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| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-11-24 09:02:26 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-11-24 09:02:26 +0100 |
| commit | af7c6de4db9981ac814362c441fbac22c8faa2d7 (patch) | |
| tree | 33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/reference/mkinerrmin.html | |
| parent | 8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff) | |
Start online docs of the development version
Diffstat (limited to 'docs/dev/reference/mkinerrmin.html')
| -rw-r--r-- | docs/dev/reference/mkinerrmin.html | 248 |
1 files changed, 102 insertions, 146 deletions
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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 @@ 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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