</span>, - main <span class='op'>=</span> <span class='st'>"auto"</span>, - legends <span class='op'>=</span> <span class='fl'>1</span>, - resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>, - ylab <span class='op'>=</span> <span class='st'>"Residue"</span>, - standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, - show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>, - errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>, - errmin_digits <span class='op'>=</span> <span class='fl'>3</span>, - cex <span class='op'>=</span> <span class='fl'>0.7</span>, - rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>, - ymax <span class='op'>=</span> <span class='st'>"auto"</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one -column.</p></td> - </tr> - <tr> - <th>main</th> - <td><p>The main title placed on the outer margin of the plot.</p></td> - </tr> - <tr> - <th>legends</th> - <td><p>An index for the fits for which legends should be shown.</p></td> - </tr> - <tr> - <th>resplot</th> - <td><p>Should the residuals plotted against time, using -<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted -values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>Should the residuals be standardized? This option -is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if -<code>resplot = "time"</code>.</p></td> - </tr> - <tr> - <th>show_errmin</th> - <td><p>Should the chi2 error level be shown on top of the plots -to the left?</p></td> - </tr> - <tr> - <th>errmin_var</th> - <td><p>The variable for which the FOCUS chi2 error value should -be shown.</p></td> - </tr> - <tr> - <th>errmin_digits</th> - <td><p>The number of significant digits for rounding the FOCUS -chi2 error percentage.</p></td> - </tr> - <tr> - <th>cex</th> - <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</p></td> - </tr> - <tr> - <th>rel.height.middle</th> - <td><p>The relative height of the middle plot, if more -than two rows of plots are shown.</p></td> - </tr> - <tr> - <th>ymax</th> - <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and -<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then -latex is being used for the formatting of the chi2 error level.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> main <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legends <span class="op">=</span> <span class="fl">1</span>,</span> +<span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span> +<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span> +<span> cex <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span> +<span> ymax <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one +column.</p></dd> + + +<dt>main</dt> +<dd><p>The main title placed on the outer margin of the plot.</p></dd> + + +<dt>legends</dt> +<dd><p>An index for the fits for which legends should be shown.</p></dd> + + +<dt>resplot</dt> +<dd><p>Should the residuals plotted against time, using +<code><a href="mkinresplot.html">mkinresplot</a></code>, or as squared residuals against predicted +values, with the error model, using <code><a href="mkinerrplot.html">mkinerrplot</a></code>.</p></dd> + + +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> + + +<dt>standardized</dt> +<dd><p>Should the residuals be standardized? This option +is passed to <code><a href="mkinresplot.html">mkinresplot</a></code>, it only takes effect if +<code>resplot = "time"</code>.</p></dd> + + +<dt>show_errmin</dt> +<dd><p>Should the chi2 error level be shown on top of the plots +to the left?</p></dd> + + +<dt>errmin_var</dt> +<dd><p>The variable for which the FOCUS chi2 error value should +be shown.</p></dd> + +<dt>errmin_digits</dt> +<dd><p>The number of significant digits for rounding the FOCUS +chi2 error percentage.</p></dd> + + +<dt>cex</dt> +<dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd> + + +<dt>rel.height.middle</dt> +<dd><p>The relative height of the middle plot, if more +than two rows of plots are shown.</p></dd> + + +<dt>ymax</dt> +<dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> and +<code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function is called for its side effect.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then +latex is being used for the formatting of the chi2 error level.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># \dontrun{</span> - <span class='co'># Only use one core not to offend CRAN checks</span> - <span class='va'>fits</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"HS"</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS B"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, <span class='co'># named list for titles</span> - cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span> - <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> - <span class='co'># generated by pkgdown, as far as I know).</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># same as plot(fits[1, 2])</span> -</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='co'># Show the error models</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core not to offend CRAN checks</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span> +<span class="r-in"><span> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span> +<span class="r-in"><span> <span class="co"># generated by pkgdown, as far as I know).</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Show the error models</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html index c24fba99..82b46336 100644 --- a/docs/dev/reference/plot.nafta.html +++ b/docs/dev/reference/plot.nafta.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ function (SFO, then IORE, then DFOP)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ function (SFO, then IORE, then DFOP)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the results of the three models used in the NAFTA scheme.</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> <div class="hidden name"><code>plot.nafta.Rd</code></div> </div> @@ -149,65 +94,65 @@ function (SFO, then IORE, then DFOP)." /> function (SFO, then IORE, then DFOP).</p> </div> - <pre class="usage"><span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, legend <span class='op'>=</span> <span class='cn'>FALSE</span>, main <span class='op'>=</span> <span class='st'>"auto"</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of class <code><a href='nafta.html'>nafta</a></code>.</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be added?</p></td> - </tr> - <tr> - <th>main</th> - <td><p>Possibility to override the main title of the plot.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nafta</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, legend <span class="op">=</span> <span class="cn">FALSE</span>, main <span class="op">=</span> <span class="st">"auto"</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of class <code><a href="nafta.html">nafta</a></code>.</p></dd> + +<dt>legend</dt> +<dd><p>Should a legend be added?</p></dd> + + +<dt>main</dt> +<dd><p>Possibility to override the main title of the plot.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function is called for its side effect.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>Calls <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/read_spreadsheet.html b/docs/dev/reference/read_spreadsheet.html index 70828765..d0ac47d4 100644 --- a/docs/dev/reference/read_spreadsheet.html +++ b/docs/dev/reference/read_spreadsheet.html @@ -22,7 +22,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'."><meta name= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -64,7 +64,10 @@ factors can be given in columns named 'Temperature' and 'Moisture'."><meta name= <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -103,7 +106,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'.</p> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_spreadsheet</span><span class="op">(</span></span> <span> <span class="va">path</span>,</span> <span> valid_datasets <span class="op">=</span> <span class="st">"all"</span>,</span> -<span> parent_only <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> parent_only <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> normalize <span class="op">=</span> <span class="cn">TRUE</span></span> <span><span class="op">)</span></span></code></pre></div> </div> diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html index 0999e346..ad825391 100644 --- a/docs/dev/reference/reexports.html +++ b/docs/dev/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -55,19 +55,25 @@ intervals, nlme <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html index 3f518ab7..009f790f 100644 --- a/docs/dev/reference/residuals.mkinfit.html +++ b/docs/dev/reference/residuals.mkinfit.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Extract residuals from an mkinfit model — residuals.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - 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- +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Extract residuals from an mkinfit model</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/residuals.mkinfit.R'><code>R/residuals.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/residuals.mkinfit.R" class="external-link"><code>R/residuals.mkinfit.R</code></a></small> <div class="hidden name"><code>residuals.mkinfit.Rd</code></div> </div> @@ -147,60 +92,59 @@ <p>Extract residuals from an mkinfit model</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>object</span>, standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>Should the residuals be standardized by dividing by the -standard deviation obtained from the fitted error model?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702 -#> [7] -0.03269080 1.45347823 -0.88423697</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208 -#> [7] -0.04695355 2.08761977 -1.27002287</div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">object</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> + + +<dt>standardized</dt> +<dd><p>Should the residuals be standardized by dividing by the +standard deviation obtained from the fitted error model?</p></dd> + + +<dt>...</dt> +<dd><p>Not used</p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702</span> +<span class="r-out co"><span class="r-pr">#></span> [7] -0.03269080 1.45347823 -0.88423697</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208</span> +<span class="r-out co"><span class="r-pr">#></span> [7] -0.04695355 2.08761977 -1.27002287</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 73382cba..131b168b 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -113,7 +113,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> -<span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">0.1</span><span class="op">)</span>,</span> +<span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span>,</span> <span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span> <span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span> <span> save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> @@ -430,10 +430,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 15 00:45:58 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 15 00:45:58 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Dec 7 16:22:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Dec 7 16:22:26 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -448,12 +448,12 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.189 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.508 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for degradation parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 93.8102 -5.3734 -0.9711 -1.8799 -4.2708 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> @@ -462,6 +462,19 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for random effects (square root of initial entries in omega):</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 4.941 0.000 0.0000 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 0.000 2.551 0.0000 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000 0.000 0.7251 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.000 0.000 0.0000 1.449 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.000 0.000 0.0000 0.000 2.228 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.000 0.000 0.0000 0.000 0.000 0.7814</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for error model parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> diff --git a/docs/dev/reference/schaefer07_complex_case-1.png b/docs/dev/reference/schaefer07_complex_case-1.png Binary files differindex 96aab2dc..eee9e0cc 100644 --- a/docs/dev/reference/schaefer07_complex_case-1.png +++ b/docs/dev/reference/schaefer07_complex_case-1.png diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html index 4ccad5c4..5ff62d34 100644 --- a/docs/dev/reference/schaefer07_complex_case.html +++ b/docs/dev/reference/schaefer07_complex_case.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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The results from the fitting are also included." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> + The results from the fitting are also included."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,44 +43,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Metabolism data set used for checking the software quality of KinGUI</h1> @@ -151,93 +96,109 @@ The results from the fitting are also included.</p> </div> - <pre class="usage"><span class='va'>schaefer07_complex_case</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">schaefer07_complex_case</span></span></code></pre></div> + </div> + + <div id="format"> + <h2>Format</h2> + <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl><dt><code>time</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>parent</code></dt> +<dd><p>a numeric vector</p></dd> + <dt><code>A1</code></dt> +<dd><p>a numeric vector</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>B1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>C1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>A2</code></dt> +<dd><p>a numeric vector</p></dd> - <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl> - <dt><code>time</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>parent</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>A1</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>B1</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>C1</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>A2</code></dt><dd><p>a numeric vector</p></dd> </dl><p>The results are a data frame with 14 results for different parameter values</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>data</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_case</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, - B1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - C1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - A2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span> - <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 -#> -#> $distimes -#> DT50 DT90 -#> parent 13.95078 46.34350 -#> A1 49.75342 165.27728 -#> B1 37.26908 123.80520 -#> C1 11.23131 37.30961 -#> A2 28.50624 94.69567 -#> </div><div class='input'> <span class='co'># }</span> - <span class='co'># Compare with the results obtained in the original publication</span> - <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span> -</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation -#> 1 parent degradation rate 0.0496 0.0506 2.0 -#> 2 parent DT50 13.9900 13.6900 2.2 -#> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9 -#> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2 -#> 5 metabolite A1 DT50 49.9600 50.8900 1.8 -#> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6 -#> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7 -#> 8 metabolite B1 DT50 39.6100 40.2400 1.6 -#> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5 -#> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9 -#> 11 metabolite C1 DT50 10.8700 9.9000 9.8 -#> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7 -#> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4 -#> 14 metabolite A2 DT50 28.2400 28.4500 0.7</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">schaefer07_complex_case</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A1"</span>, <span class="st">"B1"</span>, <span class="st">"C1"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> B1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> C1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="schaefer07_complex_case-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 13.95078 46.34350</span> +<span class="r-out co"><span class="r-pr">#></span> A1 49.75342 165.27728</span> +<span class="r-out co"><span class="r-pr">#></span> B1 37.26908 123.80520</span> +<span class="r-out co"><span class="r-pr">#></span> C1 11.23131 37.30961</span> +<span class="r-out co"><span class="r-pr">#></span> A2 28.50624 94.69567</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span> <span class="co"># Compare with the results obtained in the original publication</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">schaefer07_complex_results</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> compound parameter KinGUI ModelMaker deviation</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent degradation rate 0.0496 0.0506 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 parent DT50 13.9900 13.6900 2.2</span> +<span class="r-out co"><span class="r-pr">#></span> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9</span> +<span class="r-out co"><span class="r-pr">#></span> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2</span> +<span class="r-out co"><span class="r-pr">#></span> 5 metabolite A1 DT50 49.9600 50.8900 1.8</span> +<span class="r-out co"><span class="r-pr">#></span> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6</span> +<span class="r-out co"><span class="r-pr">#></span> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7</span> +<span class="r-out co"><span class="r-pr">#></span> 8 metabolite B1 DT50 39.6100 40.2400 1.6</span> +<span class="r-out co"><span class="r-pr">#></span> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9</span> +<span class="r-out co"><span class="r-pr">#></span> 11 metabolite C1 DT50 10.8700 9.9000 9.8</span> +<span class="r-out co"><span class="r-pr">#></span> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7</span> +<span class="r-out co"><span class="r-pr">#></span> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4</span> +<span class="r-out co"><span class="r-pr">#></span> 14 metabolite A2 DT50 28.2400 28.4500 0.7</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html index 6c6a5d46..fab0a72d 100644 --- a/docs/dev/reference/set_nd_nq.html +++ b/docs/dev/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><meta name="robots" content= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ it automates the proposal of Boesten et al (2015)."><meta name="robots" content= <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/sigma_twocomp-1.png b/docs/dev/reference/sigma_twocomp-1.png Binary files differindex 6e61684e..0353b72c 100644 --- a/docs/dev/reference/sigma_twocomp-1.png +++ b/docs/dev/reference/sigma_twocomp-1.png diff --git a/docs/dev/reference/sigma_twocomp.html b/docs/dev/reference/sigma_twocomp.html index b7d295b2..292bf8e8 100644 --- a/docs/dev/reference/sigma_twocomp.html +++ b/docs/dev/reference/sigma_twocomp.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Two-component error model — sigma_twocomp • mkin</title> - - -<!-- jquery --> 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describing the standard deviation of the measurement error in +dependence of the measured value \(y\):"><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ dependence of the measured value \(y\):" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ dependence of the measured value \(y\):" /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Two-component error model</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/sigma_twocomp.R'><code>R/sigma_twocomp.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/sigma_twocomp.R" class="external-link"><code>R/sigma_twocomp.R</code></a></small> <div class="hidden name"><code>sigma_twocomp.Rd</code></div> </div> @@ -149,40 +94,43 @@ dependence of the measured value \(y\):" /> dependence of the measured value \(y\):</p> </div> - <pre class="usage"><span class='fu'>sigma_twocomp</span><span class='op'>(</span><span class='va'>y</span>, <span class='va'>sigma_low</span>, <span class='va'>rsd_high</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>y</th> - <td><p>The magnitude of the observed value</p></td> - </tr> - <tr> - <th>sigma_low</th> - <td><p>The asymptotic minimum of the standard deviation for low -observed values</p></td> - </tr> - <tr> - <th>rsd_high</th> - <td><p>The coefficient describing the increase of the standard -deviation with the magnitude of the observed value</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The standard deviation of the response variable.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>y</dt> +<dd><p>The magnitude of the observed value</p></dd> + +<dt>sigma_low</dt> +<dd><p>The asymptotic minimum of the standard deviation for low +observed values</p></dd> + + +<dt>rsd_high</dt> +<dd><p>The coefficient describing the increase of the standard +deviation with the magnitude of the observed value</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The standard deviation of the response variable.</p> + </div> + <div id="details"> + <h2>Details</h2> <p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)</p> <p>This is the error model used for example by Werner et al. (1978). The model proposed by Rocke and Lorenzato (1995) can be written in this form as well, but assumes approximate lognormal distribution of errors for high values of y.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898.</p> @@ -190,61 +138,62 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a> +<a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>times</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> -<span class='va'>d_pred</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>time <span class='op'>=</span> <span class='va'>times</span>, parent <span class='op'>=</span> <span class='fl'>100</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>exp</a></span><span class='op'>(</span><span class='op'>-</span> <span class='fl'>0.03</span> <span class='op'>*</span> <span class='va'>times</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456</span><span class='op'>)</span> -<span class='va'>d_syn</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_pred</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>y</span><span class='op'>)</span> <span class='fu'>sigma_twocomp</span><span class='op'>(</span><span class='va'>y</span>, <span class='fl'>1</span>, <span class='fl'>0.07</span><span class='op'>)</span>, - reps <span class='op'>=</span> <span class='fl'>2</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> -<span class='va'>f_nls</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/nls.html'>nls</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='fu'><a href='https://rdrr.io/r/stats/SSasymp.html'>SSasymp</a></span><span class='op'>(</span><span class='va'>time</span>, <span class='fl'>0</span>, <span class='va'>parent_0</span>, <span class='va'>lrc</span><span class='op'>)</span>, data <span class='op'>=</span> <span class='va'>d_syn</span>, - start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> -<span class='va'>f_gnls</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/gnls.html'>gnls</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='fu'><a href='https://rdrr.io/r/stats/SSasymp.html'>SSasymp</a></span><span class='op'>(</span><span class='va'>time</span>, <span class='fl'>0</span>, <span class='va'>parent_0</span>, <span class='va'>lrc</span><span class='op'>)</span>, - data <span class='op'>=</span> <span class='va'>d_syn</span>, na.action <span class='op'>=</span> <span class='va'>na.omit</span>, - start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> - <span class='va'>f_gnls_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_gnls</span>, weights <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/varConstProp.html'>varConstProp</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> - <span class='va'>f_gnls_tc_sf</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_gnls_tc</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>sigma <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> -<span class='op'>}</span> -<span class='va'>f_mkin</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>d_syn</span>, error_model <span class='op'>=</span> <span class='st'>"const"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>f_mkin_tc</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>d_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>f_mkin_tc</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='sigma_twocomp-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nls</span>, <span class='va'>f_gnls</span>, <span class='va'>f_gnls_tc</span>, <span class='va'>f_gnls_tc_sf</span>, <span class='va'>f_mkin</span>, <span class='va'>f_mkin_tc</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> f_nls 3 114.4817 -#> f_gnls 3 114.4817 -#> f_gnls_tc 5 103.6447 -#> f_gnls_tc_sf 4 101.6447 -#> f_mkin 3 114.4817 -#> f_mkin_tc 4 101.6446</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">times</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_pred</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_syn</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_pred</span>, <span class="kw">function</span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="fl">1</span>, <span class="fl">0.07</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> reps <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="va">f_nls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>, data <span class="op">=</span> <span class="va">d_syn</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_gnls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/gnls.html" class="external-link">gnls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">d_syn</span>, na.action <span class="op">=</span> <span class="va">na.omit</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">f_gnls_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls</span>, weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/varConstProp.html" class="external-link">varConstProp</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_gnls_tc_sf</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls_tc</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sigma <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="va">f_mkin</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">f_mkin_tc</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sigma_twocomp-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nls</span>, <span class="va">f_gnls</span>, <span class="va">f_gnls_tc</span>, <span class="va">f_gnls_tc_sf</span>, <span class="va">f_mkin</span>, <span class="va">f_mkin_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_nls 3 114.4817</span> +<span class="r-out co"><span class="r-pr">#></span> f_gnls 3 114.4817</span> +<span class="r-out co"><span class="r-pr">#></span> f_gnls_tc 5 103.6447</span> +<span class="r-out co"><span class="r-pr">#></span> f_gnls_tc_sf 4 101.6447</span> +<span class="r-out co"><span class="r-pr">#></span> f_mkin 3 114.4817</span> +<span class="r-out co"><span class="r-pr">#></span> f_mkin_tc 4 101.6446</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html index 4c856100..c3516f07 100644 --- a/docs/dev/reference/status.html +++ b/docs/dev/reference/status.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index 3994a424..ad8432bf 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -211,10 +214,10 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Nov 14 21:06:31 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Nov 14 21:06:31 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:06 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:06 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html index 96c2d0e5..0c0248fb 100644 --- a/docs/dev/reference/summary.mmkin.html +++ b/docs/dev/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -132,7 +135,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.767 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.842 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index 067efcfe..dcf2bd3d 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -48,19 +48,25 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -229,11 +235,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.158 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:27:32 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:27:32 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.160 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:11 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:11 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -243,7 +249,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.534 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.542 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index d8a41356..3b5869f1 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -99,7 +102,7 @@ endpoints such as formation fractions and DT50 values. Optionally <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for summary.saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> @@ -243,56 +246,58 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 828.1 822.7 -400.1</span> +<span class="r-out co"><span class="r-pr">#></span> 810.8 805.4 -391.4</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.74378 97.81291 103.67465</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06168 -4.17104 -3.95231</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92584 -1.31273 -0.53894</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.81914 -3.60206 -2.03623</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63916 -4.32672 -2.95161</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02927 -1.15247 1.09394</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.86164 0.67928 1.04400</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07973 0.06437 0.09509</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.73313 -7.46512 8.93137</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.06488 -0.06041 0.19017</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.41955 0.15206 0.68705</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.81750 0.29140 1.34361</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75265 0.27939 1.22590</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34411 -1.70964 2.39786</span> +<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.86947 97.81542 103.92353</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06947 -4.16944 -3.96950</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.93256 -1.34200 -0.52312</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.37017 -2.72660 -2.01375</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.06264 -4.21344 -3.91184</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02174 -0.45898 0.41549</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87598 0.67275 1.07922</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07949 0.06389 0.09509</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.19170 -30.36286 30.74626</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.01883 -0.28736 0.32502</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44300 0.16391 0.72209</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35320 0.09661 0.60978</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.13707 0.02359 0.25056</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.37478 0.04490 0.70467</span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)" "sd(g_qlogis)"</span> -<span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)"</span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span> +<span class="r-in"><span> no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"parent_0"</span>, <span class="st">"log_k_m1"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Approximate 95% confidence intervals</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 97.54844979 100.46239264 103.37633550</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01575805 0.01729111 0.01897331</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.21014925 0.28626877 0.37680664</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.02651112 0.05601399 0.11834908</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01326524 0.02649799 0.05293107</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.31467778 0.51297098 0.70726363</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.36731429 101.42508066 104.48284703</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01513234 0.01670094 0.01843214</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20221431 0.27608850 0.36461630</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.06915073 0.09759718 0.13774560</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01487068 0.01740389 0.02036863</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.37365671 0.48384821 0.59563299</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.1658367 0.4471180 0.7283993</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.2768757 0.7929203 1.3089649</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.2693629 0.7566116 1.2438602</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16439770 0.4427585 0.7211193</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.08304243 0.3345213 0.5860002</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.03146410 0.1490210 0.2665779</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.06216385 0.4023430 0.7425221</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.70273100 0.88750764 1.07228428</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06781347 0.08328016 0.09874685</span> -<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.67696663 0.87777355 1.07858048</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.06363957 0.07878001 0.09392044</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:12:50 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:12:50 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Dec 15 14:47:14 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Dec 15 14:47:14 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -307,12 +312,12 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 25.006 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.623 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for degradation parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> @@ -321,237 +326,291 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for random effects (square root of initial entries in omega):</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 6.742 0.0000 0.0000 0.0000 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.000 0.2236 0.0000 0.0000 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000 0.0000 0.5572 0.0000 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.000 0.0000 0.0000 0.8031 0.0000 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.000 0.0000 0.0000 0.0000 0.2931 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.000 0.0000 0.0000 0.0000 0.0000 0.807</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for error model parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 b.1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 825.6 821.3 -401.8</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 807 802.3 -391.5</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.46239 97.54845 103.37634</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.05756 -4.15040 -3.96472</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.91358 -1.32403 -0.50312</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.88215 -3.63019 -2.13412</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63069 -4.32261 -2.93876</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.05190 -0.77834 0.88213</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88751 0.70273 1.07228</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08328 0.06781 0.09875</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44712 0.16584 0.72840</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.79292 0.27688 1.30896</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75661 0.26936 1.24386</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.42508 98.36731 104.48285</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.09229 -4.19092 -3.99366</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.96395 -1.37251 -0.55538</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.32691 -2.67147 -1.98235</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.05106 -4.20836 -3.89376</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.06463 -0.51656 0.38730</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87777 0.67697 1.07858</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07878 0.06364 0.09392</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44276 0.16440 0.72112</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.33452 0.08304 0.58600</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.14902 0.03146 0.26658</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.40234 0.06216 0.74252</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4102 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2113 0.2439 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1308 -0.1305 -0.0504 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -0.0383 0.0592 0.0151 0.0001 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0029 -0.0118 0.0131 -0.2547 -0.1942</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4693 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2378 0.2595 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1720 -0.1593 -0.0669 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0179 0.0594 0.0035 0.1995 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.1073 -0.1060 -0.0322 -0.2299 -0.3168</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4471 0.1658 0.7284</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.7929 0.2769 1.3090</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.7566 0.2694 1.2439</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4428 0.16440 0.7211</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3345 0.08304 0.5860</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1490 0.03146 0.2666</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4023 0.06216 0.7425</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88751 0.70273 1.07228</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08328 0.06781 0.09875</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87777 0.67697 1.07858</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07878 0.06364 0.09392</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.46239 97.54845 103.37634</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01729 0.01576 0.01897</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28627 0.21015 0.37681</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.05601 0.02651 0.11835</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.02650 0.01327 0.05293</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.51297 0.31468 0.70726</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.4251 98.36731 104.48285</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0167 0.01513 0.01843</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.2761 0.20221 0.36462</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.0976 0.06915 0.13775</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.0174 0.01487 0.02037</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.4838 0.37366 0.59563</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2863</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7137</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2761</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7239</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 17.44 65.15 19.61 12.37 26.16</span> -<span class="r-out co"><span class="r-pr">#></span> m1 40.09 133.17 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 15.54 94.33 28.4 7.102 39.83</span> +<span class="r-out co"><span class="r-pr">#></span> m1 41.50 137.87 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.005e+02 -10.662393 8.4135 -1.267301</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.005e+02 3.637607 8.4135 0.432355</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.576e+01 -7.063498 8.0244 -0.880249</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.576e+01 -0.263498 8.0244 -0.032837</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.717e+01 -5.369491 7.3135 -0.734185</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.717e+01 7.330509 7.3135 1.002320</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.274e+01 -1.238672 6.1224 -0.202319</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.274e+01 -2.438672 6.1224 -0.398322</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.418e+01 0.022691 4.5984 0.004935</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.418e+01 -4.577309 4.5984 -0.995423</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.241e+01 -0.914545 2.8416 -0.321837</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.241e+01 -3.614545 2.8416 -1.271993</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.283e+01 -0.730904 1.3891 -0.526186</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.283e+01 0.769096 1.3891 0.553681</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.128e+00 0.071981 1.0238 0.070309</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.128e+00 2.171981 1.0238 2.121538</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.022e+00 -0.822164 0.9225 -0.891230</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.022e+00 -0.622164 0.9225 -0.674429</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.163e+00 -0.863423 0.8928 -0.967116</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.163e+00 -0.963423 0.8928 -1.079126</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.233e+00 -1.032930 0.9274 -1.113734</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.233e+00 -0.232930 0.9274 -0.251152</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.495e+00 0.005314 1.0393 0.005113</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.495e+00 -1.494686 1.0393 -1.438116</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.010e+01 0.096372 1.2230 0.078801</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.010e+01 -0.603628 1.2230 -0.493572</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.269e+01 -0.492073 1.3802 -0.356526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.269e+01 0.707927 1.3802 0.512922</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.086e+01 0.944360 1.2669 0.745420</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.086e+01 2.344360 1.2669 1.850494</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.723e+00 -1.123088 1.0961 -1.024658</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.723e+00 1.576912 1.0961 1.438708</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.184e+00 -1.683936 0.9869 -1.706219</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.184e+00 0.216064 0.9869 0.218923</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.005e+02 17.537607 8.4135 2.084469</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.005e+02 -0.662393 8.4135 -0.078730</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.566e+01 -5.456414 8.0156 -0.680727</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.566e+01 -1.056414 8.0156 -0.131795</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.702e+01 9.082833 7.3009 1.244062</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.702e+01 -8.617167 7.3009 -1.180281</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.298e+01 4.919834 6.1423 0.800981</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.298e+01 4.719834 6.1423 0.768420</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.588e+01 0.124003 4.7372 0.026176</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.588e+01 -1.175997 4.7372 -0.248245</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.719e+01 -0.587869 3.2217 -0.182474</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.719e+01 -0.387869 3.2217 -0.120394</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.013e+01 1.973728 1.8966 1.040673</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.013e+01 4.573728 1.8966 2.411556</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.259e+01 -0.185933 1.3734 -0.135379</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.259e+01 -1.785933 1.3734 -1.300347</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.981e+00 -1.180542 1.1088 -1.064723</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.981e+00 -0.080542 1.1088 -0.072640</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.306e+00 -0.006246 0.8941 -0.006986</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.589e+00 0.110879 0.9365 0.118399</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.589e+00 1.110879 0.9365 1.186217</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.062e+00 1.038045 1.0647 0.974978</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.062e+00 0.838045 1.0647 0.787129</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.065e+01 -0.553713 1.2549 -0.441227</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.065e+01 -0.353713 1.2549 -0.281857</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.284e+01 -2.144854 1.3900 -1.543111</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.284e+01 -0.644854 1.3900 -0.463939</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.082e+01 -0.115278 1.2645 -0.091165</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.082e+01 1.684722 1.2645 1.332337</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.014e+00 1.085607 1.1105 0.977610</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.014e+00 -0.614393 1.1105 -0.553272</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.736e+00 0.363593 1.0079 0.360737</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.736e+00 -1.236407 1.0079 -1.226697</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.005e+02 5.737607 8.4135 0.681955</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.005e+02 6.437607 8.4135 0.765155</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.343e+01 13.972212 7.8311 1.784188</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.343e+01 2.672212 7.8311 0.341229</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.160e+01 -2.196297 6.8531 -0.320484</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.160e+01 1.003703 6.8531 0.146460</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.464e+01 -0.737220 5.4557 -0.135129</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.464e+01 -2.237220 5.4557 -0.410072</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.772e+01 3.278433 4.0722 0.805086</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.772e+01 -0.621567 4.0722 -0.152638</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.303e+01 3.070676 2.8903 1.062400</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.303e+01 3.570676 2.8903 1.235391</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.929e+01 0.808039 1.8355 0.440235</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.929e+01 0.508039 1.8355 0.276789</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.209e+01 -0.794443 1.3425 -0.591785</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.209e+01 -1.394443 1.3425 -1.038728</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.590e+00 0.610002 1.0896 0.559843</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.590e+00 -0.289998 1.0896 -0.266152</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -4.263e-14 0.800000 0.8875 0.901401</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.692e+00 0.107665 0.8986 0.119811</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.692e+00 0.607665 0.8986 0.676214</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.455e+00 -0.255347 0.9619 -0.265449</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.455e+00 -0.355347 0.9619 -0.369404</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.124e+00 -1.324338 1.1160 -1.186685</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.124e+00 1.975662 1.1160 1.770309</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.104e+01 0.361860 1.2778 0.283196</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.104e+01 1.761860 1.2778 1.378852</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.177e+01 -0.272554 1.3225 -0.206097</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.177e+01 -1.172554 1.3225 -0.886648</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.242e+00 -1.741667 1.1747 -1.482591</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.242e+00 -0.641667 1.1747 -0.546218</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.837e+00 0.463318 1.0544 0.439398</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.837e+00 1.263318 1.0544 1.198095</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 4.906e+00 0.394322 0.9770 0.403595</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 4.906e+00 -1.105678 0.9770 -1.131677</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.005e+02 4.237607 8.4135 0.503670</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.005e+02 -12.162393 8.4135 -1.445587</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.723e+01 -3.029220 8.1458 -0.371877</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.723e+01 -2.629220 8.1458 -0.322772</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.114e+01 -13.041804 7.6420 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parent 60 23.5 2.110e+01 2.400596 1.9686 1.219459</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.183e+01 -0.034206 1.3263 -0.025791</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.183e+01 0.265794 1.3263 0.200408</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.985e+00 0.014647 1.0612 0.013803</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.985e+00 -0.785353 1.0612 -0.740078</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 -1.705e-13 1.600000 0.8875 1.802801</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.803e-01 0.219655 0.8893 0.246994</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.927e+00 1.773027 0.9019 1.965880</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.927e+00 0.073027 0.9019 0.080970</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.013e+00 -0.412926 0.9483 -0.435417</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.013e+00 -0.212926 0.9483 -0.224523</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.604e+00 0.495843 1.0441 0.474896</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.604e+00 -0.004157 1.0441 -0.003981</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.077e+00 0.422700 1.1658 0.362576</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.077e+00 0.222700 1.1658 0.191024</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.818e+00 -0.518498 1.1520 -0.450099</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.818e+00 0.181502 1.1520 0.157559</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.738e+00 -0.137785 1.0500 -0.131222</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.738e+00 0.962215 1.0500 0.916383</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.794e+00 -1.093754 0.9732 -1.123914</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.794e+00 -1.293754 0.9732 -1.329429</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.005e+02 9.937607 8.4135 1.181155</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.005e+02 11.637607 8.4135 1.383212</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.372e+01 -0.215694 7.8550 -0.027460</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.372e+01 -2.715694 7.8550 -0.345730</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.226e+01 -11.257156 6.9076 -1.629667</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.226e+01 7.442844 6.9076 1.077480</span> 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11.3 1.172e+01 -0.423434 1.3194 -0.320923</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.172e+01 0.176566 1.3194 0.133820</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.281e+00 1.719138 1.0749 1.599402</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.281e+00 0.819138 1.0749 0.762086</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 -2.842e-13 0.700000 0.8875 0.788726</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.252e+00 -0.252227 0.9279 -0.271821</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.252e+00 -0.652227 0.9279 -0.702895</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.615e+00 -3.515326 1.1413 -3.080237</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.615e+00 -1.115326 1.1413 -0.977283</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.588e+01 0.619041 1.5928 0.388661</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.588e+01 3.119041 1.5928 1.958272</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.189e+01 1.014705 2.0272 0.500543</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.189e+01 1.314705 2.0272 0.648529</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.369e+01 -1.487604 2.1632 -0.687701</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.369e+01 0.712396 2.1632 0.329332</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.869e+01 -3.193942 1.7920 -1.782295</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.869e+01 1.106058 1.7920 0.617206</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.380e+01 1.103454 1.4518 0.760041</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.380e+01 0.403454 1.4518 0.277892</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.864e+00 1.035963 1.2093 0.856637</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.864e+00 0.535963 1.2093 0.443187</span> +<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.014e+02 -11.62508 8.0383 -1.44620</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.014e+02 2.67492 8.0383 0.33277</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.650e+01 -7.80311 7.6530 -1.01961</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.650e+01 -1.00311 7.6530 -0.13107</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.753e+01 -5.72638 6.9510 -0.82382</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.753e+01 6.97362 6.9510 1.00326</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.254e+01 -1.04133 5.7818 -0.18010</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.254e+01 -2.24133 5.7818 -0.38765</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.349e+01 0.71029 4.3044 0.16502</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.349e+01 -3.88971 4.3044 -0.90366</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.167e+01 -0.16616 2.6446 -0.06283</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.167e+01 -2.86616 2.6446 -1.08379</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.279e+01 -0.69287 1.3365 -0.51843</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.279e+01 0.80713 1.3365 0.60392</span> 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class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.236e+00 -1.73617 0.9699 -1.79010</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.236e+00 0.16383 0.9699 0.16892</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.014e+02 16.57492 8.0383 2.06198</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.014e+02 -1.62508 8.0383 -0.20217</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.599e+01 -5.79045 7.6129 -0.76061</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.599e+01 -1.39045 7.6129 -0.18264</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.652e+01 9.57931 6.8724 1.39388</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.652e+01 -8.12069 6.8724 -1.18164</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.197e+01 5.93429 5.7370 1.03439</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.197e+01 5.73429 5.7370 0.99953</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.555e+01 0.44657 4.4637 0.10005</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.555e+01 -0.85343 4.4637 -0.19120</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.853e+01 -1.93170 3.1599 -0.61132</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.853e+01 -1.73170 3.1599 -0.54803</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.110e+01 1.00360 1.8795 0.53396</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.110e+01 3.60360 1.8795 1.91728</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.250e+01 -0.09712 1.3190 -0.07363</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.250e+01 -1.69712 1.3190 -1.28667</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.419e+00 -0.61913 1.0546 -0.58709</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.419e+00 0.48087 1.0546 0.45599</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.422e+00 -0.12194 0.8849 -0.13781</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.831e+00 -0.13149 0.9282 -0.14166</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.831e+00 0.86851 0.9282 0.93567</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.292e+00 0.80812 1.0490 0.77034</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.292e+00 0.60812 1.0490 0.57969</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.055e+01 -0.45332 1.2090 -0.37495</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.055e+01 -0.25332 1.2090 -0.20953</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.230e+01 -1.59960 1.3074 -1.22347</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.230e+01 -0.09960 1.3074 -0.07618</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.065e+01 0.05342 1.2141 0.04400</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.065e+01 1.85342 1.2141 1.52661</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.196e+00 0.90368 1.0897 0.82930</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.196e+00 -0.79632 1.0897 -0.73078</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.997e+00 0.10252 0.9969 0.10284</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.997e+00 -1.49748 0.9969 -1.50220</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.014e+02 4.77492 8.0383 0.59402</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.014e+02 5.47492 8.0383 0.68110</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.390e+01 13.49935 7.4494 1.81214</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.390e+01 2.19935 7.4494 0.29524</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.152e+01 -2.12307 6.4821 -0.32753</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.152e+01 1.07693 6.4821 0.16614</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.446e+01 -0.55834 5.1533 -0.10834</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.446e+01 -2.05834 5.1533 -0.39942</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.826e+01 2.74073 3.9019 0.70241</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.826e+01 -1.15927 3.9019 -0.29711</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.424e+01 1.86399 2.8364 0.65718</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.424e+01 2.36399 2.8364 0.83346</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.968e+01 0.42172 1.7815 0.23672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.968e+01 0.12172 1.7815 0.06833</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.195e+01 -0.64633 1.2869 -0.50222</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.195e+01 -1.24633 1.2869 -0.96844</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.255e+00 0.94532 1.0474 0.90251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.255e+00 0.04532 1.0474 0.04327</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 2.956e-11 0.80000 0.8778 0.91140</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.758e+00 0.04187 0.8886 0.04712</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.758e+00 0.54187 0.8886 0.60978</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.567e+00 -0.36697 0.9486 -0.38683</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.567e+00 -0.46697 0.9486 -0.49224</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.151e+00 -1.35124 1.0876 -1.24242</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.151e+00 1.94876 1.0876 1.79182</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.083e+01 0.57098 1.2240 0.46647</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.083e+01 1.97098 1.2240 1.61022</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.147e+01 0.03175 1.2597 0.02520</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.147e+01 -0.86825 1.2597 -0.68928</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.298e+00 -1.79834 1.1433 -1.57298</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.298e+00 -0.69834 1.1433 -0.61083</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 7.038e+00 0.26249 1.0382 0.25283</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 7.038e+00 1.06249 1.0382 1.02340</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 5.116e+00 0.18417 0.9659 0.19068</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 5.116e+00 -1.31583 0.9659 -1.36232</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.014e+02 3.27492 8.0383 0.40741</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.014e+02 -13.12508 8.0383 -1.63281</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.781e+01 -3.61183 7.7555 -0.46572</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.781e+01 -3.21183 7.7555 -0.41414</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.110e+01 -13.00467 7.2307 -1.79853</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.110e+01 5.39533 7.2307 0.74617</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 7.951e+01 -3.30511 6.3246 -0.52258</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 7.951e+01 -1.70511 6.3246 -0.26960</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.376e+01 7.03783 5.0993 1.38016</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.376e+01 3.53783 5.0993 0.69379</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.340e+01 -0.30456 3.5303 -0.08627</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.340e+01 1.69544 3.5303 0.48026</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.142e+01 -0.12077 1.9022 -0.06349</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.142e+01 2.07923 1.9022 1.09308</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.207e+01 -0.26813 1.2940 -0.20721</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.207e+01 0.03187 1.2940 0.02463</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.954e+00 0.04554 1.0347 0.04402</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.954e+00 -0.75446 1.0347 -0.72914</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 1.990e-13 1.60000 0.8778 1.82279</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 7.305e-01 0.16949 0.8797 0.19267</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 2.051e+00 1.64896 0.8925 1.84753</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 2.051e+00 -0.05104 0.8925 -0.05719</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.204e+00 -0.60375 0.9382 -0.64354</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.204e+00 -0.40375 0.9382 -0.43036</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.760e+00 0.34021 1.0267 0.33137</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.760e+00 -0.15979 1.0267 -0.15563</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.011e+00 0.48856 1.1289 0.43277</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.011e+00 0.28856 1.1289 0.25561</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.611e+00 -0.31077 1.1093 -0.28014</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.611e+00 0.38923 1.1093 0.35086</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.678e+00 -0.07753 1.0233 -0.07576</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.678e+00 1.02247 1.0233 0.99915</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.847e+00 -1.14679 0.9572 -1.19804</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.847e+00 -1.34679 0.9572 -1.40698</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.014e+02 8.97492 8.0383 1.11651</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.014e+02 10.67492 8.0383 1.32800</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.466e+01 -1.16118 7.5089 -0.15464</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.466e+01 -3.66118 7.5089 -0.48758</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.302e+01 -12.01844 6.5988 -1.82130</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.302e+01 6.68156 6.5988 1.01254</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.563e+01 -5.22574 5.2440 -0.99652</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.563e+01 -6.52574 5.2440 -1.24442</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.727e+01 9.22621 3.8263 2.41128</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.727e+01 -0.27379 3.8263 -0.07156</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.103e+01 -0.83405 2.5977 -0.32108</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.103e+01 -7.13405 2.5977 -2.74634</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.800e+01 -0.99696 1.6675 -0.59787</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.800e+01 0.70304 1.6675 0.42161</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.167e+01 -0.36809 1.2710 -0.28961</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.167e+01 0.23191 1.2710 0.18246</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.595e+00 1.40496 1.0623 1.32256</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.595e+00 0.50496 1.0623 0.47535</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 0.000e+00 0.70000 0.8778 0.79747</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.158e+00 -0.15799 0.9123 -0.17317</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.158e+00 -0.55799 0.9123 -0.61160</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.443e+00 -3.34286 1.1013 -3.03535</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.443e+00 -0.94286 1.1013 -0.85613</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.580e+01 0.69781 1.5232 0.45811</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.580e+01 3.19781 1.5232 2.09935</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.216e+01 0.73604 1.9543 0.37663</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.216e+01 1.03604 1.9543 0.53014</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.423e+01 -2.03128 2.1011 -0.96678</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.423e+01 0.16872 2.1011 0.08030</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.876e+01 -3.25610 1.7187 -1.89455</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.876e+01 1.04390 1.7187 0.60739</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.366e+01 1.23585 1.3890 0.88976</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.366e+01 0.53585 1.3890 0.38579</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.761e+00 1.13911 1.1670 0.97613</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.761e+00 0.63911 1.1670 0.54767</span> +<span class="r-in"><span><span class="co"># Add a correlation between random effects of g and k2</span></span></span> +<span class="r-in"><span><span class="va">cov_model_3</span> <span class="op"><-</span> <span class="va">f_saem_dfop_sfo_2</span><span class="op">$</span><span class="va">so</span><span class="op">@</span><span class="va">model</span><span class="op">@</span><span class="va">covariance.model</span></span></span> +<span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"log_k2"</span>, <span class="st">"g_qlogis"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="va">cov_model_3</span><span class="op">[</span><span class="st">"g_qlogis"</span>, <span class="st">"log_k2"</span><span class="op">]</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo_3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>,</span></span> +<span class="r-in"><span> covariance.model <span class="op">=</span> <span class="va">cov_model_3</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Approximate 95% confidence intervals</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.39888363 101.48951337 104.58014311</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01508704 0.01665986 0.01839665</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20141557 0.27540583 0.36418131</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.07708759 0.10430866 0.14114200</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01476621 0.01786384 0.02161129</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.33679867 0.45083525 0.57028162</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.38085375 0.4441841 0.5075145</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.04774819 0.2660384 0.4843286</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.63842736 0.1977024 1.0338321</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.22711289 0.4502227 0.6733326</span> +<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.83271473 -0.6176939 -0.4026730</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.67347568 0.87437392 1.07527216</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.06393032 0.07912417 0.09431802</span> +<span class="r-in"><span><span class="co"># The correlation does not improve the fit judged by AIC and BIC, although</span></span></span> +<span class="r-in"><span><span class="co"># the likelihood is higher with the additional parameter</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, <span class="va">f_saem_dfop_sfo_2</span>, <span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 171 observations of 2 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_2 12 806.96 802.27 -391.48</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.99 802.91 -391.00</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo 14 810.83 805.36 -391.42</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> diff --git a/docs/dev/reference/summary_listing.html b/docs/dev/reference/summary_listing.html new file mode 100644 index 00000000..876412cc --- /dev/null +++ b/docs/dev/reference/summary_listing.html @@ -0,0 +1,147 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Display the output of a summary function according to the output format — summary_listing • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" 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href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Display the output of a summary function according to the output format — summary_listing"><meta property="og:description" content='This function is intended for use in a R markdown code chunk with the chunk +option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--></head><body data-spy="scroll" 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data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Display the output of a summary function according to the output format</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary_listing.R" class="external-link"><code>R/summary_listing.R</code></a></small> + <div class="hidden name"><code>summary_listing.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function is intended for use in a R markdown code chunk with the chunk +option <code>results = "asis"</code>.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summary_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span>, label <span class="op">=</span> <span class="cn">NULL</span>, clearpage <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">tex_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span>, label <span class="op">=</span> <span class="cn">NULL</span>, clearpage <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">html_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>The object for which the summary is to be listed</p></dd> + + +<dt>caption</dt> +<dd><p>An optional caption</p></dd> + + +<dt>label</dt> +<dd><p>An optional label, ignored in html output</p></dd> + + +<dt>clearpage</dt> +<dd><p>Should a new page be started after the listing? Ignored in html output</p></dd> + +</dl></div> + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 89975db5..132380a8 100644 --- a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014.html b/docs/dev/reference/synthetic_data_for_UBA_2014.html index 33a0ace2..729d991a 100644 --- a/docs/dev/reference/synthetic_data_for_UBA_2014.html +++ b/docs/dev/reference/synthetic_data_for_UBA_2014.html @@ -1,46 +1,5 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> -<meta property="og:description" content="The 12 datasets were generated using four different models and three different +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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The four models are either the SFO or the DFOP model with either two sequential or two parallel metabolites. Variance component 'a' is based on a normal distribution with standard deviation of 3, @@ -55,28 +14,14 @@ Initial concentrations for metabolites and all values where adding the variance in a value below the assumed limit of detection of 0.1 were set to NA. As an example, the first dataset has the title SFO_lin_a and is based on the SFO model with two sequential metabolites (linear pathway), with added variance component 'a'. -Compare also the code in the example section to see the degradation models." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +Compare also the code in the example section to see the degradation models."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -87,23 +32,21 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -113,44 +56,46 @@ Compare also the code in the example section to see the degradation models." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Synthetic datasets for one parent compound with two metabolites</h1> @@ -177,300 +122,308 @@ Compare also the code in the example section to see the degradation models." /> <p>Compare also the code in the example section to see the degradation models.</p> </div> - <pre class="usage"><span class='va'>synthetic_data_for_UBA_2014</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">synthetic_data_for_UBA_2014</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>, + each containing, among others, the following components</p><dl><dt><code>title</code></dt> +<dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>data</code></dt> +<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd> - <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='co'># The data have been generated using the following kinetic models</span> -<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - -<span class='va'>m_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>m_synth_DFOP_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># The model predictions without intentional error were generated as follows</span> -<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> - -<span class='va'>d_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.7</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.8</span>, - k_M1 <span class='op'>=</span> <span class='fl'>0.3</span>, f_M1_to_M2 <span class='op'>=</span> <span class='fl'>0.7</span>, - k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='va'>d_synth_DFOP_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_lin</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='fl'>0.2</span>, k2 <span class='op'>=</span> <span class='fl'>0.02</span>, g <span class='op'>=</span> <span class='fl'>0.5</span>, - f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.3</span>, - f_M1_to_M2 <span class='op'>=</span> <span class='fl'>0.7</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='va'>d_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.2</span>, - f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.8</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.01</span>, - f_parent_to_M2 <span class='op'>=</span> <span class='fl'>0.2</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='va'>d_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='fl'>0.3</span>, k2 <span class='op'>=</span> <span class='fl'>0.02</span>, g <span class='op'>=</span> <span class='fl'>0.7</span>, - f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.6</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.04</span>, - f_parent_to_M2 <span class='op'>=</span> <span class='fl'>0.4</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='co'># Construct names for datasets with errors</span> -<span class='va'>d_synth_names</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"d_synth_"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO_lin"</span>, <span class='st'>"SFO_par"</span>, - <span class='st'>"DFOP_lin"</span>, <span class='st'>"DFOP_par"</span><span class='op'>)</span><span class='op'>)</span> - -<span class='co'># Original function used or adding errors. The add_err function now published</span> -<span class='co'># with this package is a slightly generalised version where the names of</span> -<span class='co'># secondary compartments that should have an initial value of zero (M1 and M2</span> -<span class='co'># in this case) are not hardcoded any more.</span> -<span class='co'># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span> -<span class='co'># {</span> -<span class='co'># set.seed(seed)</span> -<span class='co'># d_long = mkin_wide_to_long(d, time = "time")</span> -<span class='co'># d_rep = data.frame(lapply(d_long, rep, each = 2))</span> -<span class='co'># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span> -<span class='co'>#</span> -<span class='co'># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span> -<span class='co'># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span> -<span class='co'># d_NA$value <- round(d_NA$value, 1)</span> -<span class='co'># return(d_NA)</span> -<span class='co'># }</span> - -<span class='co'># The following is the simplified version of the two-component model of Rocke</span> -<span class='co'># and Lorenzato (1995)</span> -<span class='va'>sdfunc_twocomp</span> <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span>, <span class='va'>sd_low</span>, <span class='va'>rsd_high</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='va'>sd_low</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='va'>rsd_high</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span> -<span class='op'>}</span> - -<span class='co'># Add the errors.</span> -<span class='kw'>for</span> <span class='op'>(</span><span class='va'>d_synth_name</span> <span class='kw'>in</span> <span class='va'>d_synth_names</span><span class='op'>)</span> -<span class='op'>{</span> - <span class='va'>d_synth</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/get.html'>get</a></span><span class='op'>(</span><span class='va'>d_synth_name</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_a"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_b"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>7</span><span class='op'>)</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_c"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, - <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'>sdfunc_twocomp</span><span class='op'>(</span><span class='va'>value</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> - -<span class='op'>}</span> - -<span class='va'>d_synth_err_names</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span> - <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='va'>d_synth_names</span>, each <span class='op'>=</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>letters</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, sep <span class='op'>=</span> <span class='st'>"_"</span><span class='op'>)</span> -<span class='op'>)</span> - -<span class='co'># This is just one example of an evaluation using the kinetic model used for</span> -<span class='co'># the generation of the data</span> - <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, - quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.3.9000 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 17:13:29 2021 -#> Date of summary: Mon Feb 15 17:13:29 2021 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 -#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted using 833 model solutions performed in 0.649 s -#> -#> Error model: Constant variance -#> -#> Error model algorithm: OLS -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.3500 state -#> k_parent 0.1000 deparm -#> k_M1 0.1001 deparm -#> k_M2 0.1002 deparm -#> f_parent_to_M1 0.5000 deparm -#> f_M1_to_M2 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 101.350000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_M1 -2.301586 -Inf Inf -#> log_k_M2 -2.300587 -Inf Inf -#> f_parent_qlogis 0.000000 -Inf Inf -#> f_M1_qlogis 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> M1_0 0 state -#> M2_0 0 state -#> -#> Results: -#> -#> AIC BIC logLik -#> 188.7274 200.3723 -87.36368 -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 102.1000 1.57000 98.8600 105.3000 -#> log_k_parent -0.3020 0.03885 -0.3812 -0.2229 -#> log_k_M1 -1.2070 0.07123 -1.3520 -1.0620 -#> log_k_M2 -3.9010 0.06571 -4.0350 -3.7670 -#> f_parent_qlogis 1.2010 0.23530 0.7216 1.6800 -#> f_M1_qlogis 0.9589 0.24890 0.4520 1.4660 -#> sigma 2.2730 0.25740 1.7490 2.7970 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_qlogis -#> parent_0 1.000e+00 3.933e-01 -1.605e-01 2.819e-02 -4.624e-01 -#> log_k_parent 3.933e-01 1.000e+00 -4.082e-01 7.166e-02 -5.682e-01 -#> log_k_M1 -1.605e-01 -4.082e-01 1.000e+00 -3.929e-01 7.478e-01 -#> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01 -#> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00 -#> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01 -#> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08 -#> f_M1_qlogis sigma -#> parent_0 1.614e-01 -2.900e-08 -#> log_k_parent 4.102e-01 -8.030e-09 -#> log_k_M1 -8.109e-01 -2.741e-08 -#> log_k_M2 5.419e-01 3.938e-08 -#> f_parent_qlogis -8.605e-01 -2.681e-08 -#> f_M1_qlogis 1.000e+00 4.971e-08 -#> sigma 4.971e-08 1.000e+00 -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 102.10000 65.000 7.281e-36 98.86000 105.30000 -#> k_parent 0.73930 25.740 2.948e-23 0.68310 0.80020 -#> k_M1 0.29920 14.040 1.577e-15 0.25880 0.34590 -#> k_M2 0.02023 15.220 1.653e-16 0.01769 0.02312 -#> f_parent_to_M1 0.76870 18.370 7.295e-19 0.67300 0.84290 -#> f_M1_to_M2 0.72290 14.500 6.418e-16 0.61110 0.81240 -#> sigma 2.27300 8.832 2.161e-10 1.74900 2.79700 -#> -#> FOCUS Chi2 error levels in percent: -#> err.min n.optim df -#> All data 8.454 6 17 -#> parent 8.660 2 6 -#> M1 10.583 2 5 -#> M2 3.586 2 6 -#> -#> Resulting formation fractions: -#> ff -#> parent_M1 0.7687 -#> parent_sink 0.2313 -#> M1_M2 0.7229 -#> M1_sink 0.2771 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 0.9376 3.114 -#> M1 2.3170 7.697 -#> M2 34.2689 113.839 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 101.5 1.021e+02 -0.56248 -#> 0 parent 101.2 1.021e+02 -0.86248 -#> 1 parent 53.9 4.873e+01 5.17118 -#> 1 parent 47.5 4.873e+01 -1.22882 -#> 3 parent 10.4 1.111e+01 -0.70773 -#> 3 parent 7.6 1.111e+01 -3.50773 -#> 7 parent 1.1 5.772e-01 0.52283 -#> 7 parent 0.3 5.772e-01 -0.27717 -#> 14 parent 3.5 3.264e-03 3.49674 -#> 28 parent 3.2 1.045e-07 3.20000 -#> 90 parent 0.6 9.530e-10 0.60000 -#> 120 parent 3.5 -5.940e-10 3.50000 -#> 1 M1 36.4 3.479e+01 1.61088 -#> 1 M1 37.4 3.479e+01 2.61088 -#> 3 M1 34.3 3.937e+01 -5.07027 -#> 3 M1 39.8 3.937e+01 0.42973 -#> 7 M1 15.1 1.549e+01 -0.38715 -#> 7 M1 17.8 1.549e+01 2.31285 -#> 14 M1 5.8 1.995e+00 3.80469 -#> 14 M1 1.2 1.995e+00 -0.79531 -#> 60 M1 0.5 2.111e-06 0.50000 -#> 90 M1 3.2 -9.670e-10 3.20000 -#> 120 M1 1.5 7.670e-10 1.50000 -#> 120 M1 0.6 7.670e-10 0.60000 -#> 1 M2 4.8 4.455e+00 0.34517 -#> 3 M2 20.9 2.153e+01 -0.62527 -#> 3 M2 19.3 2.153e+01 -2.22527 -#> 7 M2 42.0 4.192e+01 0.07941 -#> 7 M2 43.1 4.192e+01 1.17941 -#> 14 M2 49.4 4.557e+01 3.83353 -#> 14 M2 44.3 4.557e+01 -1.26647 -#> 28 M2 34.6 3.547e+01 -0.87275 -#> 28 M2 33.0 3.547e+01 -2.47275 -#> 60 M2 18.8 1.858e+01 0.21837 -#> 60 M2 17.6 1.858e+01 -0.98163 -#> 90 M2 10.6 1.013e+01 0.47130 -#> 90 M2 10.8 1.013e+01 0.67130 -#> 120 M2 9.8 5.521e+00 4.27893 -#> 120 M2 3.3 5.521e+00 -2.22107</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># The data have been generated using the following kinetic models</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The model predictions without intentional error were generated as follows</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.7</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>,</span></span> +<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fl">0.3</span>, f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>,</span></span> +<span class="r-in"><span> k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_lin</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.5</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fl">0.3</span>,</span></span> +<span class="r-in"><span> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.2</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>, k_M1 <span class="op">=</span> <span class="fl">0.01</span>,</span></span> +<span class="r-in"><span> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.2</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.3</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.6</span>, k_M1 <span class="op">=</span> <span class="fl">0.04</span>,</span></span> +<span class="r-in"><span> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.4</span>, k_M2 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Construct names for datasets with errors</span></span></span> +<span class="r-in"><span><span class="va">d_synth_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"d_synth_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO_lin"</span>, <span class="st">"SFO_par"</span>,</span></span> +<span class="r-in"><span> <span class="st">"DFOP_lin"</span>, <span class="st">"DFOP_par"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Original function used or adding errors. The add_err function now published</span></span></span> +<span class="r-in"><span><span class="co"># with this package is a slightly generalised version where the names of</span></span></span> +<span class="r-in"><span><span class="co"># secondary compartments that should have an initial value of zero (M1 and M2</span></span></span> +<span class="r-in"><span><span class="co"># in this case) are not hardcoded any more.</span></span></span> +<span class="r-in"><span><span class="co"># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span></span></span> +<span class="r-in"><span><span class="co"># {</span></span></span> +<span class="r-in"><span><span class="co"># set.seed(seed)</span></span></span> +<span class="r-in"><span><span class="co"># d_long = mkin_wide_to_long(d, time = "time")</span></span></span> +<span class="r-in"><span><span class="co"># d_rep = data.frame(lapply(d_long, rep, each = 2))</span></span></span> +<span class="r-in"><span><span class="co"># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span></span></span> +<span class="r-in"><span><span class="co"># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span></span></span> +<span class="r-in"><span><span class="co"># d_NA$value <- round(d_NA$value, 1)</span></span></span> +<span class="r-in"><span><span class="co"># return(d_NA)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following is the simplified version of the two-component model of Rocke</span></span></span> +<span class="r-in"><span><span class="co"># and Lorenzato (1995)</span></span></span> +<span class="r-in"><span><span class="va">sdfunc_twocomp</span> <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span>, <span class="va">sd_low</span>, <span class="va">rsd_high</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">sd_low</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">rsd_high</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Add the errors.</span></span></span> +<span class="r-in"><span><span class="kw">for</span> <span class="op">(</span><span class="va">d_synth_name</span> <span class="kw">in</span> <span class="va">d_synth_names</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">d_synth</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/get.html" class="external-link">get</a></span><span class="op">(</span><span class="va">d_synth_name</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_a"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_b"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_c"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu">sdfunc_twocomp</span><span class="op">(</span><span class="va">value</span>, <span class="fl">0.5</span>, <span class="fl">0.07</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_err_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="va">d_synth_names</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, sep <span class="op">=</span> <span class="st">"_"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is just one example of an evaluation using the kinetic model used for</span></span></span> +<span class="r-in"><span><span class="co"># the generation of the data</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:54 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:54 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Equations:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1</span> +<span class="r-out co"><span class="r-pr">#></span> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.574 s</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Error model algorithm: OLS </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for parameters to be optimised:</span> +<span class="r-out co"><span class="r-pr">#></span> value type</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.3500 state</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.1000 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.1001 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.1002 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.5000 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M2 0.5000 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for the transformed parameters actually optimised:</span> +<span class="r-out co"><span class="r-pr">#></span> value lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.350000 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.302585 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -2.301586 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 -2.300587 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000000 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 0.000000 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed parameter values:</span> +<span class="r-out co"><span class="r-pr">#></span> value type</span> +<span class="r-out co"><span class="r-pr">#></span> M1_0 0 state</span> +<span class="r-out co"><span class="r-pr">#></span> M2_0 0 state</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Results:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 188.7274 200.3723 -87.36368</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Optimised, transformed parameters with symmetric confidence intervals:</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 102.1000 1.57000 98.8600 105.3000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -0.3020 0.03885 -0.3812 -0.2229</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -1.2070 0.07123 -1.3520 -1.0620</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 -3.9010 0.06571 -4.0350 -3.7670</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 1.2010 0.23530 0.7216 1.6800</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 0.9589 0.24890 0.4520 1.4660</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.2730 0.25740 1.7490 2.7970</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 3.933e-01 -1.605e-01 2.819e-02 -4.624e-01</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 3.933e-01 1.000e+00 -4.082e-01 7.166e-02 -5.682e-01</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -1.605e-01 -4.082e-01 1.000e+00 -3.929e-01 7.478e-01</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis sigma</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -2.900e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -8.030e-09</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 -2.741e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 3.938e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 4.971e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.971e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> +<span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> +<span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 102.10000 65.000 7.281e-36 98.86000 105.30000</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.73930 25.740 2.948e-23 0.68310 0.80020</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.29920 14.040 1.577e-15 0.25880 0.34590</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.02023 15.220 1.653e-16 0.01769 0.02312</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.76870 18.370 7.295e-19 0.67300 0.84290</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M2 0.72290 14.500 6.418e-16 0.61110 0.81240</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.27300 8.832 2.161e-10 1.74900 2.79700</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> FOCUS Chi2 error levels in percent:</span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 8.454 6 17</span> +<span class="r-out co"><span class="r-pr">#></span> parent 8.660 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> M1 10.583 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M2 3.586 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> +<span class="r-out co"><span class="r-pr">#></span> ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_M1 0.7687</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.2313</span> +<span class="r-out co"><span class="r-pr">#></span> M1_M2 0.7229</span> +<span class="r-out co"><span class="r-pr">#></span> M1_sink 0.2771</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.9376 3.114</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.3170 7.697</span> +<span class="r-out co"><span class="r-pr">#></span> M2 34.2689 113.839</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> time variable observed predicted residual</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56248</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86248</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent 53.9 4.873e+01 5.17118</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent 47.5 4.873e+01 -1.22882</span> +<span class="r-out co"><span class="r-pr">#></span> 3 parent 10.4 1.111e+01 -0.70773</span> +<span class="r-out co"><span class="r-pr">#></span> 3 parent 7.6 1.111e+01 -3.50773</span> +<span class="r-out co"><span class="r-pr">#></span> 7 parent 1.1 5.772e-01 0.52283</span> +<span class="r-out co"><span class="r-pr">#></span> 7 parent 0.3 5.772e-01 -0.27717</span> +<span class="r-out co"><span class="r-pr">#></span> 14 parent 3.5 3.264e-03 3.49674</span> +<span class="r-out co"><span class="r-pr">#></span> 28 parent 3.2 1.045e-07 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.530e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.940e-10 3.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 M1 36.4 3.479e+01 1.61088</span> +<span class="r-out co"><span class="r-pr">#></span> 1 M1 37.4 3.479e+01 2.61088</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M1 34.3 3.937e+01 -5.07027</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M1 39.8 3.937e+01 0.42973</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M1 15.1 1.549e+01 -0.38715</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M1 17.8 1.549e+01 2.31285</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M1 5.8 1.995e+00 3.80469</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M1 1.2 1.995e+00 -0.79531</span> +<span class="r-out co"><span class="r-pr">#></span> 60 M1 0.5 2.111e-06 0.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.670e-10 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.670e-10 1.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.670e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 M2 4.8 4.455e+00 0.34517</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M2 20.9 2.153e+01 -0.62527</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M2 19.3 2.153e+01 -2.22527</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M2 42.0 4.192e+01 0.07941</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M2 43.1 4.192e+01 1.17941</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M2 49.4 4.557e+01 3.83353</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M2 44.3 4.557e+01 -1.26647</span> +<span class="r-out co"><span class="r-pr">#></span> 28 M2 34.6 3.547e+01 -0.87275</span> +<span class="r-out co"><span class="r-pr">#></span> 28 M2 33.0 3.547e+01 -2.47275</span> +<span class="r-out co"><span class="r-pr">#></span> 60 M2 18.8 1.858e+01 0.21837</span> +<span class="r-out co"><span class="r-pr">#></span> 60 M2 17.6 1.858e+01 -0.98163</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M2 10.6 1.013e+01 0.47130</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M2 10.8 1.013e+01 0.67130</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M2 9.8 5.521e+00 4.27893</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M2 3.3 5.521e+00 -2.22107</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,44 +42,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Three experimental datasets from two water sediment systems and one soil</h1> @@ -149,113 +94,126 @@ software packages (Ranke, 2014).</p> </div> - <pre class="usage"><span class='va'>test_data_from_UBA_2014</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A list containing three datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>. + Each dataset has, among others, the following components</p><dl><dt><code>title</code></dt> +<dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>data</code></dt> +<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd> - <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>. - Each dataset has, among others, the following components</p><dl> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> - <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span> - <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span> - <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span> - <span class='co'># generally considered deprecated due to the frequent occurrence of such</span> - <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> - <span class='co'># model).</span> - <span class='va'>m_ws</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent_w <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span><span class='op'>)</span>, - parent_s <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>f_river</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_ws</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span> -</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_w_0 95.91998118 NA NA NA NA NA -#> k_parent_w 0.41145375 NA NA NA NA NA -#> k_parent_s 0.04663944 NA NA NA NA NA -#> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA -#> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA -#> sigma 3.13612618 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.1090929 5 6 -#> parent_w 0.0817436 3 3 -#> parent_s 0.1619965 2 3</div><div class='input'> - <span class='co'># This is the evaluation used for the validation of software packages</span> - <span class='co'># in the expertise from 2014</span> - <span class='va'>m_soil</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>, - M3 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - <span class='va'>f_soil</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_soil</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418 -#> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575 -#> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609 -#> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857 -#> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431 -#> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA -#> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA -#> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205 -#> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509 -#> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 -#> Upper -#> parent_0 78.35255358 -#> k_parent 0.13084582 -#> k_M1 6.23970702 -#> k_M2 0.09843260 -#> k_M3 0.04333992 -#> f_parent_to_M1 NA -#> f_parent_to_M2 NA -#> f_M1_to_M3 0.86450775 -#> f_M2_to_M3 0.99489895 -#> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.09649963 9 20 -#> parent 0.04721283 2 6 -#> M1 0.26551208 2 5 -#> M2 0.20327575 2 5 -#> M3 0.05196550 3 4</div><div class='input'> <span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span> +<span class="r-in"><span> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span> +<span class="r-in"><span> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span></span> +<span class="r-in"><span> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span></span> +<span class="r-in"><span> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span></span> +<span class="r-in"><span> <span class="co"># model).</span></span></span> +<span class="r-in"><span> <span class="va">m_ws</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">f_river</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Could not calculate correlation; no covariance matrix</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w_0 95.91998118 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_w 0.41145375 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_s 0.04663944 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.13612618 NA NA NA NA NA</span> +<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.1090929 5 6</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w 0.0817436 3 3</span> +<span class="r-out co"><span class="r-pr">#></span> parent_s 0.1619965 2 3</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># This is the evaluation used for the validation of software packages</span></span></span> +<span class="r-in"><span> <span class="co"># in the expertise from 2014</span></span></span> +<span class="r-in"><span> <span class="va">m_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778</span> +<span class="r-out co"><span class="r-pr">#></span> Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 78.35255358</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.13084582</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 6.23970702</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.09843260</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.04333992</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.86450775</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.99489895</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.45337221</span> +<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.09649963 9 20</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.04721283 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> M1 0.26551208 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M2 0.20327575 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M3 0.05196550 3 4</span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/tex_listing.html b/docs/dev/reference/tex_listing.html index c82138b7..03bd83f2 100644 --- a/docs/dev/reference/tex_listing.html +++ b/docs/dev/reference/tex_listing.html @@ -18,7 +18,7 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 75d6a1f9..a7a01043 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -1,72 +1,17 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, -the ilr transformation is used." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +the ilr transformation is used."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -77,23 +22,21 @@ the ilr transformation is used." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -103,48 +46,50 @@ the ilr transformation is used." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/transform_odeparms.R" class="external-link"><code>R/transform_odeparms.R</code></a></small> <div class="hidden name"><code>transform_odeparms.Rd</code></div> </div> @@ -154,205 +99,221 @@ restricted values to the full scale of real numbers. For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, -the <a href='ilr.html'>ilr</a> transformation is used.</p> +the <a href="ilr.html">ilr</a> transformation is used.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">transform_odeparms</span><span class="op">(</span></span> +<span> <span class="va">parms</span>,</span> +<span> <span class="va">mkinmod</span>,</span> +<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">backtransform_odeparms</span><span class="op">(</span></span> +<span> <span class="va">transparms</span>,</span> +<span> <span class="va">mkinmod</span>,</span> +<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span><span class='op'>(</span> - <span class='va'>parms</span>, - <span class='va'>mkinmod</span>, - transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, - transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>parms</dt> +<dd><p>Parameters of kinetic models as used in the differential +equations.</p></dd> -<span class='fu'>backtransform_odeparms</span><span class='op'>(</span> - <span class='va'>transparms</span>, - <span class='va'>mkinmod</span>, - transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, - transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span></pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>parms</th> - <td><p>Parameters of kinetic models as used in the differential -equations.</p></td> - </tr> - <tr> - <th>mkinmod</th> - <td><p>The kinetic model of class <a href='mkinmod.html'>mkinmod</a>, containing +<dt>mkinmod</dt> +<dd><p>The kinetic model of class <a href="mkinmod.html">mkinmod</a>, containing the names of the model variables that are needed for grouping the -formation fractions before <a href='ilr.html'>ilr</a> transformation, the parameter -names and the information if the pathway to sink is included in the model.</p></td> - </tr> - <tr> - <th>transform_rates</th> - <td><p>Boolean specifying if kinetic rate constants should +formation fractions before <a href="ilr.html">ilr</a> transformation, the parameter +names and the information if the pathway to sink is included in the model.</p></dd> + + +<dt>transform_rates</dt> +<dd><p>Boolean specifying if kinetic rate constants should be transformed in the model specification used in the fitting for better compliance with the assumption of normal distribution of the estimator. If TRUE, also alpha and beta parameters of the FOMC model are log-transformed, as well as k1 and k2 rate constants for the DFOP and HS -models and the break point tb of the HS model.</p></td> - </tr> - <tr> - <th>transform_fractions</th> - <td><p>Boolean specifying if formation fractions +models and the break point tb of the HS model.</p></dd> + + +<dt>transform_fractions</dt> +<dd><p>Boolean specifying if formation fractions constants should be transformed in the model specification used in the fitting for better compliance with the assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP model is also seen as a fraction. If a single fraction is transformed (g parameter of DFOP or only a single target variable e.g. a single metabolite plus a pathway to sink), a -logistic transformation is used <code><a href='https://rdrr.io/r/stats/Logistic.html'>stats::qlogis()</a></code>. In other cases, i.e. if +logistic transformation is used <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">stats::qlogis()</a></code>. In other cases, i.e. if two or more formation fractions need to be transformed whose sum cannot -exceed one, the <a href='ilr.html'>ilr</a> transformation is used.</p></td> - </tr> - <tr> - <th>transparms</th> - <td><p>Transformed parameters of kinetic models as used in the -fitting procedure.</p></td> - </tr> - </table> +exceed one, the <a href="ilr.html">ilr</a> transformation is used.</p></dd> + - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>transparms</dt> +<dd><p>Transformed parameters of kinetic models as used in the +fitting procedure.</p></dd> - <p>A vector of transformed or backtransformed parameters</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>A vector of transformed or backtransformed parameters</p> + </div> + <div id="details"> + <h2>Details</h2> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. -This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - +This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='va'>FOCUS_D</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># remove zero values to avoid warning</span> -<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -<span class='co'># Transformed and backtransformed parameters</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='co'># Compare to the version without transforming rate parameters (does not work</span> -<span class='co'># with analytical solution, we get NA values for m1 in predictions)</span> -<span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.57022 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</span> - -<span class='va'>initials</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>$</span><span class='va'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>initials</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span> -<span class='va'>transformed</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span> -<span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink -#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='co'># The case of formation fractions (this is now the default)</span> -<span class='va'>SFO_SFO.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.5985 1.5702 96.404 102.79 -#> log_k_parent -2.3157 0.0409 -2.399 -2.23 -#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 -#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 -#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 -#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 -#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='va'>initials</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"f_parent_to_m1"</span> <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>transformed</span> <span class='op'><-</span> <span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO.ff</span><span class='op'>)</span> -<span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO.ff</span><span class='op'>)</span> -</div><div class='output co'>#> f_parent_to_m1 -#> 0.5 </div><div class='input'> -<span class='co'># And without sink</span> -<span class='va'>SFO_SFO.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - -<span class='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 84.79 3.012 78.67 90.91 -#> log_k_parent -2.76 0.082 -2.92 -2.59 -#> log_k_m1 -4.21 0.123 -4.46 -3.96 -#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 -#> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 -#> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 -#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div><div class='input'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># remove zero values to avoid warning</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Transformed and backtransformed parameters</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.60 1.5702 96.40 102.79</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.04 0.0763 -3.19 -2.88</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1_sink -5.25 0.1332 -5.52 -4.98</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.13 0.3585 2.40 3.85</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># Compare to the version without transforming rate parameters (does not work</span></span></span> +<span class="r-in"><span><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span></span> +<span class="r-in"><span><span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, transform_rates <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 96.40384 1.03e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 2.39609 3.85e+00</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">$</span><span class="va">value</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">initials</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 100.750000 -2.302585 -2.301586 -2.300587 </span> +<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent_sink k_parent_m1 k_m1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 100.7500 0.1000 0.1001 0.1002 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># The case of formation fractions (this is now the default)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.ff.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.5985 1.5702 96.404 102.79</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.3157 0.0409 -2.399 -2.23</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.2475 0.1332 -5.518 -4.98</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.0579 0.0893 -0.124 0.24</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.1255 0.3585 2.396 3.85</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> +<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"f_parent_to_m1"</span> <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.5 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And without sink</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff.2</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.ff.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff.2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 84.79 3.012 78.67 90.91</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.76 0.082 -2.92 -2.59</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.21 0.123 -4.46 -3.96</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.22 0.943 6.31 10.14</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/update.mkinfit-1.png b/docs/dev/reference/update.mkinfit-1.png Binary files differindex df8473c1..12fe1f5b 100644 --- a/docs/dev/reference/update.mkinfit-1.png +++ b/docs/dev/reference/update.mkinfit-1.png diff --git a/docs/dev/reference/update.mkinfit-2.png b/docs/dev/reference/update.mkinfit-2.png Binary files differindex 13c99b44..21817f94 100644 --- a/docs/dev/reference/update.mkinfit-2.png +++ b/docs/dev/reference/update.mkinfit-2.png diff --git a/docs/dev/reference/update.mkinfit.html b/docs/dev/reference/update.mkinfit.html index 83f45028..cf611716 100644 --- a/docs/dev/reference/update.mkinfit.html +++ b/docs/dev/reference/update.mkinfit.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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The fitted degradation +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Update an mkinfit model with different arguments — update.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Update an mkinfit model with different arguments — update.mkinfit"><meta property="og:description" content="This function will return an updated mkinfit object. The fitted degradation model parameters from the old fit are used as starting values for the updated fit. Values specified as 'parms.ini' and/or 'state.ini' will -override these starting values." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +override these starting values."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,48 +44,50 @@ override these starting values." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Update an mkinfit model with different arguments</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/update.mkinfit.R'><code>R/update.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/update.mkinfit.R" class="external-link"><code>R/update.mkinfit.R</code></a></small> <div class="hidden name"><code>update.mkinfit.Rd</code></div> </div> @@ -153,66 +98,67 @@ updated fit. Values specified as 'parms.ini' and/or 'state.ini' will override these starting values.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, evaluate <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An mkinfit object to be updated</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Arguments to <code><a href='mkinfit.html'>mkinfit</a></code> that should replace + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, evaluate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An mkinfit object to be updated</p></dd> + + +<dt>...</dt> +<dd><p>Arguments to <code><a href="mkinfit.html">mkinfit</a></code> that should replace the arguments from the original call. Arguments set to NULL will -remove arguments given in the original call</p></td> - </tr> - <tr> - <th>evaluate</th> - <td><p>Should the call be evaluated or returned as a call</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent sigma -#> 99.44423885 0.09793574 3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='va'>fit_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>fit</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -<span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent sigma_low rsd_high -#> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span> -</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> -</div></pre> +remove arguments given in the original call</p></dd> + + +<dt>evaluate</dt> +<dd><p>Should the call be evaluated or returned as a call</p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 99.44423885 0.09793574 3.39632469 </span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="update.mkinfit-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma_low rsd_high </span> +<span class="r-out co"><span class="r-pr">#></span> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="update.mkinfit-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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