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| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-13 05:19:08 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-13 05:19:08 +0100 |
| commit | 8d1a84ac2190538ed3bac53a303064e281595868 (patch) | |
| tree | acb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/reference/schaefer07_complex_case.html | |
| parent | 51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff) | |
| parent | 4200e566ad2600f56bc3987669aeab88582139eb (diff) | |
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/dev/reference/schaefer07_complex_case.html')
| -rw-r--r-- | docs/dev/reference/schaefer07_complex_case.html | 249 |
1 files changed, 105 insertions, 144 deletions
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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> |