diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-11-01 12:19:03 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-11-01 12:19:03 +0100 |
| commit | bbb74d4f60033899cd5cdd36aa70f157bc52209e (patch) | |
| tree | ca0f620ba0ffd59ff242071260d2346e4ca254ff /docs/reference | |
| parent | 70e48e8360875f22970174d409c46cb3f076fa99 (diff) | |
Fix bug in yesterdays release, add methods for BIC
Diffstat (limited to 'docs/reference')
31 files changed, 141 insertions, 627 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 103bcb4a..7ca12302 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin</title> +<title>Calculate the AIC for a column of an mmkin object — AIC.mmkin • mkin</title> <!-- jquery --> @@ -35,7 +35,7 @@ -<meta property="og:title" content="Calculated the AIC for a column of an mmkin object — AIC.mmkin" /> +<meta property="og:title" content="Calculate 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" /> @@ -70,7 +70,7 @@ same dataset." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -128,7 +128,7 @@ same dataset." /> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Calculated the AIC for a column of an mmkin object</h1> + <h1>Calculate the AIC for a column of an mmkin object</h1> <div class="hidden name"><code>AIC.mmkin.Rd</code></div> </div> @@ -139,7 +139,10 @@ 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> +<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>) + +<span class='co'># S3 method for mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='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"> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 879c1444..7273b5de 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -176,16 +176,16 @@ either a list of mkinfit objects or a single mkinfit object.</p></td> <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,40 List,40 +#> FOMC List,41 List,41 #> 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,40 -#> FOMC List,40 +#> SFO List,41 +#> FOMC List,41 #> 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,40 +#> SFO List,41 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>( diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 8f418b75..83d624bb 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -8,11 +8,13 @@ <title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" /> +<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -43,6 +45,7 @@ in this fit." /> + <!-- 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 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -160,7 +161,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -168,7 +168,6 @@ in this fit.</p> 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/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> @@ -176,11 +175,8 @@ in this fit.</p> <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index a457a4a2..75a0da96 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -8,11 +8,13 @@ <title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> +<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -43,6 +45,7 @@ in this fit." /> + <!-- 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 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -159,7 +160,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -167,7 +167,6 @@ in this fit.</p> 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/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> @@ -175,11 +174,8 @@ in this fit.</p> <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 4285c70c..d9d24bdf 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -8,11 +8,13 @@ <title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • 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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" /> +<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -43,6 +45,7 @@ in this fit." /> + <!-- 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 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_HS_ref_A_to_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -160,7 +161,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -168,7 +168,6 @@ in this fit.</p> 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/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> @@ -176,11 +175,8 @@ in this fit.</p> <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index d1dab9a9..8c0f5bc9 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -8,11 +8,13 @@ <title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • 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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" /> +<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" /> <meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -43,6 +45,7 @@ in this fit." /> + <!-- 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 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_SFO_ref_A_to_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -158,7 +159,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -166,7 +166,6 @@ in this fit.</p> 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/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> @@ -174,11 +173,8 @@ in this fit.</p> <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 2f183654..8ccf363e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -8,11 +8,13 @@ <title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • 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="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> +<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> <meta property="og:description" content="Data taken from FOCUS (2006), p. 258." /> <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> @@ -131,9 +133,7 @@ </div> <div class="ref-description"> - <p>Data taken from FOCUS (2006), p. 258.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_A</span> @@ -142,7 +142,8 @@ <span class='no'>FOCUS_2006_D</span> <span class='no'>FOCUS_2006_E</span> <span class='no'>FOCUS_2006_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>6 datasets with observations on the following variables.</p><dl class='dl-horizontal'> @@ -152,7 +153,6 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -160,7 +160,6 @@ 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'>FOCUS_2006_C</span></div><div class='output co'>#> name time value @@ -177,11 +176,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - 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<li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - </ul> -</li> -<li> - <a href="../news/index.html">News</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Example datasets from the NAFTA guidance published 2015</h1> - - <div class="hidden name"><code>NAFTA_2015_datasets.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Data taken from US EPA (2015), p. 23.</p> - - </div> - - <pre class="usage"><span class='no'>NAFTA_2015_datasets</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>1 dataset with observations on the following variables.</p><dl class='dl-horizontal'> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</p></dd> - </dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <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="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'><a href='nafta.html'>nafta</a></span>(<span class='no'>MRID_555555</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://www.rdocumentation.org/packages/base/topics/print'>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 -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -#> k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08 -#> N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -#> k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -#> k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -#> g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1352 407 -#> IORE 541 5192066 1562968 -#> DFOP 429 2383 841 -#> -#> Representative half-life: -#> [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_2015_datasets-1.png' alt='' width='700' height='433' /></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="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> -</div> - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 84d5508a..5ad02bf9 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -8,11 +8,13 @@ <title>Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015 • 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="Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015" /> +<meta property="og:title" content="Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015" /> <meta property="og:description" content="Data taken from US EPA (2015), p. 19 and 23." /> <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 +133,13 @@ </div> <div class="ref-description"> - <p>Data taken from US EPA (2015), p. 19 and 23.</p> - </div> <pre class="usage"><span class='no'>NAFTA_SOP_Appendix_B</span> <span class='no'>NAFTA_SOP_Appendix_D</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>2 datasets with observations on the following variables.</p><dl class='dl-horizontal'> @@ -148,7 +149,6 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics @@ -159,7 +159,6 @@ Calculate Representative Half-life Values and Characterizing Pesticide Degradation <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></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: @@ -204,11 +203,8 @@ <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index a0498a31..110ccc86 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -8,11 +8,13 @@ <title>Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • 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="Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment" /> +<meta property="og:title" content="Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment" /> <meta property="og:description" content="Data taken from from Attachment 1 of the SOP." /> <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> @@ -131,18 +133,16 @@ </div> <div class="ref-description"> - <p>Data taken from from Attachment 1 of the SOP.</p> - </div> <pre class="usage"><span class='no'>NAFTA_SOP_Attachment</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable for the evaluation with <code><a href='nafta.html'>nafta</a></code></p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics @@ -153,7 +153,6 @@ Calculate Representative Half-life Values and Characterizing Pesticide Degradation <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</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 half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#> Sums of squares: @@ -198,11 +197,8 @@ <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 6fb806fc..54696ff5 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -236,7 +236,7 @@ machines, cores > 1 is not supported.</p></td> <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</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/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</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'>#> User System verstrichen -#> 50.987 0.008 51.023 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span> +#> 51.646 0.000 51.673 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span> <span class='co'># system.time(ci_profile <- confint(f_d_1, cores = 5))</span> <span class='co'># system.time(ci_profile <- confint(f_d_1,</span> <span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))</span> diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index f35aee5f..18e11261 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -8,11 +8,13 @@ <title>Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • 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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019" /> +<meta property="og:title" content="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019" /> <meta property="og:description" content="The 12 datasets were extracted from active substance evaluation dossiers published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some @@ -67,6 +69,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + <!-- 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> @@ -137,7 +140,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -159,7 +161,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </div> <div class="ref-description"> - <p>The 12 datasets were extracted from active substance evaluation dossiers published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some @@ -189,11 +190,11 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl to one half of the LOD reported to be 1% AR.</p> <p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).</p> - </div> <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, @@ -203,7 +204,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> @@ -225,7 +225,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed Decision of the United Kingdom made to the European Commission under Regulation (EC) No. 1141/2010 for renewal of an active substance</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> @@ -264,11 +263,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/index.html b/docs/reference/index.html index 8987db96..4279f6de 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -255,9 +255,9 @@ of an mmkin object</p></td> </tr><tr> <td> - <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> </p> + <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p> </td> - <td><p>Calculated the AIC for a column of an mmkin object</p></td> + <td><p>Calculate the AIC for a column of an mmkin object</p></td> </tr> </tbody><tbody> <tr> @@ -448,6 +448,12 @@ kinetic models fitted with mkinfit</p></td> </tr><tr> <td> + <p><code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Number of observations on which an mkinfit object was fitted</p></td> + </tr><tr> + + <td> <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p> </td> <td><p>Function to plot residuals stored in an mkin object</p></td> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex b9a42571..5b70455c 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 91c55a6a..ce2d40cd 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -8,11 +8,13 @@ <title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • 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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> +<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> <meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts." /> @@ -41,6 +43,7 @@ + <!-- 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> @@ -133,15 +135,14 @@ </div> <div class="ref-description"> - <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts.</p> - </div> <pre class="usage"><span class='no'>mccall81_245T</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing the following variables.</p><dl class='dl-horizontal'> @@ -156,12 +157,10 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</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_SFO</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='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'>"phenol"</span>), @@ -228,11 +227,8 @@ <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index c72d1cd0..7ee73f15 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -402,15 +402,15 @@ estimators.</p> <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: Thu Oct 31 01:48:29 2019 -#> Date of summary: Thu Oct 31 01:48:29 2019 +#> Date of fit: Fri Nov 1 10:08:21 2019 +#> Date of summary: Fri Nov 1 10:08:21 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 0.455 s +#> Fitted using 222 model solutions performed in 0.456 s #> #> Error model: Constant variance #> @@ -482,7 +482,7 @@ estimators.</p> <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 -#> 1.464 0.000 1.465 </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 +#> 1.488 0.000 1.491 </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 #> @@ -555,7 +555,7 @@ estimators.</p> #> 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 -#> 1.047 0.000 1.047 </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 +#> 1.058 0.000 1.059 </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 #> @@ -591,8 +591,8 @@ estimators.</p> <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: Thu Oct 31 01:48:44 2019 -#> Date of summary: Thu Oct 31 01:48:44 2019 +#> Date of fit: Fri Nov 1 10:08:36 2019 +#> Date of summary: Fri Nov 1 10:08:36 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -600,7 +600,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.136 s +#> Fitted using 421 model solutions performed in 1.083 s #> #> Error model: Constant variance #> @@ -708,8 +708,8 @@ estimators.</p> #> 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: Thu Oct 31 01:48:47 2019 -#> Date of summary: Thu Oct 31 01:48:47 2019 +#> Date of fit: Fri Nov 1 10:08:39 2019 +#> Date of summary: Fri Nov 1 10:08:39 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -717,7 +717,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 978 model solutions performed in 2.512 s +#> Fitted using 978 model solutions performed in 2.553 s #> #> Error model: Variance unique to each observed variable #> @@ -840,8 +840,8 @@ estimators.</p> #> 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: Thu Oct 31 01:48:56 2019 -#> Date of summary: Thu Oct 31 01:48:56 2019 +#> Date of fit: Fri Nov 1 10:08:48 2019 +#> Date of summary: Fri Nov 1 10:08:48 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -849,7 +849,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.124 s +#> Fitted using 2289 model solutions performed in 9.253 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 2eefdc2e..317ffe5f 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -239,7 +239,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <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 file59d942b9ac06.c 2> file59d942b9ac06.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file12cd48616f1.c 2> file12cd48616f1.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f7d543ad..0eca973c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -350,7 +350,7 @@ solver is used.</p></td> <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'>"eigen"</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 -#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>( +#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>( <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</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'>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='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 @@ -360,7 +360,7 @@ solver is used.</p></td> <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 -#> 0.021 0.000 0.021 </div><div class='input'> +#> 0.021 0.000 0.022 </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 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 8312c17c..d1ea7a52 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -202,8 +202,8 @@ for parallel execution.</p></td> <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 -#> 0.011 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'> +#> 0.014 0.024 4.895 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 19.047 0.004 19.063 </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 diff --git a/docs/reference/print.nafta.html b/docs/reference/nobs.mkinfit.html index fa8223ad..1bd97732 100644 --- a/docs/reference/print.nafta.html +++ b/docs/reference/nobs.mkinfit.html @@ -6,13 +6,15 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Print nafta objects — print.nafta • mkin</title> +<title>Number of observations on which an mkinfit object was fitted — nobs.mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/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 +34,14 @@ -<meta property="og:title" content="Print nafta objects — print.nafta" /> -<meta property="og:description" content="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 property="og:title" content="Number of observations on which an mkinfit object was fitted — nobs.mkinfit" /> +<meta property="og:description" content="Number of observations on which an mkinfit object was fitted" /> <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> @@ -68,7 +69,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -111,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -127,50 +127,42 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Print nafta objects</h1> + <h1>Number of observations on which an mkinfit object was fitted</h1> - <div class="hidden name"><code>print.nafta.Rd</code></div> + <div class="hidden name"><code>nobs.mkinfit.Rd</code></div> </div> <div class="ref-description"> - - <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> - + <p>Number of observations on which an mkinfit object was fitted</p> </div> - <pre class="usage"><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> - + <pre class="usage"><span class='co'># S3 method for mkinfit</span> +<span class='fu'><a href='https://rdrr.io/r/stats/nobs.html'>nobs</a></span>(<span class='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> <tr> - <th>x</th> - <td><p>An <code><a href='nafta.html'>nafta</a></code> object.</p></td> - </tr> - <tr> - <th>quiet</th> - <td><p>Should the evaluation text be shown?</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to be used for printing parameters and dissipation times.</p></td> + <th>object</th> + <td><p>An mkinfit object</p></td> </tr> <tr> <th>...</th> - <td><p>Not used.</p></td> + <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>The number of rows in the data included in the mkinfit object</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> - </ul> + <li><a href="#value">Value</a></li> + </ul> </div> </div> diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differdeleted file mode 100644 index ad2ffa8c..00000000 --- a/docs/reference/plot.mkinfit-6.png +++ /dev/null diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 13d96256..44037bb4 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c6635409..27b19430 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -8,11 +8,13 @@ <title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/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 --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> +<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> <meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the software quality of KinGUI in the original publication (Schäfer et al., 2007). The results from the fitting are also included." /> @@ -41,6 +43,7 @@ + <!-- 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> @@ -133,15 +135,14 @@ </div> <div class="ref-description"> - <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the software quality of KinGUI in the original publication (Schäfer et al., 2007). The results from the fitting are also included.</p> - </div> <pre class="usage"><span class='no'>schaefer07_complex_case</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl class='dl-horizontal'> @@ -153,14 +154,12 @@ <dt><code>A2</code></dt><dd><p>a numeric vector</p></dd> </dl><p>The results are a data frame with 14 results for different parameter values</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) @@ -206,11 +205,8 @@ <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="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 65bc6326..fb3c43ef 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -225,15 +225,15 @@ distribution</p></td> <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: Fri Oct 25 02:09:45 2019 -#> Date of summary: Fri Oct 25 02:09:45 2019 +#> Date of fit: Fri Nov 1 10:10:07 2019 +#> Date of summary: Fri Nov 1 10:10:07 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.274 s +#> Fitted using 131 model solutions performed in 0.265 s #> #> Error model: Constant variance #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html deleted file mode 100644 index b3da0016..00000000 --- a/docs/reference/synthetic_data_for_UBA.html +++ /dev/null @@ -1,225 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/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 --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> - -<meta property="og:description" content="The 12 datasets were generated using four different models and three different - variance components. The four models are either the SFO or the DFOP model with either - two sequential or two parallel metabolites. -Variance component 'a' is based on a normal distribution with standard deviation of 3, - Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. - Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the - minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 - for the increase of the standard deviation with y. Note that this is a simplified version - of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the - measured values approximates lognormal distribution for high values, whereas we are using - normally distributed error components all along. -Initial concentrations for metabolites and all values where adding the variance component resulted - in a value below the assumed limit of detection of 0.1 were set to NA. -As an example, the first dataset has the title SFO_lin_a and is based on the SFO model - with two sequential metabolites (linear pathway), with added variance component 'a'. -Compare also the code in the example section to see the degradation models." /> -<meta name="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> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../reference/index.html">Functions and data</a> -</li> -<li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> - Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"> - <li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </ul> -</li> -<li> - <a href="../news/index.html">News</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Synthetic datasets for one parent compound with two metabolites</h1> - - <div class="hidden name"><code>synthetic_data_for_UBA.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>The 12 datasets were generated using four different models and three different - variance components. The four models are either the SFO or the DFOP model with either - two sequential or two parallel metabolites.</p> -<p>Variance component 'a' is based on a normal distribution with standard deviation of 3, - Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. - Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the - minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 - for the increase of the standard deviation with y. Note that this is a simplified version - of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the - measured values approximates lognormal distribution for high values, whereas we are using - normally distributed error components all along.</p> -<p>Initial concentrations for metabolites and all values where adding the variance component resulted - in a value below the assumed limit of detection of 0.1 were set to <code>NA</code>.</p> -<p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model - with two sequential metabolites (linear pathway), with added variance component 'a'.</p> -<p>Compare also the code in the example section to see the degradation models.</p> - - </div> - - <pre class="usage"><span class='no'>synthetic_data_for_UBA_2014</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl class='dl-horizontal'> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> - -</dl> - - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative - zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> -<p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for - measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"></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="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> -</div> - - </footer> - </div> - - - - - </body> -</html> - - diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index eb5b8c65..6ac7403a 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -282,8 +282,8 @@ Compare also the code in the example section to see the degradation models." /> <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/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 22:49:25 2019 -#> Date of summary: Mon Oct 21 22:49:25 2019 +#> Date of fit: Fri Nov 1 10:10:17 2019 +#> Date of summary: Fri Nov 1 10:10:17 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -292,7 +292,7 @@ Compare also the code in the example section to see the degradation models." /> #> #> Model predictions using solution type deSolve #> -#> Fitted using 847 model solutions performed in 2.43 s +#> Fitted using 847 model solutions performed in 2.468 s #> #> Error model: Constant variance #> diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex fc05f896..51b38eda 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex b0dfdd5a..a40f7553 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 5c1a3bed..0040c331 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -8,11 +8,13 @@ <title>Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • 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="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> +<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> <meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014)." /> <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 +134,13 @@ </div> <div class="ref-description"> - <p>The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014).</p> - </div> <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>. @@ -149,12 +150,10 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</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> @@ -222,11 +221,8 @@ <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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index b4040a1b..b9f6f9a9 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -264,7 +264,7 @@ remove arguments given in the original call</p></td> #> #> $time #> User System verstrichen -#> 10.314 0.000 10.320 +#> 10.251 0.000 10.257 #> #> $mkinmod #> <mkinmod> model generated with @@ -413,8 +413,8 @@ remove arguments given in the original call</p></td> #> $rss #> function (P) #> cost_function(P, OLS = TRUE, update_data = FALSE) -#> <bytecode: 0x555557c557c8> -#> <environment: 0x55555bb0e330> +#> <bytecode: 0x555558e48258> +#> <environment: 0x55555caa08e0> #> #> $ll #> function (P, fixed_degparms = FALSE, fixed_errparms = FALSE) @@ -422,8 +422,8 @@ remove arguments given in the original call</p></td> #> -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms, #> fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE) #> } -#> <bytecode: 0x555557c55bf0> -#> <environment: 0x55555bb0e330> +#> <bytecode: 0x555558e47e30> +#> <environment: 0x55555caa08e0> #> #> $start #> value type @@ -500,7 +500,7 @@ remove arguments given in the original call</p></td> #> [1] 12 #> #> $date -#> [1] "Thu Oct 31 01:49:09 2019" +#> [1] "Fri Nov 1 10:10:42 2019" #> #> $version #> [1] "0.9.49.6" |
