diff options
Diffstat (limited to 'docs')
48 files changed, 1275 insertions, 1277 deletions
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index ec138595..9caabec8 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -90,7 +90,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-10-25</h4> <div class="hidden name"><code>mkin.Rmd</code></div> @@ -223,6 +223,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex 751a79e1..e21b4233 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/news/index.html b/docs/news/index.html index 20a71657..67f64150 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -136,7 +136,6 @@ <ul> <li><p>Move long-running tests to tests/testthat/slow with a separate test log. They currently take around 7 minutes on my system</p></li> <li><p>‘mkinfit’: Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals</p></li> -<li><p>‘mkinfit’: The default algorithm for fitting the ‘obs’ error model is now IRLS</p></li> <li><p>Vignette ‘twa.html’: Add the maximum time weighted average formulas for the hockey stick model</p></li> <li><p>Support frameless plots (‘frame = FALSE’)</p></li> <li><p>Support to suppress the chi2 error level (‘show_errmin = FALSE’) in ‘plot.mmkin’</p></li> diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 2fe02c97..103bcb4a 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -8,11 +8,13 @@ <title>Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Calculated the AIC for a column of an mmkin object — AIC.mmkin" /> -<meta property="og:description" content="Provides a convenient way to compare different kineti models fitted to the - same dataset." /> +<meta property="og:title" content="Calculated the AIC for a column of an mmkin object — AIC.mmkin" /> +<meta property="og:description" content="Provides a convenient way to compare different kinetic models fitted to the +same dataset." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,21 +134,20 @@ </div> <div class="ref-description"> - - <p>Provides a convenient way to compare different kineti models fitted to the - same dataset.</p> - + <p>Provides a convenient way to compare different kinetic models fitted to the +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='no'>object</span>, <span class='no'>...</span>, <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>2</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> + <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, containing only one +column.</p></td> </tr> <tr> <th>...</th> @@ -157,15 +158,15 @@ <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> - + <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="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> + <pre class="examples"><div class='input'> + <span class='co'># skip, as it takes > 10 s on winbuilder</span> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> @@ -184,15 +185,14 @@ #> SFO 3 59.29336 #> FOMC 4 44.68652 #> DFOP 5 29.02372</div><div class='input'> + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 52d00ac2..47536237 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -8,11 +8,13 @@ <title>Export a list of datasets format to a CAKE study file — CAKE_export • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Export a list of datasets format to a CAKE study file — CAKE_export" /> -<meta property="og:description" content="In addition to the datasets, the pathways in the degradation - model can be specified as well." /> +<meta property="og:title" content="Export a list of datasets format to a CAKE study file — CAKE_export" /> +<meta property="og:description" content="In addition to the datasets, the pathways in the degradation model can be +specified as well." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,46 +134,40 @@ </div> <div class="ref-description"> - - <p>In addition to the datasets, the pathways in the degradation - model can be specified as well.</p> - + <p>In addition to the datasets, the pathways in the degradation model can be +specified as well.</p> </div> - <pre class="usage"><span class='fu'>CAKE_export</span>(<span class='no'>ds</span>, <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), - <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <pre class="usage"><span class='fu'>CAKE_export</span>(<span class='no'>ds</span>, <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"CAKE_export.csf"</span>, <span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>, - <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>, - <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>, - <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>, - <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>, - <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), + <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>, <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>, + <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>, <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>, + <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>, <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), <span class='kw'>optimiser</span> <span class='kw'>=</span> <span class='st'>"IRLS"</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 named list of datasets in long format as compatible with - <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> +<code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> <tr> <th>map</th> <td><p>A character vector with CAKE compartment names (Parent, A1, ...), - named with the names used in the list of datasets.</p></td> +named with the names used in the list of datasets.</p></td> </tr> <tr> <th>links</th> <td><p>An optional character vector of target compartments, named with - the names of the source compartments. In order to make this - easier, the names are used as in the datasets supplied.</p></td> +the names of the source compartments. In order to make this easier, the +names are used as in the datasets supplied.</p></td> </tr> <tr> <th>filename</th> - <td><p>Where to write the result. Should end in .csf in order to be compatible - with CAKE.</p></td> + <td><p>Where to write the result. Should end in .csf in order to be +compatible with CAKE.</p></td> </tr> <tr> <th>path</th> @@ -210,20 +206,18 @@ <td><p>Can be OLS or IRLS.</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> - </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - </ul> + </ul> <h2>Author</h2> <p>Johannes Ranke</p> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index b34d00a1..eef4f902 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -8,11 +8,13 @@ <title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" /> -<meta property="og:description" content="Function describing decline from a defined starting value using the sum - of two exponential decline functions." /> +<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" /> +<meta property="og:description" content="Function describing decline from a defined starting value using the sum of +two exponential decline functions." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,12 @@ </div> <div class="ref-description"> - - <p>Function describing decline from a defined starting value using the sum - of two exponential decline functions.</p> - + <p>Function describing decline from a defined starting value using the sum of +two exponential decline functions.</p> </div> <pre class="usage"><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</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> @@ -161,36 +161,33 @@ </tr> <tr> <th>g</th> - <td><p>Fraction of the starting value declining according to the - first kinetic constant.</p></td> + <td><p>Fraction of the starting value declining according to the first +kinetic constant.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable at time <code>t</code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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 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='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div></pre> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index ae120587..879c1444 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -8,11 +8,13 @@ <title>Subsetting method for mmkin objects — [.mmkin • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" /> +<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" /> <meta property="og:description" content="Subsetting method for mmkin objects." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,14 +133,12 @@ </div> <div class="ref-description"> - <p>Subsetting method for mmkin objects.</p> - </div> <pre class="usage"># S3 method for mmkin [(x, i, j, ..., drop = FALSE)</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> @@ -160,32 +160,32 @@ </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> + <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> <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <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> + <pre class="examples"><div class='input'> + <span class='co'># Only use one core, to pass R CMD check --as-cran</span> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset #> model B C -#> FOMC List,39 List,39 +#> FOMC List,40 List,40 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B -#> SFO List,39 -#> FOMC List,39 +#> SFO List,40 +#> FOMC List,40 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B -#> SFO List,39 +#> SFO List,40 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>( @@ -210,15 +210,14 @@ #> #> $message #> [1] "both X-convergence and relative convergence (5)" -#> </div></pre> +#> </div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index df05afbd..f44ad713 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -8,11 +8,13 @@ <title>First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,17 +34,15 @@ -<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" /> -<meta property="og:description" content="Function describing exponential decline from a defined starting value, with - a decreasing rate constant. -The form given here differs slightly from the original reference by Gustafson - and Holden (1990). The parameter beta corresponds to 1/beta in the - original equation." /> +<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" /> +<meta property="og:description" content="Function describing exponential decline from a defined starting value, with +a decreasing rate constant." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -113,7 +113,6 @@ The form given here differs slightly from the original reference by Gustafson <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +134,12 @@ The form given here differs slightly from the original reference by Gustafson </div> <div class="ref-description"> - - <p>Function describing exponential decline from a defined starting value, with - a decreasing rate constant.</p> -<p>The form given here differs slightly from the original reference by Gustafson - and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta in the - original equation.</p> - + <p>Function describing exponential decline from a defined starting value, with +a decreasing rate constant.</p> </div> <pre class="usage"><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>alpha</span>, <span class='no'>beta</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> @@ -159,52 +153,52 @@ The form given here differs slightly from the original reference by Gustafson </tr> <tr> <th>alpha</th> - <td><p>Shape parameter determined by coefficient of variation of rate constant - values.</p></td> + <td><p>Shape parameter determined by coefficient of variation of rate +constant values.</p></td> </tr> <tr> <th>beta</th> <td><p>Location parameter.</p></td> </tr> </table> - - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The solution of the FOMC kinetic model reduces to the - <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and - <code>beta</code> with - \(k = \frac{\beta}{\alpha}\).</p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable at time <code>t</code>.</p> - + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>The form given here differs slightly from the original reference by +Gustafson and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta +in the original equation.</p> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>The solution of the FOMC kinetic model reduces to the + <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and + <code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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 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> -<p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A - new model based on spatial variability. <em>Environmental Science and +<p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: + A new model based on spatial variability. <em>Environmental Science and Technology</em> <b>24</b>, 1032-1038</p> - <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/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div></pre> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - - <li><a href="#note">Note</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#details">Details</a></li> + <li><a href="#note">Note</a></li> <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index b46902c5..82b9324c 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -8,11 +8,13 @@ <title>Hockey-Stick kinetics — HS.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" /> +<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" /> <meta property="og:description" content="Function describing two exponential decline functions with a break point - between them." /> +between them." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,12 @@ </div> <div class="ref-description"> - <p>Function describing two exponential decline functions with a break point - between them.</p> - +between them.</p> </div> <pre class="usage"><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</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> @@ -161,37 +161,34 @@ </tr> <tr> <th>tb</th> - <td><p>Break point. Before this time, exponential decline according - to <code>k1</code> is calculated, after this time, exponential decline proceeds - according to <code>k2</code>.</p></td> + <td><p>Break point. Before this time, exponential decline according to +<code>k1</code> is calculated, after this time, exponential decline proceeds +according to <code>k2</code>.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable at time <code>t</code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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 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='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div></pre> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 082c2f41..6af44ab8 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -8,11 +8,13 @@ <title>Indeterminate order rate equation kinetics — IORE.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" /> -<meta property="og:description" content="Function describing exponential decline from a defined starting value, with - a concentration dependent rate constant." /> +<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" /> +<meta property="og:description" content="Function describing exponential decline from a defined starting value, with +a concentration dependent rate constant." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,12 @@ </div> <div class="ref-description"> - - <p>Function describing exponential decline from a defined starting value, with - a concentration dependent rate constant.</p> - + <p>Function describing exponential decline from a defined starting value, with +a concentration dependent rate constant.</p> </div> <pre class="usage"><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k__iore</span>, <span class='no'>N</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> @@ -153,34 +153,32 @@ </tr> <tr> <th>k__iore</th> - <td><p>Rate constant. Note that this depends on the concentration units used.</p></td> + <td><p>Rate constant. Note that this depends on the concentration +units used.</p></td> </tr> <tr> <th>N</th> <td><p>Exponent describing the nonlinearity of the rate equation</p></td> </tr> </table> - - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The solution of the IORE kinetic model reduces to the - <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1. - The parameters of the IORE model can be transformed to equivalent parameters - of the FOMC mode - see the NAFTA guidance for details.</p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable at time <code>t</code>.</p> - + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>The solution of the IORE kinetic model reduces to the + <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1. The parameters of the IORE model can + be transformed to equivalent parameters of the FOMC mode - see the NAFTA + guidance for details.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental - Media</p> - + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance + for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <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/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># \dontrun{</span> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># \dontrun{</span> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fit.iore.deS</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -195,19 +193,16 @@ #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 #> iore.deS 1.785233 15.1479 4.559973</div><div class='input'> # } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - - <li><a href="#note">Note</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#note">Note</a></li> <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index cb0870a8..55fd61a4 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -8,11 +8,13 @@ <title>Single First-Order kinetics — SFO.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Single First-Order kinetics — SFO.solution" /> +<meta property="og:title" content="Single First-Order kinetics — SFO.solution" /> <meta property="og:description" content="Function describing exponential decline from a defined starting value." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,13 +133,11 @@ </div> <div class="ref-description"> - <p>Function describing exponential decline from a defined starting value.</p> - </div> <pre class="usage"><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</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> @@ -154,32 +154,29 @@ <td><p>Kinetic constant.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable at time <code>t</code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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 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='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div></pre> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 398f787f..fbf067af 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -8,11 +8,13 @@ <title>Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,17 +34,18 @@ -<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" /> +<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" /> <meta property="og:description" content="Function describing the solution of the differential equations describing - the kinetic model with first-order terms for a two-way transfer from a free - to a bound fraction, and a first-order degradation term for the free - fraction. The initial condition is a defined amount in the free fraction and - no substance in the bound fraction." /> +the kinetic model with first-order terms for a two-way transfer from a free +to a bound fraction, and a first-order degradation term for the free +fraction. The initial condition is a defined amount in the free fraction +and no substance in the bound fraction." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -113,7 +116,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,15 @@ </div> <div class="ref-description"> - <p>Function describing the solution of the differential equations describing - the kinetic model with first-order terms for a two-way transfer from a free - to a bound fraction, and a first-order degradation term for the free - fraction. The initial condition is a defined amount in the free fraction and - no substance in the bound fraction.</p> - +the kinetic model with first-order terms for a two-way transfer from a free +to a bound fraction, and a first-order degradation term for the free +fraction. The initial condition is a defined amount in the free fraction +and no substance in the bound fraction.</p> </div> <pre class="usage"><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</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> @@ -167,36 +167,34 @@ </tr> <tr> <th>k_1output</th> - <td><p>Kinetic constant describing degradation of the free fraction.</p></td> + <td><p>Kinetic constant describing degradation of the free +fraction.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The value of the response variable, which is the sum of free and bound - fractions at time <code>t</code>.</p> - + <p>The value of the response variable, which is the sum of free and + bound fractions at time <code>t</code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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 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='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div></pre> + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex df843300..d476bba1 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index eeaf9e5b..67789694 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -8,11 +8,13 @@ <title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,15 +34,16 @@ -<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" /> +<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" /> <meta property="og:description" content="Normally distributed errors are added to data predicted for a specific - degradation model using mkinpredict. The variance of the error - may depend on the predicted value and is specified as a standard deviation." /> +degradation model using mkinpredict. The variance of the error +may depend on the predicted value and is specified as a standard deviation." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -111,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,33 +135,32 @@ </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 - may depend on the predicted value and is specified as a standard deviation.</p> - +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='no'>prediction</span>, <span class='no'>sdfunc</span>, <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), - <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, - <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> - + <pre class="usage"><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>, <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, + <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</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> + <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 returning - a standard deviation that should be used for generating the random error - terms for this value.</p></td> + <td><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> + <td><p>The names of state variables that should have an initial +value of zero</p></td> </tr> <tr> <th>n</th> @@ -167,8 +168,8 @@ </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> + <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> @@ -180,25 +181,25 @@ </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> + <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> - + <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> - <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 - http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> - + <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 +http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> <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> + <pre class="examples"><div class='input'> +<span class='co'># The kinetic model</span> <span class='no'>m_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># Generate a prediction for a specific set of parameters</span> @@ -235,17 +236,15 @@ <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.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index f0abb0b6..e81bdbb5 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,13 +6,16 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title> +<title>Function to calculate endpoints for further use from kinetic models fitted +with mkinfit — endpoints • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,16 +35,19 @@ -<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" /> -<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models -fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, -the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but -with the advantage that the SFORB model can also be used for metabolites." /> +<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted +with mkinfit — endpoints" /> +<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions +from kinetic models fitted with mkinfit. If the SFORB model was specified +for one of the parents or metabolites, the Eigenvalues are returned. These +are equivalent to the rate constantes of the DFOP model, but with the +advantage that the SFORB model can also be used for metabolites." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -112,7 +118,6 @@ with the advantage that the SFORB model can also be used for metabolites." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -128,22 +133,22 @@ with the advantage that the SFORB model can also be used for metabolites." /> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> + <h1>Function to calculate endpoints for further use from kinetic models fitted +with mkinfit</h1> <div class="hidden name"><code>endpoints.Rd</code></div> </div> <div class="ref-description"> - - <p>This function calculates DT50 and DT90 values as well as formation fractions from kinetic models -fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, -the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but -with the advantage that the SFORB model can also be used for metabolites.</p> - + <p>This function calculates DT50 and DT90 values as well as formation fractions +from kinetic models fitted with mkinfit. If the SFORB model was specified +for one of the parents or metabolites, the Eigenvalues are returned. These +are equivalent to the rate constantes of the DFOP model, but with the +advantage that the SFORB model can also be used for metabolites.</p> </div> <pre class="usage"><span class='fu'>endpoints</span>(<span class='no'>fit</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> @@ -152,18 +157,17 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> </table> - - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with the components mentioned above.</p> - + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <pre class="examples"><div class='input'> + <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> logical(0) #> @@ -173,17 +177,15 @@ with the advantage that the SFORB model can also be used for metabolites.</p> #> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 -#> </div></pre> +#> </div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - - <li><a href="#note">Note</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#note">Note</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 925698d9..76ce2233 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -8,11 +8,13 @@ <title>Function to perform isometric log-ratio transformation — ilr • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,15 @@ -<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" /> -<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." /> +<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" /> +<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio +transformations." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,40 +134,41 @@ </div> <div class="ref-description"> - - <p>This implementation is a special case of the class of isometric log-ratio transformations.</p> - + <p>This implementation is a special case of the class of isometric log-ratio +transformations.</p> </div> <pre class="usage"><span class='fu'>ilr</span>(<span class='no'>x</span>) - <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre> - + +<span class='fu'>invilr</span>(<span class='no'>x</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>A numeric vector. Naturally, the forward transformation is only sensible for - vectors with all elements being greater than zero.</p></td> + <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> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <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> - + <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> - <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> - + <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 <code>robCompositions</code>.</p></div> - + <div class='dont-index'><p>Another implementation can be found in R package + <code>robCompositions</code>.</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> + <pre class="examples"><div class='input'> +<span class='co'># Order matters</span> <span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</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> @@ -173,19 +177,16 @@ <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='fu'>invilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(-<span class='fl'>10</span>, <span class='fl'>0</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='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>) <span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>) -<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>b</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</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></pre> +<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>b</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</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> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/index.html b/docs/reference/index.html index 17a879a9..328f5aca 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -160,11 +160,12 @@ <td> <p><code><a href="mmkin.html">mmkin()</a></code> </p> </td> - <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td> + <td><p>Fit one or more kinetic models with one or more state variables to one or +more datasets</p></td> </tr><tr> <td> - <p><code><a href="nafta.html">nafta()</a></code> </p> + <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> </p> </td> <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td> </tr> @@ -210,7 +211,8 @@ <td> <p><code><a href="endpoints.html">endpoints()</a></code> </p> </td> - <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td> + <td><p>Function to calculate endpoints for further use from kinetic models fitted +with mkinfit</p></td> </tr><tr> <td> @@ -242,7 +244,8 @@ <td> <p><code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> </p> </td> - <td><p>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</p></td> + <td><p>Plot model fits (observed and fitted) and the residuals for a row or column +of an mmkin object</p></td> </tr><tr> <td> @@ -352,23 +355,15 @@ <tr> <td> - <p><code><a href="nafta.html">nafta()</a></code> </p> + <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> </p> </td> <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td> </tr><tr> <td> - <p><code><a href="print.nafta.html">print(<i><nafta></i>)</a></code> </p> - </td> - <td><p>Print nafta objects</p></td> - </tr><tr> - - <td> <p><code><a href="plot.nafta.html">plot(<i><nafta></i>)</a></code> </p> </td> - <td><p>Plot the results of the three models used in the NAFTA scheme. The plots - are ordered with increasing complexity of the model in this function - (SFO, then IORE, then DFOP).</p></td> + <td><p>Plot the results of the three models used in the NAFTA scheme.</p></td> </tr> </tbody><tbody> <tr> @@ -388,7 +383,8 @@ <td> <p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p> </td> - <td><p>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</p></td> + <td><p>Function to calculate maximum time weighted average concentrations from +kinetic models fitted with mkinfit</p></td> </tr><tr> <td> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index dbe0c116..c79146a9 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -8,11 +8,13 @@ <title>Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,19 +34,17 @@ -<meta property="og:title" content="Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit" /> +<meta property="og:title" content="Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit" /> <meta property="og:description" content="This function simply calculates the product of the likelihood densities - calculated using dnorm, i.e. assuming normal distribution, - with of the mean predicted by the degradation model, and the - standard deviation predicted by the error model. -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." /> +calculated using dnorm, i.e. assuming normal distribution, +with of the mean predicted by the degradation model, and the standard +deviation predicted by the error model." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -115,7 +115,6 @@ The total number of estimated parameters returned with the value <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -137,20 +136,15 @@ The total number of estimated parameters returned with the value </div> <div class="ref-description"> - <p>This function simply calculates the product of the likelihood densities - calculated using <code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution, - with of the mean predicted by the degradation model, and the - standard deviation predicted by the error model.</p> -<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> - +calculated using <code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution, +with of the mean predicted by the degradation model, and the standard +deviation 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='no'>object</span>, <span class='no'>...</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> @@ -163,21 +157,25 @@ The total number of estimated parameters returned with the value <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 parameters (degradation model parameters plus variance - model parameters) as attribute.</p> - + <p>An object of class <code><a href='https://rdrr.io/r/stats/logLik.html'>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> + + <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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> + <pre class="examples"><div class='input'> + <span class='co'># \dontrun{</span> <span class='no'>sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>) @@ -186,17 +184,16 @@ The total number of estimated parameters returned with the value #> f_nw 5 204.4486 #> f_obs 6 205.8727 #> f_tc 6 141.9656</div><div class='input'> # } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#details">Details</a></li> <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png Binary files differindex 752fd9d4..78a31f93 100644 --- a/docs/reference/logistic.solution-2.png +++ b/docs/reference/logistic.solution-2.png diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 91fe035e..b2f24d45 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -8,11 +8,13 @@ <title>Logistic kinetics — logistic.solution • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Logistic kinetics — logistic.solution" /> +<meta property="og:title" content="Logistic kinetics — logistic.solution" /> <meta property="og:description" content="Function describing exponential decline from a defined starting value, with - an increasing rate constant, supposedly caused by microbial growth" /> +an increasing rate constant, supposedly caused by microbial growth" /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,12 @@ </div> <div class="ref-description"> - <p>Function describing exponential decline from a defined starting value, with - an increasing rate constant, supposedly caused by microbial growth</p> - +an increasing rate constant, supposedly caused by microbial growth</p> </div> <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</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> @@ -164,28 +164,25 @@ <td><p>Growth rate of the increase in the rate constant.</p></td> </tr> </table> - - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The solution of the logistic model reduces to the - <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to - <code>kmax</code>.</p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable at time <code>t</code>.</p> - + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>The solution of the logistic model reduces to the + <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <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, + <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, 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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span> + <pre class="examples"><div class='input'> + <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>), <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>), @@ -221,19 +218,16 @@ #> k0 0.4448750 #> r 1.1821121 #> sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#> DT50 DT90 DT50_k0 DT50_kmax -#> parent 36.86533 62.41511 4297.854 10.83349</div></pre> +#> parent 36.86533 62.41511 4297.854 10.83349</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - - <li><a href="#note">Note</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#note">Note</a></li> <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index d1c2a805..ef2a55bf 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -6,13 +6,16 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent • mkin</title> +<title>Function to calculate maximum time weighted average concentrations from +kinetic models fitted with mkinfit — max_twa_parent • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,17 +35,19 @@ -<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" /> -<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations -(TWAs) for kinetic models fitted with mkinfit. 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 property="og:title" content="Function to calculate maximum time weighted average concentrations from +kinetic models fitted with mkinfit — max_twa_parent" /> +<meta property="og:description" content="This function calculates maximum moving window time weighted average +concentrations (TWAs) for kinetic models fitted with mkinfit. +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="twitter:card" content="summary" /> + <!-- 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> @@ -113,7 +118,6 @@ guidance." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -129,27 +133,30 @@ guidance." /> <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> + <h1>Function to calculate maximum time weighted average concentrations from +kinetic models fitted with mkinfit</h1> <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>. 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> - + <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>. +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='no'>fit</span>, <span class='no'>windows</span>) - <span class='fu'>max_twa_sfo</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k</span>, <span class='no'>t</span>) - <span class='fu'>max_twa_fomc</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>, <span class='no'>t</span>) - <span class='fu'>max_twa_dfop</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>, <span class='no'>t</span>) - <span class='fu'>max_twa_hs</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>, <span class='no'>t</span>)</pre> - + +<span class='fu'>max_twa_sfo</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k</span>, <span class='no'>t</span>) + +<span class='fu'>max_twa_fomc</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>, <span class='no'>t</span>) + +<span class='fu'>max_twa_dfop</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>, <span class='no'>t</span>) + +<span class='fu'>max_twa_hs</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>, <span class='no'>t</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> @@ -159,14 +166,15 @@ guidance.</p> </tr> <tr> <th>windows</th> - <td><p>The width of the time windows for which the TWAs should be calculated.</p></td> + <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 - 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> +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> @@ -201,36 +209,33 @@ guidance.</p> <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 <code>windows</code> argument. - For the other functions, a numeric vector of length one (also known as 'a - number').</p> - + <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 and - Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + <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 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='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <pre class="examples"><div class='input'> + <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#> 7 21 -#> 34.71343 18.22124 </div></pre> +#> 34.71343 18.22124 </div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 169aefd4..bb7c263a 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -8,11 +8,13 @@ <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/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,15 +34,16 @@ -<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 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="twitter:card" content="summary" /> + <!-- 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> @@ -111,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,23 +135,22 @@ </div> <div class="ref-description"> - - <p>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.</p> - + <p>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.</p> </div> <pre class="usage"><span class='fu'>mkin_long_to_wide</span>(<span class='no'>long_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>outtime</span> <span class='kw'>=</span> <span class='st'>"time"</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>long_data</th> - <td><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> + <td><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> @@ -160,14 +161,14 @@ <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="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='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> time parent m1 + <pre class="examples"><div class='input'> +<span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</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 @@ -189,15 +190,14 @@ #> 19 100 NA 31.04 #> 20 100 NA 33.13 #> 21 120 NA 25.15 -#> 22 120 NA 33.31</div></pre> +#> 22 120 NA 33.31</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index d8ae913f..523d45e1 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -8,11 +8,13 @@ <title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,16 @@ -<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" /> -<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several - dependent variable and converts it into the long form as required by mkinfit." /> +<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" /> +<meta property="og:description" content="This function simply takes a dataframe with one independent variable and +several dependent variable and converts it into the long form as required by +mkinfit." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,50 +135,49 @@ </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> - + <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> </div> <pre class="usage"><span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"t"</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>wide_data</th> - <td><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> + <td><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> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>Dataframe in long format as needed for <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>)) + <pre class="examples"><div class='input'> +<span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>)) <span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</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></pre> +#> 6 y 3 5</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index e0f4fbb6..386c00d7 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -8,11 +8,13 @@ <title>A dataset class for mkin — mkinds • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="A dataset class for mkin — mkinds" /> +<meta property="og:title" content="A dataset class for mkin — mkinds" /> <meta property="og:description" content="A dataset class for mkin" /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,51 +133,47 @@ </div> <div class="ref-description"> - <p>A dataset class for mkin</p> - </div> <pre class="usage"><span class='no'>mkinds</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> -<dl class='dl-horizontal'> -<dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd> -<dt><code>sampling</code></dt><dd><p>times The sampling times</p></dd> +<dl class='dl-horizontal'> +<dt>list("title")</dt><dd><p>A full title for the dataset</p></dd> -<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd> +<dt>list("sampling")</dt><dd><p>times The sampling times</p></dd> -<dt><code>observed</code></dt><dd><p>Names of the observed compounds</p></dd> +<dt>list("time_unit")</dt><dd><p>The time unit</p></dd> -<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd> +<dt>list("observed")</dt><dd><p>Names of the observed compounds</p></dd> -<dt><code>replicates</code></dt><dd><p>The number of replicates</p></dd> +<dt>list("unit")</dt><dd><p>The unit of the observations</p></dd> -<dt><code>data</code></dt><dd><p>A dataframe with at least the columns name, time and value -in order to be compatible with mkinfit</p></dd> +<dt>list("replicates")</dt><dd><p>The number of replicates</p></dd> +<dt>list("data")</dt><dd><p>A dataframe with at least the columns name, time and +value in order to be compatible with mkinfit</p></dd> </dl> - + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> + <pre class="examples"><div class='input'> +<span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#fields">Fields</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 941e30f5..1a31bc60 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -8,11 +8,13 @@ <title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" /> -<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the -chi-squared test as defined in the FOCUS kinetics report from 2006." /> +<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" /> +<meta property="og:description" content="This function finds the smallest relative error still resulting in passing +the chi-squared test as defined in the FOCUS kinetics report from 2006." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,12 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> </div> <div class="ref-description"> - - <p>This function finds the smallest relative error still resulting in passing the -chi-squared test as defined in the FOCUS kinetics report from 2006.</p> - + <p>This function finds the smallest relative error still resulting in passing +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='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</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> @@ -152,35 +152,33 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> <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 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 dataframe has one row for the total dataset and one further row for - each observed state variable in the model. +<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 +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 and - Degradation Kinetics from Environmental Fate Studies on Pesticides in 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> - + <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 +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='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <pre class="examples"><div class='input'> +<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df @@ -192,19 +190,16 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> #> All data 0.1544 4 13 #> parent 0.1659 2 7 #> m1 0.1095 2 6</div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 4386673c..079a6708 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -37,11 +37,10 @@ <meta property="og:title" content="Function to plot squared residuals and the error model for an mkin object — mkinerrplot" /> <meta property="og:description" content="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 plot.mkinfit - using the argument show_errplot = TRUE." /> +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 plot.mkinfit +using the argument show_errplot = TRUE." /> <meta name="twitter:card" content="summary" /> @@ -139,21 +138,17 @@ <div class="ref-description"> <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> - using the argument <code>show_errplot = TRUE</code>.</p> +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> +using the argument <code>show_errplot = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>, - <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>, - <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span><span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='no'>...</span>)</pre> + <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, + <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, + <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>, <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -164,8 +159,9 @@ </tr> <tr> <th>obs_vars</th> - <td><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> + <td><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> @@ -182,7 +178,7 @@ <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> +the y axis and defaults to "auto".</p></td> </tr> <tr> <th>legend</th> @@ -190,8 +186,8 @@ </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> + <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> @@ -213,15 +209,18 @@ <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> + <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> - <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 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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> + <pre class="examples"><div class='input'> +<span class='co'># \dontrun{</span> <span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit</span>)</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index e07d1f13..6c98bc38 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -8,11 +8,13 @@ <title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,21 +34,20 @@ -<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" /> -<meta property="og:description" content="This function maximises the likelihood of the observed data using - the Port algorithm nlminb, and the specified initial or fixed - parameters and starting values. In each step of the optimsation, the kinetic - model is solved using the function mkinpredict. The parameters - of the selected error model are fitted simultaneously with the degradation - model parameters, as both of them are arguments of the likelihood function. -Per default, parameters in the kinetic models are internally transformed in - order to better satisfy the assumption of a normal distribution of their - estimators." /> +<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" /> +<meta property="og:description" content="This function maximises the likelihood of the observed data using the Port +algorithm nlminb, and the specified initial or fixed +parameters and starting values. In each step of the optimsation, the +kinetic model is solved using the function mkinpredict. The +parameters of the selected error model are fitted simultaneously with the +degradation model parameters, as both of them are arguments of the +likelihood function." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -117,7 +118,6 @@ Per default, parameters in the kinetic models are internally transformed in <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -139,135 +139,126 @@ Per default, parameters in the kinetic models are internally transformed in </div> <div class="ref-description"> - - <p>This function maximises the likelihood of the observed data using - the Port algorithm <code><a href='https://rdrr.io/r/stats/nlminb.html'>nlminb</a></code>, and the specified initial or fixed - parameters and starting values. In each step of the optimsation, the kinetic - model is solved using the function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The parameters - of the selected error model are fitted simultaneously with the degradation - model parameters, as both of them are arguments of the likelihood function.</p> -<p>Per default, parameters in the kinetic models are internally transformed in - order to better satisfy the assumption of a normal distribution of their - estimators.</p> - + <p>This function maximises the likelihood of the observed data using the Port +algorithm <code><a href='https://rdrr.io/r/stats/nlminb.html'>nlminb</a></code>, and the specified initial or fixed +parameters and starting values. In each step of the optimsation, the +kinetic model is solved using the function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The +parameters of the selected error model are fitted simultaneously with the +degradation model parameters, as both of them are arguments of the +likelihood function.</p> </div> - <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, - <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], - <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), - <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, - <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>eval.max</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>iter.max</span> <span class='kw'>=</span> <span class='fl'>200</span>), - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>), - <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, - <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), - <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, - <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> - + <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, + <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, + <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</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>mkinmod</th> - <td><p>A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic model to be - fitted to the data, or one of the shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB", "IORE"). If a shorthand name is given, a parent only degradation - model is generated for the variable with the highest value in - <code>observed</code>.</p></td> + <td><p>A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic +model to be fitted to the data, or one of the shorthand names ("SFO", +"FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a +parent only degradation model is generated for the variable with the +highest value in <code>observed</code>.</p></td> </tr> <tr> <th>observed</th> - <td><p>A dataframe with the observed data. The first column called "name" must - contain the name of the observed variable for each data point. The second - column must contain the times of observation, named "time". The third - column must be named "value" and contain the observed values. Zero values - in the "value" column will be removed, with a warning, in order to - avoid problems with fitting the two-component error model. This is not - expected to be a problem, because in general, values of zero are not - observed in degradation data, because there is a lower limit of detection.</p></td> + <td><p>A dataframe with the observed data. The first column called +"name" must contain the name of the observed variable for each data point. +The second column must contain the times of observation, named "time". +The third column must be named "value" and contain the observed values. +Zero values in the "value" column will be removed, with a warning, in +order to avoid problems with fitting the two-component error model. This +is not expected to be a problem, because in general, values of zero are +not observed in degradation data, because there is a lower limit of +detection.</p></td> </tr> <tr> <th>parms.ini</th> - <td><p>A named vector of initial values for the parameters, including parameters - to be optimised and potentially also fixed parameters as indicated by - <code>fixed_parms</code>. If set to "auto", initial values for rate constants - are set to default values. Using parameter names that are not in the model - gives an error.</p> + <td><p>A named vector of initial values for the parameters, + including parameters to be optimised and potentially also fixed parameters + as indicated by <code>fixed_parms</code>. If set to "auto", initial values for + rate constants are set to default values. Using parameter names that are + not in the model gives an error.</p> <p>It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from this - model. This works nicely if the models are nested. An example is given - below.</p></td> + needs. You can use the parameter lists "bparms.ode" from a previously + fitted model, which contains the differential equation parameters from + this model. This works nicely if the models are nested. An example is + given below.</p></td> </tr> <tr> <th>state.ini</th> - <td><p>A named vector of initial values for the state variables of the model. In - case the observed variables are represented by more than one model - variable, the names will differ from the names of the observed variables - (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default is to set - the initial value of the first model variable to the mean of the time zero - values for the variable with the maximum observed value, and all others to 0. - If this variable has no time zero observations, its initial value is set to 100.</p></td> + <td><p>A named vector of initial values for the state variables of +the model. In case the observed variables are represented by more than one +model variable, the names will differ from the names of the observed +variables (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default +is to set the initial value of the first model variable to the mean of the +time zero values for the variable with the maximum observed value, and all +others to 0. If this variable has no time zero observations, its initial +value is set to 100.</p></td> </tr> <tr> <th>err.ini</th> - <td><p>A named vector of initial values for the error model parameters to be - optimised. If set to "auto", initial values are set to default values. - Otherwise, inital values for all error model parameters must be - given.</p></td> + <td><p>A named vector of initial values for the error model +parameters to be optimised. If set to "auto", initial values are set to +default values. Otherwise, inital values for all error model parameters +must be given.</p></td> </tr> <tr> <th>fixed_parms</th> - <td><p>The names of parameters that should not be optimised but rather kept at the - values specified in <code>parms.ini</code>.</p></td> + <td><p>The names of parameters that should not be optimised but +rather kept at the values specified in <code>parms.ini</code>.</p></td> </tr> <tr> <th>fixed_initials</th> - <td><p>The names of model variables for which the initial state at time 0 should - be excluded from the optimisation. Defaults to all state variables except - for the first one.</p></td> + <td><p>The names of model variables for which the initial +state at time 0 should be excluded from the optimisation. Defaults to all +state variables except for the first one.</p></td> </tr> <tr> <th>from_max_mean</th> - <td><p>If this is set to TRUE, and the model has only one observed variable, then - data before the time of the maximum observed value (after averaging for each - sampling time) are discarded, and this time is subtracted from all - remaining time values, so the time of the maximum observed mean value is - the new time zero.</p></td> + <td><p>If this is set to TRUE, and the model has only one +observed variable, then data before the time of the maximum observed value +(after averaging for each sampling time) are discarded, and this time is +subtracted from all remaining time values, so the time of the maximum +observed mean value is the new time zero.</p></td> </tr> <tr> <th>solution_type</th> - <td><p>If set to "eigen", the solution of the system of differential equations is - based on the spectral decomposition of the coefficient matrix in cases that - this is possible. If set to "deSolve", a numerical ode solver from package - <code>deSolve</code> is used. If set to "analytical", an analytical - solution of the model is used. This is only implemented for simple - degradation experiments with only one state variable, i.e. with no - metabolites. The default is "auto", which uses "analytical" if possible, - otherwise "deSolve" if a compiler is present, and "eigen" if no - compiler is present and the model can be expressed using eigenvalues and - eigenvectors. This argument is passed on to the helper function - <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> + <td><p>If set to "eigen", the solution of the system of +differential equations is based on the spectral decomposition of the +coefficient matrix in cases that this is possible. If set to "deSolve", a +numerical ode solver from package <code>deSolve</code> is used. If set to +"analytical", an analytical solution of the model is used. This is only +implemented for simple degradation experiments with only one state +variable, i.e. with no metabolites. The default is "auto", which uses +"analytical" if possible, otherwise "deSolve" if a compiler is present, +and "eigen" if no compiler is present and the model can be expressed using +eigenvalues and eigenvectors. This argument is passed on to the helper +function <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> </tr> <tr> <th>method.ode</th> - <td><p>The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> to - <code>ode</code> in case the solution type is "deSolve". The default - "lsoda" is performant, but sometimes fails to converge.</p></td> + <td><p>The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> +to <code>ode</code> in case the solution type is "deSolve". The default +"lsoda" is performant, but sometimes fails to converge.</p></td> </tr> <tr> <th>use_compiled</th> - <td><p>If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> - model is used in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if a compiled - version is present.</p></td> + <td><p>If set to <code>FALSE</code>, no compiled version of the +<code><a href='mkinmod.html'>mkinmod</a></code> model is used in the calls to +<code><a href='mkinpredict.html'>mkinpredict</a></code> even if a compiled version is present.</p></td> </tr> <tr> <th>control</th> @@ -275,92 +266,90 @@ Per default, parameters in the kinetic models are internally transformed in </tr> <tr> <th>transform_rates</th> - <td><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. If FALSE, zero is used as a lower bound for the rates - in the optimisation.</p></td> + <td><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. If FALSE, zero is used as +a lower bound for the rates in the optimisation.</p></td> </tr> <tr> <th>transform_fractions</th> - <td><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. If TRUE, the g parameter of the DFOP and HS - models are also transformed, as they can also be seen as compositional - data. The transformation used for these transformations is the - <code><a href='ilr.html'>ilr</a></code> transformation.</p></td> + <td><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. If TRUE, +the g parameter of the DFOP and HS models are also transformed, as they +can also be seen as compositional data. The transformation used for these +transformations is the <code><a href='ilr.html'>ilr</a></code> transformation.</p></td> </tr> <tr> <th>quiet</th> - <td><p>Suppress printing out the current value of the negative log-likelihood - after each improvement?</p></td> + <td><p>Suppress printing out the current value of the negative +log-likelihood after each improvement?</p></td> </tr> <tr> <th>atol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8, - lower than in <code>lsoda</code>.</p></td> + <td><p>Absolute error tolerance, passed to <code>ode</code>. Default +is 1e-8, lower than in <code>lsoda</code>.</p></td> </tr> <tr> <th>rtol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10, - much lower than in <code>lsoda</code>.</p></td> + <td><p>Absolute error tolerance, passed to <code>ode</code>. Default +is 1e-10, much lower than in <code>lsoda</code>.</p></td> </tr> <tr> <th>n.outtimes</th> - <td><p>The length of the dataseries that is produced by the model prediction - function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy of - the numerical solver if that is used (see <code>solution_type</code> argument. - The default value is 100.</p></td> + <td><p>The length of the dataseries that is produced by the model +prediction function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy +of the numerical solver if that is used (see <code>solution_type</code> +argument. The default value is 100.</p></td> </tr> <tr> <th>error_model</th> - <td><p>If the error model is "const", a constant standard deviation - is assumed.</p> + <td><p>If the error model is "const", a constant standard + deviation is assumed.</p> <p>If the error model is "obs", each observed variable is assumed to have its - own variance.</p> + own variance.</p> <p>If the error model is "tc" (two-component error model), a two component - error model similar to the one described by Rocke and Lorenzato (1995) is - used for setting up the likelihood function. Note that this model deviates - from the model by Rocke and Lorenzato, as their model implies that the - errors follow a lognormal distribution for large values, not a normal - distribution as assumed by this method.</p></td> + error model similar to the one described by Rocke and Lorenzato (1995) is + used for setting up the likelihood function. Note that this model + deviates from the model by Rocke and Lorenzato, as their model implies + that the errors follow a lognormal distribution for large values, not a + normal distribution as assumed by this method.</p></td> </tr> <tr> <th>error_model_algorithm</th> - <td><p>If "auto", the selected algorithm depends on the error model. - If the error model is "const", nonlinear least squares fitting ("OLS") is - selected. If the error model is "obs", iteratively reweighted least squares - fitting ("IRLS") is selected. If the error model is "tc", the "d_3" - algorithm is selected.</p> -<p>The algorithm "d_3" will directly minimize the negative - log-likelihood and - independently - also use the three step algorithm - described below. The fit with the higher likelihood is returned.</p> -<p>The algorithm "direct" will directly minimize the negative - log-likelihood.</p> -<p>The algorithm "twostep" will minimize the negative log-likelihood - after an initial unweighted least squares optimisation step.</p> -<p>The algorithm "threestep" starts with unweighted least squares, - then optimizes only the error model using the degradation model - parameters found, and then minimizes the negative log-likelihood - with free degradation and error model parameters.</p> -<p>The algorithm "fourstep" starts with unweighted least squares, - then optimizes only the error model using the degradation model - parameters found, then optimizes the degradation model again - with fixed error model parameters, and finally minimizes the negative - log-likelihood with free degradation and error model parameters.</p> + <td><p>If "auto", the selected algorithm depends on + the error model. If the error model is "const", unweighted nonlinear + least squares fitting ("OLS") is selected. If the error model is "obs", or + "tc", the "d_3" algorithm is selected.</p> +<p>The algorithm "d_3" will directly minimize the negative log-likelihood and + - independently - also use the three step algorithm described below. The + fit with the higher likelihood is returned.</p> +<p>The algorithm "direct" will directly minimize the negative log-likelihood.</p> +<p>The algorithm "twostep" will minimize the negative log-likelihood after an + initial unweighted least squares optimisation step.</p> +<p>The algorithm "threestep" starts with unweighted least squares, then + optimizes only the error model using the degradation model parameters + found, and then minimizes the negative log-likelihood with free + degradation and error model parameters.</p> +<p>The algorithm "fourstep" starts with unweighted least squares, then + optimizes only the error model using the degradation model parameters + found, then optimizes the degradation model again with fixed error model + parameters, and finally minimizes the negative log-likelihood with free + degradation and error model parameters.</p> <p>The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with - unweighted least squares, and then iterates optimization of the error model - parameters and subsequent - optimization of the degradation model using those error model parameters, - until the error model parameters converge.</p></td> + unweighted least squares, and then iterates optimization of the error + model parameters and subsequent optimization of the degradation model + using those error model parameters, until the error model parameters + converge.</p></td> </tr> <tr> <th>reweight.tol</th> - <td><p>Tolerance for the convergence criterion calculated from the error model - parameters in IRLS fits.</p></td> + <td><p>Tolerance for the convergence criterion calculated from +the error model parameters in IRLS fits.</p></td> </tr> <tr> <th>reweight.max.iter</th> @@ -372,50 +361,54 @@ Per default, parameters in the kinetic models are internally transformed in </tr> <tr> <th>...</th> - <td><p>Further arguments that will be passed on to <code>deSolve</code>.</p></td> + <td><p>Further arguments that will be passed on to +<code>deSolve</code>.</p></td> </tr> </table> - + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model + for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list with "mkinfit" in the class attribute. A summary can be obtained by - <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + <p>A list with "mkinfit" in the class attribute. A summary can be + obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> -<p>Comparisons of models fitted to the same data can be made using <code><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></code> - by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p> -<p>Fitting of several models to several datasets in a single call to - <code><a href='mmkin.html'>mmkin</a></code>.</p></div> - + <p>Per default, parameters in the kinetic models are internally transformed in +order to better satisfy the assumption of a normal distribution of their +estimators.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>When using the "IORE" submodel for metabolites, fitting with "transform_rates = TRUE" (the default) often leads to failures of the numerical ODE solver. In this situation it may help to switch off the internal rate transformation.</p> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <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 class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and + <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> +<p>Comparisons of models fitted to the same data can be made using + <code><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></code> by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p> +<p>Fitting of several models to several datasets in a single call to + <code><a href='mmkin.html'>mmkin</a></code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> + <pre class="examples"><div class='input'> +<span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Mon Oct 21 12:07:39 2019 -#> Date of summary: Mon Oct 21 12:07:39 2019 +#> Date of fit: Fri Oct 25 02:08:07 2019 +#> Date of summary: Fri Oct 25 02:08:07 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.459 s +#> Fitted using 222 model solutions performed in 0.453 s #> #> Error model: Constant variance #> @@ -487,7 +480,7 @@ Per default, parameters in the kinetic models are internally transformed in <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>#> User System verstrichen -#> 1.462 0.000 1.463 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> 1.447 0.000 1.448 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -560,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.04 0.00 1.04 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff +#> 1.032 0.000 1.032 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -596,8 +589,8 @@ Per default, parameters in the kinetic models are internally transformed in <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Mon Oct 21 12:07:54 2019 -#> Date of summary: Mon Oct 21 12:07:54 2019 +#> Date of fit: Fri Oct 25 02:08:22 2019 +#> Date of summary: Fri Oct 25 02:08:22 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -605,7 +598,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.07 s +#> Fitted using 421 model solutions performed in 1.062 s #> #> Error model: Constant variance #> @@ -713,8 +706,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Mon Oct 21 12:07:56 2019 -#> Date of summary: Mon Oct 21 12:07:56 2019 +#> Date of fit: Fri Oct 25 02:08:25 2019 +#> Date of summary: Fri Oct 25 02:08:25 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -722,11 +715,12 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 897 model solutions performed in 2.363 s +#> Fitted using 978 model solutions performed in 2.523 s #> #> Error model: Variance unique to each observed variable #> -#> Error model algorithm: IRLS +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -761,16 +755,16 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent -#> parent_0 1.00000 0.51078 -0.19132 -0.59997 0.035676 -#> log_k_parent 0.51078 1.00000 -0.37457 -0.59239 0.069834 -#> log_k_m1 -0.19132 -0.37457 1.00000 0.74398 -0.026158 -#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041371 -#> sigma_parent 0.03568 0.06983 -0.02616 -0.04137 1.000000 -#> sigma_m1 -0.03385 -0.06626 0.02482 0.03926 -0.004628 +#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035670 +#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069833 +#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158 +#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369 +#> sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000 +#> sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628 #> sigma_m1 #> parent_0 -0.033847 #> log_k_parent -0.066265 -#> log_k_m1 0.024824 +#> log_k_m1 0.024823 #> f_parent_ilr_1 0.039256 #> sigma_parent -0.004628 #> sigma_m1 1.000000 @@ -784,7 +778,7 @@ Per default, parameters in the kinetic models are internally transformed in #> k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01 #> k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03 #> f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01 -#> sigma_parent 3.401000 5.985 5.661e-07 2.244000 4.559e+00 +#> sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00 #> sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00 #> #> FOCUS Chi2 error levels in percent: @@ -805,47 +799,47 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 99.65420 -1.942e-01 -#> 0 parent 102.04 99.65420 2.386e+00 -#> 1 parent 93.50 90.26335 3.237e+00 -#> 1 parent 92.50 90.26335 2.237e+00 -#> 3 parent 63.23 74.05308 -1.082e+01 -#> 3 parent 68.99 74.05308 -5.063e+00 -#> 7 parent 52.32 49.84326 2.477e+00 -#> 7 parent 55.13 49.84326 5.287e+00 +#> 0 parent 99.46 99.65417 -1.942e-01 +#> 0 parent 102.04 99.65417 2.386e+00 +#> 1 parent 93.50 90.26332 3.237e+00 +#> 1 parent 92.50 90.26332 2.237e+00 +#> 3 parent 63.23 74.05306 -1.082e+01 +#> 3 parent 68.99 74.05306 -5.063e+00 +#> 7 parent 52.32 49.84325 2.477e+00 +#> 7 parent 55.13 49.84325 5.287e+00 #> 14 parent 27.27 24.92971 2.340e+00 #> 14 parent 26.64 24.92971 1.710e+00 #> 21 parent 11.50 12.46890 -9.689e-01 #> 21 parent 11.64 12.46890 -8.289e-01 #> 35 parent 2.85 3.11925 -2.692e-01 #> 35 parent 2.91 3.11925 -2.092e-01 -#> 50 parent 0.69 0.70678 -1.678e-02 -#> 50 parent 0.63 0.70678 -7.678e-02 +#> 50 parent 0.69 0.70679 -1.679e-02 +#> 50 parent 0.63 0.70679 -7.679e-02 #> 75 parent 0.05 0.05952 -9.523e-03 #> 75 parent 0.06 0.05952 4.772e-04 #> 1 m1 4.84 4.81075 2.925e-02 #> 1 m1 5.64 4.81075 8.292e-01 -#> 3 m1 12.91 13.04197 -1.320e-01 -#> 3 m1 12.96 13.04197 -8.197e-02 -#> 7 m1 22.97 25.06848 -2.098e+00 -#> 7 m1 24.47 25.06848 -5.985e-01 +#> 3 m1 12.91 13.04196 -1.320e-01 +#> 3 m1 12.96 13.04196 -8.196e-02 +#> 7 m1 22.97 25.06847 -2.098e+00 +#> 7 m1 24.47 25.06847 -5.985e-01 #> 14 m1 41.69 36.70308 4.987e+00 #> 14 m1 33.21 36.70308 -3.493e+00 #> 21 m1 44.37 41.65115 2.719e+00 #> 21 m1 46.44 41.65115 4.789e+00 #> 35 m1 41.22 43.29465 -2.075e+00 #> 35 m1 37.95 43.29465 -5.345e+00 -#> 50 m1 41.19 41.19948 -9.477e-03 +#> 50 m1 41.19 41.19948 -9.479e-03 #> 50 m1 40.01 41.19948 -1.189e+00 #> 75 m1 40.09 36.44035 3.650e+00 #> 75 m1 33.85 36.44035 -2.590e+00 -#> 100 m1 31.04 31.98772 -9.477e-01 -#> 100 m1 33.13 31.98772 1.142e+00 -#> 120 m1 25.15 28.80428 -3.654e+00 -#> 120 m1 33.31 28.80428 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 +#> 100 m1 31.04 31.98773 -9.477e-01 +#> 100 m1 33.13 31.98773 1.142e+00 +#> 120 m1 25.15 28.80429 -3.654e+00 +#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Mon Oct 21 12:08:06 2019 -#> Date of summary: Mon Oct 21 12:08:06 2019 +#> Date of fit: Fri Oct 25 02:08:34 2019 +#> Date of summary: Fri Oct 25 02:08:34 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -853,7 +847,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.175 s +#> Fitted using 2289 model solutions performed in 9.136 s #> #> Error model: Two-component variance function #> @@ -969,21 +963,18 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 29.04130 -3.891304 #> 120 m1 33.31 29.04130 4.268696</div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - + <li><a href="#source">Source</a></li> <li><a href="#value">Value</a></li> - - <li><a href="#see-also">See also</a></li> - + <li><a href="#details">Details</a></li> <li><a href="#note">Note</a></li> - - <li><a href="#source">Source</a></li> - + <li><a href="#see-also">See also</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f592af1c..2eefdc2e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -8,11 +8,13 @@ <title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,18 +34,17 @@ -<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> -<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to - a list, specifying the kinetic model type and reaction or transfer to other - observed compartments. Instead of specifying several expressions, a list - of lists can be given in the speclist argument. -For the definition of model types and their parameters, the equations given - in the FOCUS and NAFTA guidance documents are used." /> +<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> +<meta property="og:description" content="The function usually takes several expressions, each assigning a compound +name to a list, specifying the kinetic model type and reaction or transfer +to other observed compartments. Instead of specifying several expressions, a +list of lists can be given in the speclist argument." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -114,7 +115,6 @@ For the definition of model types and their parameters, the equations given <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -136,49 +136,47 @@ For the definition of model types and their parameters, the equations given </div> <div class="ref-description"> - - <p>The function usually takes several expressions, each assigning a compound name to - a list, specifying the kinetic model type and reaction or transfer to other - observed compartments. Instead of specifying several expressions, a list - of lists can be given in the speclist argument.</p> -<p>For the definition of model types and their parameters, the equations given - in the FOCUS and NAFTA guidance documents are used.</p> - + <p>The function usually takes several expressions, each assigning a compound +name to a list, specifying the kinetic model type and reaction or transfer +to other observed compartments. Instead of specifying several expressions, a +list of lists can be given in the speclist argument.</p> </div> - <pre class="usage"><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - + <pre class="usage"><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>...</th> - <td><p>For each observed variable, a list has to be specified as an argument, containing - at least a component <code>type</code>, specifying the type of kinetics to use - for the variable. Currently, single first order kinetics "SFO", - indeterminate order rate equation kinetics "IORE", or - single first order with reversible binding "SFORB" are implemented for all - variables, while - "FOMC", "DFOP" and "HS" can additionally be chosen for the first - variable which is assumed to be the source compartment. - Additionally, each component of the list can include a character vector <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 additional component of the list - can be "sink=FALSE" effectively fixing the flux to sink to zero.</p></td> + <td><p>For each observed variable, a list has to be specified as an +argument, containing at least a component <code>type</code>, specifying the type +of kinetics to use for the variable. Currently, single first order +kinetics "SFO", indeterminate order rate equation kinetics "IORE", or +single first order with reversible binding "SFORB" are implemented for all +variables, while "FOMC", "DFOP" and "HS" can additionally be chosen for +the first variable which is assumed to be the source compartment. +Additionally, each component of the list can include a character vector +<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 +additional component of the list can be "sink=FALSE" effectively fixing +the flux to sink to zero.</p></td> </tr> <tr> <th>use_of_ff</th> - <td><p>Specification of the use of formation fractions in the model equations and, if - applicable, the coefficient matrix. If "min", a minimum use of formation - fractions is made in order to avoid fitting the product of formation fractions - and rate constants. If "max", formation fractions are always used.</p></td> + <td><p>Specification of the use of formation fractions in the +model equations and, if applicable, the coefficient matrix. If "min", a +minimum use of formation fractions is made in order to avoid fitting the +product of formation fractions and rate constants. If "max", formation +fractions are always used.</p></td> </tr> <tr> <th>speclist</th> - <td><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></td> + <td><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></td> </tr> <tr> <th>quiet</th> @@ -186,44 +184,46 @@ For the definition of model types and their parameters, the equations given </tr> <tr> <th>verbose</th> - <td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give - detailed information about the C function being built.</p></td> + <td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if +applicable to give detailed information about the C function being built.</p></td> </tr> </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing</p> -<dt>diffs</dt><dd><p>A vector of string representations of differential equations, - one for each modelling variable.</p></dd> - <dt>parms</dt><dd><p>A vector of parameter names occurring in the differential equations.</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>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be - represented by one.</p></dd> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - + <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, + containing, among others,</p> +<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>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be + represented by one.</p></dd> + <dt>ll</dt><dd><p>The likelihood function, taking the parameter vector as the first argument.</p></dd> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>For the definition of model types and their parameters, the equations given +in the FOCUS and NAFTA guidance documents are used.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The IORE submodel is not well tested (yet). When using this model for metabolites, - you may want to read the second note in the help page to - <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - + <p>The IORE submodel is not well tested for metabolites. When using this + model for metabolites, you may want to read the second note in the help + page to <code><a href='mkinfit.html'>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 and - Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + <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 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> <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental - Media</p> - + Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> + <pre class="examples"><div class='input'> +<span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) <span class='co'># One parent compound, one metabolite, both single first order</span> @@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file663b71dc323f.c 2> file663b71dc323f.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file59d942b9ac06.c 2> file59d942b9ac06.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: @@ -260,7 +260,7 @@ For the definition of model types and their parameters, the equations given #> 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0]; #> 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1]; #> 19: }</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='co'># If we have several parallel metabolites </span> +<span class='co'># If we have several parallel metabolites</span> <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> <span class='no'>m_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), @@ -276,13 +276,10 @@ For the definition of model types and their parameters, the equations given <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#details">Details</a></li> <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 79a4cc2b..af936795 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -8,11 +8,13 @@ <title>Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> -<meta property="og:description" content="This function plots the confidence intervals for the parameters - fitted using mkinfit." /> +<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> +<meta property="og:description" content="This function plots the confidence intervals for the parameters fitted using +mkinfit." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,12 @@ </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> - + <p>This function plots the confidence intervals for the parameters fitted using +<code><a href='mkinfit.html'>mkinfit</a></code>.</p> </div> <pre class="usage"><span class='fu'>mkinparplot</span>(<span class='no'>object</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> @@ -148,26 +148,26 @@ <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</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> - + <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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> + <pre class="examples"><div class='input'> +<span class='co'># \dontrun{</span> <span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'># }</div></pre> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'># } +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 33d69b6d..d078e239 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -8,11 +8,13 @@ <title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,15 @@ -<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" /> -<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." /> +<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" /> +<meta property="og:description" content="Deprecated function. It now only calls the plot method +plot.mkinfit." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,13 +134,12 @@ </div> <div class="ref-description"> - - <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> - + <p>Deprecated function. It now only calls the plot method +<code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> </div> <pre class="usage"><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</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> @@ -150,20 +152,18 @@ <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> <p>The function is called for its side effect.</p> - </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - </ul> + </ul> <h2>Author</h2> <p>Johannes Ranke</p> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5faff3c7..f7d543ad 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -8,11 +8,13 @@ <title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,15 +34,16 @@ -<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> +<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> <meta property="og:description" content="This function produces a time series for all the observed variables in a - kinetic model as specified by mkinmod, using a specific set of - kinetic parameters and initial values for the state variables." /> +kinetic model as specified by mkinmod, using a specific set of +kinetic parameters and initial values for the state variables." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -111,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,89 +135,105 @@ </div> <div class="ref-description"> - <p>This function produces a time series for all the observed variables in a - kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of - kinetic parameters and initial values for the state variables.</p> - +kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of +kinetic parameters and initial values for the state variables.</p> </div> <pre class="usage"><span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, - <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> - + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinmod</span> +<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>, + <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</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>A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>, or a kinetic - fit as fitted by <code><a href='mkinfit.html'>mkinfit</a></code>. In the latter case, the fitted - parameters are used for the prediction.</p></td> +fit as fitted by <code><a href='mkinfit.html'>mkinfit</a></code>. In the latter case, the fitted +parameters are used for the prediction.</p></td> </tr> <tr> <th>odeparms</th> - <td><p>A numeric vector specifying the parameters used in the kinetic model, which - is generally defined as a set of ordinary differential equations.</p></td> + <td><p>A numeric vector specifying the parameters used in the +kinetic model, which is generally defined as a set of ordinary +differential equations.</p></td> </tr> <tr> <th>odeini</th> - <td><p>A numeric vectory containing the initial values of the state variables of - the model. Note that the state variables can differ from the observed - variables, for example in the case of the SFORB model.</p></td> + <td><p>A numeric vectory containing the initial values of the state +variables of the model. Note that the state variables can differ from the +observed variables, for example in the case of the SFORB model.</p></td> </tr> <tr> <th>outtimes</th> - <td><p>A numeric vector specifying the time points for which model predictions - should be generated.</p></td> + <td><p>A numeric vector specifying the time points for which model +predictions should be generated.</p></td> </tr> <tr> <th>solution_type</th> - <td><p>The method that should be used for producing the predictions. This should - generally be "analytical" if there is only one observed variable, and - usually "deSolve" in the case of several observed variables. The third - possibility "eigen" is faster but not applicable to some models e.g. - using FOMC for the parent compound.</p></td> + <td><p>The method that should be used for producing the +predictions. This should generally be "analytical" if there is only one +observed variable, and usually "deSolve" in the case of several observed +variables. The third possibility "eigen" is faster but not applicable to +some models e.g. using FOMC for the parent compound.</p></td> </tr> <tr> - <th>method.ode</th> - <td><p>The solution method passed via <code>mkinpredict</code> to - <code>ode</code> in case the solution type is "deSolve". The default - "lsoda" is performant, but sometimes fails to converge.</p></td> + <th>use_compiled</th> + <td><p>If set to <code>FALSE</code>, no compiled version of the +<code><a href='mkinmod.html'>mkinmod</a></code> model is used, even if is present.</p></td> </tr> <tr> - <th>use_compiled</th> - <td><p>If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> - model is used, even if is present.</p></td> + <th>method.ode</th> + <td><p>The solution method passed via <code>mkinpredict</code> +to <code>ode</code> in case the solution type is "deSolve". The default +"lsoda" is performant, but sometimes fails to converge.</p></td> </tr> <tr> <th>atol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8, - lower than in <code>lsoda</code>.</p></td> + <td><p>Absolute error tolerance, passed to <code>ode</code>. Default +is 1e-8, lower than in <code>lsoda</code>.</p></td> </tr> <tr> <th>rtol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10, - much lower than in <code>lsoda</code>.</p></td> + <td><p>Absolute error tolerance, passed to <code>ode</code>. Default +is 1e-10, much lower than in <code>lsoda</code>.</p></td> </tr> <tr> <th>map_output</th> - <td><p>Boolean to specify if the output should list values for the observed - variables (default) or for all state variables (if set to FALSE).</p></td> + <td><p>Boolean to specify if the output should list values for +the observed variables (default) or for all state variables (if set to +FALSE).</p></td> </tr> <tr> <th>...</th> - <td><p>Further arguments passed to the ode solver in case such a solver is used.</p></td> + <td><p>Further arguments passed to the ode solver in case such a +solver is used.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A matrix in the same format as the output of <code>ode</code>.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) + <pre class="examples"><div class='input'> + <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#> time degradinol @@ -342,7 +360,7 @@ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.022 0.000 0.021 </div><div class='input'> +#> 0.021 0.000 0.021 </div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 @@ -380,15 +398,14 @@ #> 4 0.3 75.25515 3.399419 #> 5 0.4 72.98675 4.441969 #> 6 0.5 70.78673 5.441679</div><div class='input'> # } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index eea5b218..1ac2cdbe 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -8,11 +8,13 @@ <title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,16 +34,17 @@ -<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" /> -<meta property="og:description" content="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 plot.mkinfit - using the argument show_residuals = TRUE." /> +<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" /> +<meta property="og:description" content="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 plot.mkinfit using the +argument show_residuals = TRUE." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -112,7 +115,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -134,23 +136,17 @@ </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 argument <code>show_residuals = TRUE</code>.</p> - + <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 +argument <code>show_residuals = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinresplot</span>(<span class='no'>object</span>, - <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>, - <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='no'>...</span>)</pre> - + <pre class="usage"><span class='fu'>mkinresplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, + <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>, + <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, + <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</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> @@ -160,8 +156,9 @@ </tr> <tr> <th>obs_vars</th> - <td><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> + <td><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> @@ -173,12 +170,13 @@ </tr> <tr> <th>ylab</th> - <td><p>Label for the y axis. Defaults to "Residual [% of applied radioactivity]".</p></td> + <td><p>Label for the y axis. Defaults to "Residual [% of applied +radioactivity]".</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> + <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> @@ -186,8 +184,8 @@ </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> + <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> @@ -206,29 +204,27 @@ <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.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> - + <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> - <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 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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div></pre> + <pre class="examples"><div class='input'> +<span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 1523138c..e38c153c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -8,11 +8,13 @@ <title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" /> +<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" /> <meta property="og:description" content="This is a convenience function to set up the lists used as arguments for - mkinmod." /> +mkinmod." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,48 +134,46 @@ </div> <div class="ref-description"> - <p>This is a convenience function to set up the lists used as arguments for - <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - +<code><a href='mkinmod.html'>mkinmod</a></code>.</p> </div> <pre class="usage"><span class='fu'>mkinsub</span>(<span class='no'>submodel</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='fl'>NA</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>submodel</th> - <td><p>Character vector of length one to specify the submodel type. See - <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td> + <td><p>Character vector of length one to specify the submodel type. +See <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td> </tr> <tr> <th>to</th> - <td><p>Vector of the names of the state variable to which a transformation - shall be included in the model.</p></td> + <td><p>Vector of the names of the state variable to which a +transformation shall be included in the model.</p></td> </tr> <tr> <th>sink</th> - <td><p>Should a pathway to sink be included in the model in addition to the - pathways to other state variables?</p></td> + <td><p>Should a pathway to sink be included in the model in addition to +the pathways to other state variables?</p></td> </tr> <tr> <th>full_name</th> - <td><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></td> + <td><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></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</span> + <pre class="examples"><div class='input'> +<span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> @@ -184,15 +184,14 @@ <span class='co'># Now supplying full names</span> <span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div></pre> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 9d8c0931..201ef0fd 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 0f384062..8312c17c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,13 +6,16 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title> +<title>Fit one or more kinetic models with one or more state variables to one or +more datasets — mmkin • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +35,16 @@ -<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" /> -<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets - specified in its first two arguments." /> +<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or +more datasets — mmkin" /> +<meta property="og:description" content="This function calls mkinfit on all combinations of models and +datasets specified in its first two arguments." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -110,7 +115,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -126,65 +130,64 @@ <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> + <h1>Fit one or more kinetic models with one or more state variables to one or +more datasets</h1> <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 datasets - specified in its first two arguments.</p> - + <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='no'>models</span>, <span class='no'>datasets</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> - + <pre class="usage"><span class='fu'>mmkin</span>(<span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>datasets</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</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>models</th> - <td><p>Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> - objects.</p></td> + <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> + <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 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.</p></td> + <td><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.</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> + <td><p>A cluster as returned by <code>makeCluster</code> to be used +for parallel execution.</p></td> </tr> <tr> <th>...</th> <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model - and dataset names as row and column indices.</p> - + <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using + the model and dataset names as row and column indices.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>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 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> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> + <pre class="examples"><div class='input'> +<span class='co'># \dontrun{</span> <span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> @@ -199,8 +202,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.016 0.029 4.960 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.084 0.004 19.099 </div><div class='input'> +#> 0.011 0.032 4.774 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 18.676 0.000 18.687 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 @@ -221,17 +224,15 @@ <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.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index c5ea9a9a..60917ff4 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -8,11 +8,13 @@ <title>Evaluate parent kinetics using the NAFTA guidance — nafta • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,15 +34,18 @@ -<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." /> +<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="twitter:card" content="summary" /> + <!-- 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> @@ -111,7 +116,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,24 +137,27 @@ </div> <div class="ref-description"> - - <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>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='no'>ds</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> - + <pre class="usage"><span class='fu'>nafta</span>(<span class='no'>ds</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</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='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='no'>...</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> + <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> @@ -162,31 +169,41 @@ </tr> <tr> <th>...</th> - <td><p>Further arguments passed to <code><a href='mmkin.html'>mmkin</a></code>.</p></td> + <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="value"><a class="anchor" href="#value"></a>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="source"><a class="anchor" href="#source"></a>Source</h2> - <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics - in environmental media. NAFTA Technical Working Group on Pesticides + <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> 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> + + <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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</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='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: + <pre class="examples"><div class='input'> + <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</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='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> @@ -223,17 +240,15 @@ #> 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.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - <li><a href="#source">Source</a></li> - + <li><a href="#value">Value</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 60203c3d..20f30221 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex 20f30221..ad2ffa8c 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index df01a00b..04ef75e4 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -8,11 +8,13 @@ <title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,18 +34,16 @@ -<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" /> +<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" /> <meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters - from a previous successful call to mkinfit and plots - the observed data together with the solution of the fitted model. -If the current plot device is a tikz device, - then latex is being used for the formatting of the chi2 error level, - if show_errmin = TRUE." /> +from a previous successful call to mkinfit and plots the +observed data together with the solution of the fitted model." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -114,7 +114,6 @@ If the current plot device is a tikz device, <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -136,42 +135,34 @@ If the current plot device is a tikz device, </div> <div class="ref-description"> - <p>Solves the differential equations with the optimised and fixed parameters - from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots - the observed data together with the solution of the fitted model.</p> -<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, - if <code>show_errmin = TRUE</code>.</p> - +from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the +observed data together with the solution of the fitted model.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, - <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>, - <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>, - <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, - <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>), + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>, + <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>, + <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) + <span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) + <span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>) + <span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</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>Alias for fit introduced for compatibility with the generic S3 method.</p></td> + <td><p>Alias for fit introduced for compatibility with the generic S3 +method.</p></td> </tr> <tr> <th>fit</th> @@ -179,9 +170,9 @@ If the current plot device is a tikz device, </tr> <tr> <th>obs_vars</th> - <td><p>A character vector of names of the observed variables for which the - data and the model should be plotted. Defauls to all observed variables - in the model.</p></td> + <td><p>A character vector of names of the observed variables for +which the data and the model should be plotted. Defauls to all observed +variables in the model.</p></td> </tr> <tr> <th>xlab</th> @@ -201,7 +192,8 @@ If the current plot device is a tikz device, </tr> <tr> <th>col_obs</th> - <td><p>Colors used for plotting the observed data and the corresponding model prediction lines.</p></td> + <td><p>Colors used for plotting the observed data and the +corresponding model prediction lines.</p></td> </tr> <tr> <th>pch_obs</th> @@ -221,41 +213,44 @@ If the current plot device is a tikz device, </tr> <tr> <th>show_residuals</th> - <td><p>Should residuals be shown? If only one plot of the fits is shown, the - residual plot is in the lower third of the plot. Otherwise, i.e. if - "sep_obs" is given, the residual plots will be located to the right of - the plots of the fitted curves.</p></td> + <td><p>Should residuals be shown? If only one plot of the +fits is shown, the residual plot is in the lower third of the plot. +Otherwise, i.e. if "sep_obs" is given, the residual plots will be located +to the right of the plots of the fitted curves.</p></td> </tr> <tr> <th>show_errplot</th> - <td><p>Should squared residuals and the error model be shown? If only one plot of - the fits is shown, this plot is in the lower third of the plot. - Otherwise, i.e. if "sep_obs" is given, the residual plots will be located - to the right of the plots of the fitted curves.</p></td> + <td><p>Should squared residuals and the error model be shown? +If only one plot of the fits is shown, this plot is in the lower third of +the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will +be located to the right of the plots of the fitted curves.</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> + <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>sep_obs</th> - <td><p>Should the observed variables be shown in separate subplots? If yes, residual plots - requested by "show_residuals" will be shown next to, not below the plot of the fits.</p></td> + <td><p>Should the observed variables be shown in separate subplots? +If yes, residual plots requested by "show_residuals" will be shown next +to, not below the plot of the fits.</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> + <td><p>The relative height of the middle plot, if more +than two rows of plots are shown.</p></td> </tr> <tr> <th>row_layout</th> - <td><p>Should we use a row layout where the residual plot or the error model plot is shown - to the right?</p></td> + <td><p>Should we use a row layout where the residual plot or the +error model plot is shown to the right?</p></td> </tr> <tr> <th>lpos</th> - <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as the first argument. - If not length one, this should be of the same length as the obs_var argument.</p></td> + <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as +the first argument. If not length one, this should be of the same length +as the obs_var argument.</p></td> </tr> <tr> <th>inset</th> @@ -263,11 +258,13 @@ If the current plot device is a tikz device, </tr> <tr> <th>show_errmin</th> - <td><p>Should the FOCUS chi2 error value be shown in the upper margin of the plot?</p></td> + <td><p>Should the FOCUS chi2 error value be shown in the upper +margin of the plot?</p></td> </tr> <tr> <th>errmin_digits</th> - <td><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></td> + <td><p>The number of significant digits for rounding the FOCUS +chi2 error percentage.</p></td> </tr> <tr> <th>frame</th> @@ -278,38 +275,41 @@ If the current plot device is a tikz device, <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</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, if +<code>show_errmin = TRUE</code>.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> + <pre class="examples"><div class='input'> +<span class='co'># One parent compound, one metabolite, both single first order, path from</span> <span class='co'># parent to sink included</span> <span class='co'># \dontrun{</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Show the observed variables separately</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> <span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>)) <span class='co'># Show the observed variables separately, with the error model</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), - <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'># } + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#details">Details</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 44037bb4..13d96256 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 9a11108f..8b68cfae 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,13 +6,16 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin</title> +<title>Plot model fits (observed and fitted) and the residuals for a row or column +of an mmkin object — plot.mmkin • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,17 +35,17 @@ -<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" /> -<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), 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. -If the current plot device is a tikz device, - then latex is being used for the formatting of the chi2 error level." /> +<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column +of an mmkin object — plot.mmkin" /> +<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), 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." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -113,7 +116,6 @@ If the current plot device is a tikz device, <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -129,32 +131,31 @@ If the current plot device is a tikz device, <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> + <h1>Plot model fits (observed and fitted) and the residuals for a row or column +of an mmkin object</h1> <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='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> -<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> - + <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.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, - <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre> - + <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, + <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</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> + <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> @@ -166,21 +167,24 @@ If the current plot device is a tikz device, </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> + <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>show_errmin</th> - <td><p>Should the chi2 error level be shown on top of the plots to the left?</p></td> + <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> + <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> + <td><p>The number of significant digits for rounding the FOCUS +chi2 error percentage.</p></td> </tr> <tr> <th>cex</th> @@ -188,21 +192,27 @@ If the current plot device is a tikz device, </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> + <td><p>The relative height of the middle plot, if more +than two rows of plots are shown.</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> + <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="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> + <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='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</span> @@ -214,15 +224,15 @@ If the current plot device is a tikz device, <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.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.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> # } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#details">Details</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index c5eed391..294a79a4 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -6,15 +6,15 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Plot the results of the three models used in the NAFTA scheme. The plots - are ordered with increasing complexity of the model in this function - (SFO, then IORE, then DFOP). — plot.nafta • mkin</title> +<title>Plot the results of the three models used in the NAFTA scheme. — plot.nafta • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -34,15 +34,15 @@ -<meta property="og:title" content="Plot the results of the three models used in the NAFTA scheme. The plots - are ordered with increasing complexity of the model in this function - (SFO, then IORE, then DFOP). — plot.nafta" /> -<meta property="og:description" content="Calls plot.mmkin." /> +<meta property="og:title" content="Plot the results of the three models used in the NAFTA scheme. — plot.nafta" /> +<meta property="og:description" content="The plots are ordered with increasing complexity of the model in this +function (SFO, then IORE, then DFOP)." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -113,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -129,22 +128,19 @@ <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. The plots - are ordered with increasing complexity of the model in this function - (SFO, then IORE, then DFOP).</h1> + <h1>Plot the results of the three models used in the NAFTA scheme.</h1> <div class="hidden name"><code>plot.nafta.Rd</code></div> </div> <div class="ref-description"> - - <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p> - + <p>The plots are ordered with increasing complexity of the model in this +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.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='no'>...</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> @@ -165,20 +161,22 @@ <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> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - </ul> + <li><a href="#details">Details</a></li> + </ul> <h2>Author</h2> <p>Johannes Ranke</p> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 810123b8..d7ba94e1 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -8,11 +8,13 @@ <title>Print mkinds objects — print.mkinds • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Print mkinds objects — print.mkinds" /> +<meta property="og:title" content="Print mkinds objects — print.mkinds" /> <meta property="og:description" content="Print mkinds objects." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,14 +133,12 @@ </div> <div class="ref-description"> - <p>Print mkinds objects.</p> - </div> <pre class="usage"><span class='co'># S3 method for mkinds</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</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> @@ -151,14 +151,14 @@ <td><p>Not used.</p></td> </tr> </table> - + </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - </ul> + </ul> </div> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 5a8feab8..03e73e29 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -8,11 +8,13 @@ <title>Print mkinmod objects — print.mkinmod • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,15 @@ -<meta property="og:title" content="Print mkinmod objects — print.mkinmod" /> -<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." /> +<meta property="og:title" content="Print mkinmod objects — print.mkinmod" /> +<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its +components." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -109,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,14 +134,13 @@ </div> <div class="ref-description"> - - <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p> - + <p>Print mkinmod objects in a way that the user finds his way to get to its +components.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinmod</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</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> @@ -151,10 +153,11 @@ <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='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), + <pre class="examples"><div class='input'> + <span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#> <mkinmod> model generated with @@ -171,13 +174,13 @@ #> Differential 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</div></pre> +#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index ef62212a..d95e1c28 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -36,13 +36,8 @@ <meta property="og:title" content="Two component error model — sigma_twocomp" /> -<meta property="og:description" content="Function describing the standard deviation of the measurement error - in dependence of the measured value \(y\): -$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ - sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2) -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." /> +<meta property="og:description" content="Function describing the standard deviation of the measurement error in +dependence of the measured value \(y\):" /> <meta name="twitter:card" content="summary" /> @@ -139,13 +134,8 @@ This is the error model used for example by Werner et al. (1978). The model </div> <div class="ref-description"> - <p>Function describing the standard deviation of the measurement error - in dependence of the measured value \(y\):</p> -<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> + <p>Function describing the standard deviation of the measurement error in +dependence of the measured value \(y\):</p> </div> <pre class="usage"><span class='fu'>sigma_twocomp</span>(<span class='no'>y</span>, <span class='no'>sigma_low</span>, <span class='no'>rsd_high</span>)</pre> @@ -159,18 +149,27 @@ This is the error model used for example by Werner et al. (1978). The model </tr> <tr> <th>sigma_low</th> - <td><p>The asymptotic minimum of the standard deviation for low observed values</p></td> + <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> + <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> + + <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> <p>Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) @@ -185,6 +184,7 @@ This is the error model used for example by Werner et al. (1978). The model <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> <li><a href="#value">Value</a></li> + <li><a href="#details">Details</a></li> <li><a href="#references">References</a></li> </ul> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 73410181..65bc6326 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -8,11 +8,13 @@ <title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,16 +34,18 @@ -<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> -<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with some - uncertainty statistics, the chi2 error levels calculated according to FOCUS - guidance (2006) as defined therein, formation fractions, DT50 values and - optionally the data, consisting of observed, predicted and residual values." /> +<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> +<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with +some uncertainty statistics, the chi2 error levels calculated according to +FOCUS guidance (2006) as defined therein, formation fractions, DT50 values +and optionally the data, consisting of observed, predicted and residual +values." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -112,7 +116,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -134,19 +137,21 @@ </div> <div class="ref-description"> - - <p>Lists model equations, initial parameter values, optimised parameters with some - uncertainty statistics, the chi2 error levels calculated according to FOCUS - guidance (2006) as defined therein, formation fractions, DT50 values and - optionally the data, consisting of observed, predicted and residual values.</p> - + <p>Lists model equations, initial parameter values, optimised parameters with +some uncertainty statistics, the chi2 error levels calculated according to +FOCUS guidance (2006) as defined therein, formation fractions, DT50 values +and optionally the data, consisting of observed, predicted and residual +values.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) + <span class='co'># S3 method for summary.mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> - +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - + <span class='fl'>3</span>), <span class='no'>...</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> @@ -155,91 +160,94 @@ <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> <tr> - <th>x</th> - <td><p>an object of class <code>summary.mkinfit</code>.</p></td> - </tr> - <tr> <th>data</th> - <td><p>logical, indicating whether the data should be included in the summary.</p></td> + <td><p>logical, indicating whether the data should be included in the +summary.</p></td> </tr> <tr> <th>distimes</th> - <td><p>logical, indicating whether DT50 and DT90 values should be included.</p></td> + <td><p>logical, indicating whether DT50 and DT90 values should be +included.</p></td> </tr> <tr> <th>alpha</th> - <td><p>error level for confidence interval estimation from t distribution</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to use for printing</p></td> + <td><p>error level for confidence interval estimation from t +distribution</p></td> </tr> <tr> <th>...</th> <td><p>optional arguments passed to methods like <code>print</code>.</p></td> </tr> + <tr> + <th>x</th> + <td><p>an object of class <code>summary.mkinfit</code>.</p></td> + </tr> + <tr> + <th>digits</th> + <td><p>Number of digits to use for printing</p></td> + </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The summary function returns a list with components, among others</p> <dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd> - <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were produced</p></dd> + <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were + produced</p></dd> + <dt>diffs</dt><dd><p>The differential equations used in the model</p></dd> <dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> - <dt>residuals, residualVariance, sigma, modVariance, df</dt><dd><p>As in summary.modFit</p></dd> - <dt>cov.unscaled, cov.scaled, info, niter, stopmess, par</dt><dd><p>As in summary.modFit</p></dd> - <dt>bpar</dt><dd><p>Optimised and backtransformed parameters</p></dd> - <dt>diffs </dt><dd><p>The differential equations used in the model</p></dd> - <dt>data </dt><dd><p>The data (see Description above).</p></dd> - <dt>start </dt><dd><p>The starting values and bounds, if applicable, for optimised parameters.</p></dd> - <dt>fixed </dt><dd><p>The values of fixed parameters.</p></dd> - <dt>errmin </dt><dd><p>The chi2 error levels for each observed variable.</p></dd> - <dt>bparms.ode </dt><dd><p>All backtransformed ODE parameters, for use as starting parameters for - related models.</p></dd> - <dt>errparms </dt><dd><p>Error model parameters.</p></dd> - <dt>ff </dt><dd><p>The estimated formation fractions derived from the fitted model.</p></dd> - <dt>distimes </dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> + <dt>bpar</dt><dd><p>Optimised and backtransformed + parameters</p></dd> + <dt>data</dt><dd><p>The data (see Description above).</p></dd> + <dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised + parameters.</p></dd> + <dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd> + <dt>errmin </dt><dd><p>The chi2 error levels for + each observed variable.</p></dd> + <dt>bparms.ode</dt><dd><p>All backtransformed ODE + parameters, for use as starting parameters for related models.</p></dd> + <dt>errparms</dt><dd><p>Error model parameters.</p></dd> + <dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted + model.</p></dd> + <dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> <dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> The print method is called for its side effect, i.e. printing the summary. - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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 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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Sep 19 09:52:40 2019 -#> Date of summary: Thu Sep 19 09:52:40 2019 +#> Date of fit: Fri Oct 25 02:09:45 2019 +#> Date of summary: Fri Oct 25 02:09:45 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.27 s +#> Fitted using 131 model solutions performed in 0.274 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.240000 state -#> k_parent_sink 0.100000 deparm -#> sigma 5.265546 error +#> value type +#> parent_0 101.24 state +#> k_parent_sink 0.10 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 101.240000 -Inf Inf #> log_k_parent_sink -2.302585 -Inf Inf -#> sigma 5.265546 0 Inf #> #> Fixed parameter values: #> None @@ -287,17 +295,15 @@ #> 30 parent 29.71 35.738 -6.0283 #> 62 parent 5.98 10.862 -4.8818 #> 90 parent 1.54 3.831 -2.2911 -#> 118 parent 0.39 1.351 -0.9613</div></pre> +#> 118 parent 0.39 1.351 -0.9613</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index b1a952d9..4d88a03e 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -8,11 +8,13 @@ <title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,21 +34,19 @@ -<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> -<meta property="og:description" content="The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - constants and other paramters 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. -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 mkinfit." /> +<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> +<meta property="og:description" content="The transformations are intended to map parameters that should only take on +restricted values to the full scale of real numbers. For kinetic rate +constants and other paramters 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="twitter:card" content="summary" /> + <!-- 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> @@ -117,7 +117,6 @@ The transformation of sets of formation fractions is fragile, as it supposes <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -139,71 +138,80 @@ The transformation of sets of formation fractions is fragile, as it supposes </div> <div class="ref-description"> - - <p>The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - constants and other paramters 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 <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> -<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 <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - + <p>The transformations are intended to map parameters that should only take on +restricted values to the full scale of real numbers. For kinetic rate +constants and other paramters 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 <code><a href='ilr.html'>ilr</a></code> transformation is used.</p> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, - <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> - + <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>transparms</th> - <td><p>Transformed parameters of kinetic models as used in the fitting procedure.</p></td> + <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 <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of - the model variables that are needed for grouping the formation fractions - before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and - the information if the pathway to sink is included in the model.</p></td> + <td><p>The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing +the names of the model variables that are needed for grouping the +formation fractions before <code><a href='ilr.html'>ilr</a></code> 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 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> + <td><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 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 and HS models are also - transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> - transformation.</p></td> + <td><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 and HS models are also transformed, as they can also +be seen as compositional data. The transformation used for these +transformations is the <code><a href='ilr.html'>ilr</a></code> transformation.</p></td> + </tr> + <tr> + <th>transparms</th> + <td><p>Transformed parameters of kinetic models as used in the +fitting procedure.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A vector of transformed or backtransformed parameters with the same names - as the original parameters.</p> + <p>A vector of transformed or backtransformed parameters with the same + names as the original parameters.</p> + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>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 <code><a href='mkinfit.html'>mkinfit</a></code>.</p> + <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2> + +<ul> +<li><p><code>backtransform_odeparms</code>: Backtransform the set of transformed parameters</p></li> +</ul> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <pre class="examples"><div class='input'> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>) @@ -278,15 +286,16 @@ The transformation of sets of formation fractions is fragile, as it supposes #> 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'># } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - + <li><a href="#details">Details</a></li> + <li><a href="#functions">Functions</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 9d241510..b62b9a44 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -133,9 +133,6 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html</loc> </url> <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/print.nafta.html</loc> - </url> - <url> <loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc> </url> <url> |
