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Diffstat (limited to 'docs/reference')
54 files changed, 1739 insertions, 1014 deletions
diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png Binary files differnew file mode 100644 index 00000000..91efcebb --- /dev/null +++ b/docs/reference/DFOP.solution-2.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3422c206..5c90809c 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>DFOP.solution. mkin</title> +<title> + — DFOP.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing decline from a defined starting value using the sum of two exponential decline functions.</p> @@ -84,7 +86,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -100,31 +102,49 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</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 + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='DFOP.solution-2.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index b513fac1..ee86854a 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>[.mmkin. mkin</title> +<title>Subsetting method for mmkin objects — [.mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1>Subsetting method for mmkin objects</h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Subsetting method for mmkin objects</h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Subsetting method for mmkin objects.</p> @@ -83,10 +84,10 @@ <pre># S3 method for mmkin [(x, i, j, ..., drop = FALSE)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> - <dd>An <code>mmkin object</code></dd> + <dd>An <code><a href='mmkin.html'>mmkin</a> object</code></dd> <dt>i</dt> <dd>Row index selecting the fits for specific models</dd> <dt>j</dt> @@ -98,15 +99,17 @@ a list of mkinfit objects or a single mkinfit object.</dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>An object of class <code>mmkin</code>.</p> - </div> + <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span> - <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</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='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</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 @@ -192,7 +195,7 @@ #> #> $time #> user system elapsed -#> 0.252 0.000 0.253 +#> 0.268 0.000 0.264 #> #> $mkinmod #> <mkinmod> model generated with @@ -378,7 +381,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3e9c368> +#> <environment: 0x49c37f0> #> #> $cost_notrans #> function (P) @@ -400,7 +403,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3e9c368> +#> <environment: 0x49c37f0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -466,7 +469,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Oct 6 10:47:28 2016" +#> [1] "Wed Oct 26 23:16:41 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -547,7 +550,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.067 +#> 0.072 0.004 0.074 #> #> $mkinmod #> <mkinmod> model generated with @@ -734,7 +737,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $cost_notrans #> function (P) @@ -756,7 +759,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -819,7 +822,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 10:47:28 2016" +#> [1] "Wed Oct 26 23:16:41 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -896,7 +899,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.067 +#> 0.072 0.004 0.074 #> #> $mkinmod #> <mkinmod> model generated with @@ -1083,7 +1086,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $cost_notrans #> function (P) @@ -1105,7 +1108,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3c1a660> +#> <environment: 0x4ae0880> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1168,14 +1171,23 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 10:47:28 2016" +#> [1] "Wed Oct 26 23:16:41 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" #> #> </div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -1184,7 +1196,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 5c0faa43..61871ba9 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_DFOP_ref_A_to_B. mkin</title> +<title> + — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -101,27 +102,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 89faecbf..4fdb5f45 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_FOMC_ref_A_to_F. mkin</title> +<title> + — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -100,27 +101,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 2dfafec6..d9e43f4a 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_HS_ref_A_to_F. mkin</title> +<title> + — FOCUS_2006_HS_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -101,27 +102,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> 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 ed3a4aff..68475b64 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_SFO_ref_A_to_F. mkin</title> +<title> + — FOCUS_2006_SFO_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.</p> <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A data frame containing the following variables. + <p>A data frame containing the following variables. <dl class='dl-horizontal'> <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> @@ -99,27 +100,45 @@ in this fit.</p> <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c1eacbd8..6221f53f 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOCUS_2006_datasets. mkin</title> +<title> + — FOCUS_2006_datasets • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,44 +68,45 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Data taken from FOCUS (2006), p. 258.</p> <pre><span class='no'>FOCUS_2006_datasets</span></pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>6 datasets with observations on the following variables. + <p>6 datasets with observations on the following variables. <dl class='dl-horizontal'> <dt><code>name</code></dt><dd>a factor containing the name of the observed variable</dd> <dt><code>time</code></dt><dd>a numeric vector containing time points</dd> <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <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 #> 1 parent 0 85.1 #> 2 parent 1 57.9 @@ -117,12 +119,29 @@ #> 9 parent 119 0.6 #> </div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png Binary files differnew file mode 100644 index 00000000..0efe8f07 --- /dev/null +++ b/docs/reference/FOMC.solution-2.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 912cf414..99d95fcb 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>FOMC.solution. mkin</title> +<title> First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> First-Order Multi-Compartment kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> First-Order Multi-Compartment kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing exponential decline from a defined starting value, with a decreasing rate constant.</p> @@ -87,7 +88,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -103,43 +104,61 @@ </dd> </dl> - <div class="Note"> - <h2>Note</h2> + <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>SFO.solution</code> for large values of <code>alpha</code> and + <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> - </div> - - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</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 + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A + <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> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='FOMC.solution-2.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <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="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png Binary files differnew file mode 100644 index 00000000..0bdb37a9 --- /dev/null +++ b/docs/reference/HS.solution-2.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 994f8373..06c6e3c1 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>HS.solution. mkin</title> +<title> Hockey-Stick kinetics — HS.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Hockey-Stick kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Hockey-Stick kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing two exponential decline functions with a break point between them.</p> @@ -83,7 +84,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -99,31 +100,49 @@ according to <code>k2</code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</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 + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='HS.solution-2.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png Binary files differnew file mode 100644 index 00000000..df268b64 --- /dev/null +++ b/docs/reference/IORE.solution-2.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 06f5c1ad..58546489 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>IORE.solution. mkin</title> +<title> Indeterminate order rate equation kinetics — IORE.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Indeterminate order rate equation kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Indeterminate order rate equation kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing exponential decline from a defined starting value, with a concentration dependent rate constant.</p> @@ -83,7 +84,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -95,53 +96,71 @@ <dd> Exponent describing the nonlinearity of the rate equation </dd> </dl> - <div class="Note"> - <h2>Note</h2> + <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>SFO.solution</code> if N = 1. + <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> - </div> - - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</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>NAFTA Technical Working Group on Pesticides (not dated) Guidance for + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='fu'>plot</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'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>fit.fomc</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='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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'>mkinfit</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>) + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='IORE.solution-2.png' alt='' width='540' height='400' /><div class='input'> <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>) <span class='fu'>print</span>(<span class='fu'>data.frame</span>(<span class='fu'>coef</span>(<span class='no'>fit.fomc</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore.deS</span>), <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS. #> model par 1 85.87489063 85.874891 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 #> model par 3 0.65096665 1.949403 1.949403 -#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, - <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back +#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, + <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 #> iore.deS 1.785233 15.1479 4.559973 #> </div></pre> </div> - <div class="col-md-3"> + <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="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 9cf069d7..b2d5526e 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>SFO.solution. mkin</title> +<title> Single First-Order kinetics — SFO.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,22 +67,23 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Single First-Order kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Single First-Order kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function describing exponential decline from a defined starting value.</p> <pre><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -92,31 +93,49 @@ <dd> Kinetic constant. </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>The value of the response variable at time <code>t</code>.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="References"> - <h2>References</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 + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 57959f26..135edb51 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>SFORB.solution. mkin</title> +<title> Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,15 +67,16 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Single First-Order Reversible Binding kinetics </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Single First-Order Reversible Binding kinetics </h1> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -86,7 +87,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>t</dt> <dd> Time. </dd> @@ -100,32 +101,50 @@ <dd> Kinetic constant describing degradation of the free fraction. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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 + <p>The value of the response variable, which is the sum of free and bound fractions at time <code>t</code>.</p> - </div> - - <div class="References"> - <h2>References</h2> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png Binary files differnew file mode 100644 index 00000000..f3d04134 --- /dev/null +++ b/docs/reference/add_err-4.png diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png Binary files differnew file mode 100644 index 00000000..05b27247 --- /dev/null +++ b/docs/reference/add_err-6.png diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png Binary files differnew file mode 100644 index 00000000..b0182d2a --- /dev/null +++ b/docs/reference/add_err-8.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index cbc925ca..9020a486 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>add_err. mkin</title> +<title> + — add_err • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,19 +68,20 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Normally distributed errors are added to data predicted for a specific - degradation model using <code>mkinpredict</code>. The variance of the error + degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error may depend on the predicted value and is specified as a standard deviation.</p> @@ -87,11 +89,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>prediction</dt> <dd> - A prediction from a kinetic model as produced by <code>mkinpredict</code>. + A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></code>. </dd> <dt>sdfunc</dt> <dd> @@ -123,31 +125,31 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list of datasets compatible with <code>mmkin</code>, i.e. + <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>mkinfit</code>.</p> - </div> - - <div class="References"> - <h2>References</h2> + <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 + <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> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># The kinetic model</span> -<span class='no'>m_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'>M1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'># Generate a prediction for a specific set of parameters</span> <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) <span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span> <span class='co'># from 2015</span> -<span class='no'>d_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinpredict</span>(<span class='no'>m_SFO_SFO</span>, +<span class='no'>d_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='fl'>1000</span>), <span class='fu'>c</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>), @@ -165,21 +167,32 @@ <span class='co'># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span> <span class='co'># are easy and examples are run often. Use only one core not to offend CRAN</span> <span class='co'># checks</span> -<span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>), +<span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>), <span class='no'>d_SFO_SFO_err</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='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) -<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><img src='add_err-4.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># We would like to inspect the fit for dataset 3 more closely</span> <span class='co'># Using double brackets makes the returned object an mkinfit object</span> <span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span> -<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='unknown-6.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='add_err-6.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># If we use single brackets, we should give two indices (model and dataset),</span> <span class='co'># and plot.mmkin is used</span> -<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><img src='unknown-8.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><img src='add_err-8.png' alt='' width='540' height='400' /><div class='input'> </div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -188,7 +201,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 8ceb39d9..89e9cf52 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>endpoints. mkin</title> +<title> + — endpoints • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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, @@ -86,27 +88,34 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <pre><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>fit</dt> <dd> - An object of class <code>mkinfit</code>. + An object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> </dl> - <div class="Note"> - <h2>Note</h2> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The function is used internally by <code>summary.mkinfit</code>.</p> - </div> + <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> + - <div class="Value"> - <h2>Value</h2> + </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> + </ul> - <p>A list with the components mentioned above.</p> - </div> - </div> - <div class="col-md-3"> <h2>Author</h2> Johannes Ranke @@ -115,7 +124,14 @@ with the advantage that the SFORB model can also be used for metabolites.</p> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 1d9a9e66..793d893c 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>geometric_mean. mkin</title> +<title> Calculate the geometric mean — geometric_mean • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,22 +67,23 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> Calculate the geometric mean </h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> Calculate the geometric mean </h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>Function calculating the geometric mean of numeric vectors</p> <pre><span class='fu'>geometric_mean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> A numeric vector </dd> @@ -90,24 +91,42 @@ <dd> Should NA values be ignored </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The geometric mean.</p> - </div> + <p>The geometric mean.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3 #> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA #> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051 #> </div></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 355cbb78..d249101d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>ilr. mkin</title> +<title> + — ilr • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This implementation is a special case of the class of isometric log-ratio transformations.</p> @@ -84,7 +86,7 @@ <pre><span class='fu'>ilr</span>(<span class='no'>x</span>) <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> @@ -93,26 +95,24 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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 + <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> - </div> - - <div class="References"> - <h2>References</h2> - - <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> - </div> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <div class="See also"> - <h2>See also</h2> + <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Another implementation can be found in R package <code>robCompositions</code>.</p> - </div> + <p>Another implementation can be found in R package <code>robCompositions</code>.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'># Order matters</span> <span class='fu'>ilr</span>(<span class='fu'>c</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'>c</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 @@ -135,7 +135,20 @@ #> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</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> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> René Lehmann and Johannes Ranke @@ -144,7 +157,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 869f61dd..60d11171 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function reference. mkin</title> +<title>Function reference • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-index"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,43 +67,61 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1>Function reference <small>version 0.9.44.9000</small></h1> -</div> - -<div class="row"> + <div class="row"> <div class="col-md-9"> - <div class="section "> - <h2>Main functions</h2> + <div class="page-header"> + <h1>Function reference</h1> + <h4>version 0.9.44.9000</h4> + </div> + + <div class="contents"> + <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2> <p class="section-desc"><p>Essential functionality</p></p> - <dl class="dl-horizontal"> - <dt><a href="mkinfit.html">mkinfit</a></dt> - <dd> -</dd> - <dt><a href="mkinmod.html">mkinmod</a></dt> - <dd> -</dd> - <dt><a href="mmkin.html">mmkin</a></dt> - <dd> -</dd> - </dl> - </div> - <div class="section "> - <h2>Show results</h2> + <p><a href="mkinfit.html"> +</a></p> + <ul> + <li><code><a href="mkinfit.html">mkinfit</a></code></li> + </ul> + <p><a href="mkinmod.html"> +</a></p> + <ul> + <li><code><a href="mkinmod.html">mkinmod</a></code></li> + </ul> + <p><a href="mmkin.html"> +</a></p> + <ul> + <li><code><a href="mmkin.html">mmkin</a></code></li> + </ul> + <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> <p class="section-desc"></p> - <dl class="dl-horizontal"> - </dl> + </div> </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="#section-main-functions">Main functions</a></li> + <li><a href="#section-show-results">Show results</a></li> + </ul> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 63635f9a..7a96be3b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mccall81_245T. mkin</title> +<title> + — mccall81_245T • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -85,31 +87,31 @@ <pre><span class='no'>mccall81_245T</span></pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A dataframe containing the following variables. + <p>A dataframe containing the following variables. <dl class='dl-horizontal'> <dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using - <code>mkinmod</code>.</dd> + <code><a href='mkinmod.html'>mkinmod</a></code>.</dd> <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after treatment</dd> <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd> <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <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 + <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> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</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>), + + <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'>list</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>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</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'>"anisole"</span>), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> @@ -117,13 +119,13 @@ <span class='co'># </span> <span class='co'>## ---------------------------------------------</span> <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span> - <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), + <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:34 2016 -#> Date of summary: Thu Oct 6 10:47:34 2016 +#> Date of fit: Wed Oct 26 23:16:47 2016 +#> Date of summary: Wed Oct 26 23:16:47 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +135,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.492 s +#> Fitted with method Port using 246 model solutions performed in 1.487 s #> #> Weighting: none #> @@ -216,12 +218,29 @@ #> anisole 103.784 344.763 #> </div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 5b1a8353..d8b616c2 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkin_long_to_wide. mkin</title> +<title> + — mkin_long_to_wide • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function takes a dataframe in the long form as required by <code>modCost</code> and converts it into a dataframe with one independent variable and several @@ -85,7 +87,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>long_data</dt> <dd> @@ -103,13 +105,15 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Dataframe in wide format.</p> - </div> + <p>Dataframe in wide format.</p> - <h2 id="examples">Examples</h2> + + <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 #> 1 0 99.46 0.00 #> 2 0 102.04 0.00 @@ -135,7 +139,16 @@ #> 22 120 NA 33.31 #> </div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -144,7 +157,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 2a70ebbe..31207861 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkin_wide_to_long. mkin</title> +<title> + — mkin_wide_to_long • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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>modCost</code>.</p> @@ -84,7 +86,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>wide_data</dt> <dd> @@ -97,13 +99,15 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Dataframe in long format as needed for <code>modCost</code>.</p> - </div> + <p>Dataframe in long format as needed for <code>modCost</code>.</p> - <h2 id="examples">Examples</h2> + + <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'>data.frame</span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'>c</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'>c</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'>c</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 @@ -114,7 +118,16 @@ #> 6 y 3 5 #> </div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -123,7 +136,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 0b4341aa..45cc315f 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -6,14 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinds. mkin</title> +<title>A dataset class for mkin — mkinds • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +21,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +34,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +55,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,52 +67,70 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1>A dataset class for mkin</h1> -</div> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>A dataset class for mkin</h1> + </div> -<div class="row"> - <div class="col-md-9"> <p>A dataset class for mkin</p> <pre><span class='no'>mkinds</span></pre> - <div class="Format"> - <h2>Format</h2> - - <p>An <code>R6Class</code> generator object.</p> - </div> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <div class="Fields"> - <h2>Fields</h2> + <p>An <code>R6Class</code> generator object.</p> + + <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> - <p></p> - <p><dl class='dl-horizontal'> + <p></p> + <p><dl class='dl-horizontal'> <dt><code>title</code></dt><dd>A full title for the dataset</dd></p> - <p><dt><code>sampling</code></dt><dd>times The sampling times</dd></p> - <p><dt><code>time_unit</code></dt><dd>The time unit</dd></p> - <p><dt><code>observed</code></dt><dd>Names of the observed compounds</dd></p> - <p><dt><code>unit</code></dt><dd>The unit of the observations</dd></p> - <p><dt><code>replicates</code></dt><dd>The number of replicates</dd></p> - <p><dt><code>data</code></dt><dd>A dataframe with at least the columns name, time and value + <p><dt><code>sampling</code></dt><dd>times The sampling times</dd></p> + <p><dt><code>time_unit</code></dt><dd>The time unit</dd></p> + <p><dt><code>observed</code></dt><dd>Names of the observed compounds</dd></p> + <p><dt><code>unit</code></dt><dd>The unit of the observations</dd></p> + <p><dt><code>replicates</code></dt><dd>The number of replicates</dd></p> + <p><dt><code>data</code></dt><dd>A dataframe with at least the columns name, time and value in order to be compatible with mkinfit</dd> </dl></p> - </div> - <h2 id="examples">Examples</h2> + + <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> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index cd9faf1a..2e1833da 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinerrmin. mkin</title> +<title> + — mkinerrmin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function uses <code>optimize</code> in order to iteratively find the smallest relative error still resulting in passing the chi-squared test @@ -85,11 +87,11 @@ as defined in the FOCUS kinetics report from 2006.</p> <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>fit</dt> <dd> - an object of class <code>mkinfit</code>. + an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>alpha</dt> <dd> @@ -97,52 +99,70 @@ as defined in the FOCUS kinetics report from 2006.</p> </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A dataframe with the following components:</p> - <p>The dataframe has one row for the total dataset and one further row for + <p>A dataframe with the following components:</p> + <p>The dataframe has one row for the total dataset and one further row for each observed state variable in the model.</p> - </div> - - <div class="Details"> - <h2>Details</h2> - - <p>This function is used internally by <code>summary.mkinfit</code>.</p> - </div> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <div class="References"> - <h2>References</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 + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><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'>list</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>), + + <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'>list</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'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> -<span class='no'>fit_FOCUS_D</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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<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>) <span class='fu'>round</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 #> All data 0.0640 4 15 #> parent 0.0646 2 7 #> m1 0.0469 2 8 -#> </div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +#> </div><div class='input'><span class='no'>fit_FOCUS_E</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_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.1544 4 13 #> parent 0.1659 2 7 #> m1 0.1095 2 6 #> </div></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7acbbe5a..3c9bd05c 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinfit. mkin</title> +<title> + — mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function uses the Flexible Modelling Environment package <code>FME</code> to create a function calculating the model cost, i.e. the @@ -86,7 +88,7 @@ Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators. In each step of the optimsation, the kinetic model is solved using the - function <code>mkinpredict</code>. The variance of the residuals for each + function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the residuals for each observed variable can optionally be iteratively reweighted until convergence using the argument <code>reweight.method = "obs"</code>.</p> @@ -111,11 +113,11 @@ <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> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>mkinmod</dt> <dd> - A list of class <code>mkinmod</code>, containing the kinetic model to be + 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"). If a shorthand name is given, a parent only degradation model is generated for the variable with the highest value in @@ -151,7 +153,7 @@ 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>mkinmod</code>). The default is to set + (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. @@ -187,18 +189,18 @@ otherwise "eigen" if the model can be expressed using eigenvalues and eigenvectors, and finally "deSolve" for the remaining models (time dependence of degradation rates and metabolites). This argument is passed - on to the helper function <code>mkinpredict</code>. + on to the helper function <code><a href='mkinpredict.html'>mkinpredict</a></code>. </dd> <dt>method.ode</dt> <dd> - The solution method passed via <code>mkinpredict</code> to + 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. </dd> <dt>use_compiled</dt> <dd> - If set to <code>FALSE</code>, no compiled version of the <code>mkinmod</code> - model is used, in the calls to <code>mkinpredict</code> even if + 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 verion is present. </dd> <dt>method.modFit</dt> @@ -251,7 +253,7 @@ 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>ilr</code> transformation. + <code><a href='ilr.html'>ilr</a></code> transformation. </dd> <dt>plot</dt> <dd> @@ -290,7 +292,7 @@ <dt>n.outtimes</dt> <dd> The length of the dataseries that is produced by the model prediction - function <code>mkinpredict</code>. This impacts the accuracy of + 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. </dd> @@ -324,54 +326,50 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by <code>summary.mkinfit</code>.</p> - </div> - - <div class="See also"> - <h2>See also</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Plotting methods <code>plot.mkinfit</code> and - <code>mkinparplot</code>.</p> - <p>Fitting of several models to several datasets in a single call to - <code>mmkin</code>.</p> - </div> + <p>A list with "mkinfit" and "modFit" 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> - <div class="Note"> - <h2>Note</h2> + <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and + <code><a href='mkinparplot.html'>mkinparplot</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> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>The implementation of iteratively reweighted least squares is inspired by the + <p>The implementation of iteratively reweighted least squares is inspired by the work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei Gao). A similar implemention can also be found in CAKE 2.0, which is the other GUI derivative of mkin, sponsored by Syngenta.</p> - </div> - - <div class="Note"> - <h2>Note</h2> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - <p>When using the "IORE" submodel for metabolites, fitting with + <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> - </div> - <h2 id="examples">Examples</h2> + + <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> <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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:36 2016 -#> Date of summary: Thu Oct 6 10:47:36 2016 +#> Date of fit: Wed Oct 26 23:16:49 2016 +#> Date of summary: Wed Oct 26 23:16:49 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.152 s +#> Fitted with method Port using 64 model solutions performed in 0.148 s #> #> Weighting: none #> @@ -436,15 +434,15 @@ #> </div><div class='input'> <span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> -<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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</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'>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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</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'>#> user system elapsed -#> 1.240 1.280 0.973 +#> 1.224 1.196 0.913 #> </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 -#> </div><div class='input'><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> </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 #> @@ -514,7 +512,22 @@ <span class='co'># summary(f.w.man.irls)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <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="#note">Note</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -523,7 +536,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 9dd8fca0..53c87e92 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinmod. mkin</title> +<title> + — mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -89,7 +91,7 @@ <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>...</dt> <dd> @@ -131,41 +133,39 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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>mkinfit</code>, containing</p> - </div> - - <div class="Note"> - <h2>Note</h2> + <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing</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, + <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>mkinfit</code>.</p> - </div> - - <div class="References"> - <h2>References</h2> + <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 + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> - </div> - <h2 id="examples">Examples</h2> + + <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> <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'>list</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> <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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> + <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> <span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> <span class='co'># SFO_SFO <- mkinmod(</span> @@ -189,7 +189,20 @@ <span class='co'># quiet = TRUE)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <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="#note">Note</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + <h2>Author</h2> Johannes Ranke @@ -198,7 +211,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png Binary files differnew file mode 100644 index 00000000..77eafd95 --- /dev/null +++ b/docs/reference/mkinparplot-4.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f2fae22d..6d4f2cfd 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinparplot. mkin</title> +<title> + — mkinparplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,45 +68,57 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function plots the confidence intervals for the parameters - fitted using <code>mkinfit</code>.</p> + fitted using <code><a href='mkinfit.html'>mkinfit</a></code>.</p> <pre><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>object</dt> <dd> - A fit represented in an <code>mkinfit</code> object. + A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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> - </div> + <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + + <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'>T245</span> <span class='kw'>=</span> <span class='fu'>list</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='fu'>c</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'>list</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='fu'>c</span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>model</span>, <span class='fu'>subset</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>) -<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /></pre> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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'>subset</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>) +<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -114,7 +127,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 51ca3992..925a6683 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinplot. mkin</title> +<title> + — mkinplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,41 +68,49 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> - <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> + <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>fit</dt> <dd> - an object of class <code>mkinfit</code>. + an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>&#8230;</dt> <dd> - further arguments passed to <code>plot.mkinfit</code>. + further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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> - <p>The function is called for its side effect.</p> - </div> - </div> - <div class="col-md-3"> <h2>Author</h2> Johannes Ranke @@ -110,7 +119,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5b7cdb32..cf04c6b6 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinpredict. mkin</title> +<title> + — mkinpredict • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,19 +68,20 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This function produces a time series for all the observed variables in a - kinetic model as specified by <code>mkinmod</code>, using a specific set of + 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> @@ -87,11 +89,11 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>mkinmod</dt> <dd> - A kinetic model as produced by <code>mkinmod</code>. + A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>. </dd> <dt>odeparms</dt> <dd> @@ -125,7 +127,7 @@ </dd> <dt>use_compiled</dt> <dd> - If set to <code>FALSE</code>, no compiled version of the <code>mkinmod</code> + 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. </dd> <dt>atol</dt> @@ -149,14 +151,16 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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> - </div> + <p>A matrix in the same format as the output of <code>ode</code>.</p> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) + + <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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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 @@ -277,31 +281,40 @@ #> 2001 20 0.2478752 #> </div><div class='input'> <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span> - <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'>list</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='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'>list</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</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'>c</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'>seq</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 elapsed -#> 0.008 0.020 0.004 +#> 0.008 0.024 0.004 #> </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</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'>c</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'>seq</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 #> 201 20 4.978707 27.46227 #> </div><div class='output co'>#> user system elapsed -#> 0.016 0.004 0.003 +#> 0.000 0.020 0.002 #> </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</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'>c</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'>seq</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 elapsed -#> 0.032 0.000 0.034 +#> 0.036 0.000 0.035 #> </div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -310,7 +323,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png Binary files differnew file mode 100644 index 00000000..7dbd7522 --- /dev/null +++ b/docs/reference/mkinresplot-4.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index fb9ab40d..f16dee5d 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinresplot. mkin</title> +<title> + — mkinresplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,20 +68,21 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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>plot.mkinfit</code> + 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> @@ -90,11 +92,11 @@ <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='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>object</dt> <dd> - A fit represented in an <code>mkinfit</code> object. + A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object. </dd> <dt>obs_vars</dt> <dd> @@ -132,24 +134,35 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> - - <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - </div> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <div class="See also"> - <h2>See also</h2> + <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code>mkinplot</code>, for a way to plot the data and the fitted lines of the + <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 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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>) -<span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /></pre> + + <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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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>) +<span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><img src='mkinresplot-4.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -158,7 +171,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 6b079c40..2432e981 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mkinsub. mkin</title> +<title> + — mkinsub • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,29 +68,30 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>This is a convenience function to set up the lists used as arguments for - <code>mkinmod</code>.</p> + <code><a href='mkinmod.html'>mkinmod</a></code>.</p> <pre><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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>submodel</dt> <dd> Character vector of length one to specify the submodel type. See - <code>mkinmod</code> for the list of allowed submodel names. + <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names. </dd> <dt>to</dt> <dd> @@ -110,27 +112,38 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list for use with <code>mkinmod</code>.</p> - </div> + <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - <h2 id="examples">Examples</h2> + + <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> -<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'>list</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'># The same model using mkinsub</span> -<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'># Now supplying full names</span> -<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -139,7 +152,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5b624893..0ad3321c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>mmkin. mkin</title> +<title> + — mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,36 +68,37 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> - <p>This function calls <code>mkinfit</code> on all combinations of models and datasets + <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> <pre><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'>round</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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>models</dt> <dd> Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB"), or an optionally named list of <code>mkinmod</code> + "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> objects. </dd> <dt>datasets</dt> <dd> An optionally named list of datasets suitable as observed data for - <code>mkinfit</code>. + <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>cores</dt> <dd> @@ -110,24 +112,24 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments that will be passed to <code>mkinfit</code>. + Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix of <code>mkinfit</code> objects that can be indexed using the model + <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> - </div> - - <div class="See also"> - <h2>See also</h2> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p><code>[.mmkin</code> for subsetting, <code>plot.mmkin</code> for plotting.</p> - </div> + <p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> <span class='co'># M1 = mkinsub("SFO", "M2"),</span> @@ -161,7 +163,18 @@ <span class='co'># plot(fits.0[1, 1])</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -170,7 +183,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png Binary files differnew file mode 100644 index 00000000..09bb687c --- /dev/null +++ b/docs/reference/plot.mkinfit-10.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differnew file mode 100644 index 00000000..1e90d789 --- /dev/null +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differnew file mode 100644 index 00000000..1dfbbe4c --- /dev/null +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png Binary files differnew file mode 100644 index 00000000..e4ab674a --- /dev/null +++ b/docs/reference/plot.mkinfit-8.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 94aebf63..631ea429 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>plot.mkinfit. mkin</title> +<title> + — plot.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,19 +68,20 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Solves the differential equations with the optimised and fixed parameters - from a previous successful call to <code>mkinfit</code> and plots + 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> @@ -98,7 +100,7 @@ plot(x, fit = x, show_errmin = FALSE, errmin_digits = 3, …) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> @@ -106,7 +108,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </dd> <dt>fit</dt> <dd> - An object of class <code>mkinfit</code>. + An object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>obs_vars</dt> <dd> @@ -194,27 +196,38 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The function is called for its side effect.</p> - </div> + <p>The function is called for its side effect.</p> - <h2 id="examples">Examples</h2> + + <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> <span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span> -<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'>mkinsub</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'>mkinsub</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) -<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='unknown-6.png' alt='' width='540' height='400' /><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='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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) +<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Show the observed variables separately</span> -<span class='fu'>plot</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'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='unknown-8.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</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'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> <span class='fu'>plot</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'>c</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><img src='unknown-10.png' alt='' width='540' height='400' /><div class='input'> + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /><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'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -223,7 +236,14 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differnew file mode 100644 index 00000000..a26e413f --- /dev/null +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differnew file mode 100644 index 00000000..f23ed172 --- /dev/null +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png Binary files differnew file mode 100644 index 00000000..dc24d92f --- /dev/null +++ b/docs/reference/plot.mmkin-6.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 358da679..44ae760f 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>plot.mmkin. mkin</title> +<title> + — plot.mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,18 +68,19 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> - <p>When x is a row selected from an mmkin object (<code>[.mmkin</code>), the same model + <p>When x is a row selected from an mmkin object (<code><a href='[.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> @@ -87,11 +89,11 @@ <span class='fu'>plot</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'>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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> - An object of class <code>mmkin</code>, with either one row or one column. + An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one column. </dd> <dt>main</dt> <dd> @@ -119,27 +121,38 @@ </dd> <dt>&#8230;</dt> <dd> - Further arguments passed to <code>plot.mkinfit</code> and <code>mkinresplot</code>. + Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The function is called for its side effect.</p> - </div> + <p>The function is called for its side effect.</p> - <h2 id="examples">Examples</h2> + + <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 not to offend CRAN checks, use Levenberg-Marquardt for speed</span> - <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</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='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</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='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='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) - <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='unknown-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'> + <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='plot.mmkin-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='plot.mmkin-4.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># We can also plot a single fit, if we like the way mmkin works, but then the plot </span> <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> <span class='co'># generated by staticdocs, as far as I know).</span> - <span class='fu'>plot</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><img src='unknown-6.png' alt='' width='540' height='400' /></pre> + <span class='fu'>plot</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><img src='plot.mmkin-6.png' alt='' width='540' height='400' /></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -148,7 +161,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index dea5f75c..c4bc08d5 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>print.mkinds. mkin</title> +<title> + — print.mkinds • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Print mkinds objects.</p> @@ -84,24 +86,38 @@ <pre><span class='co'># S3 method for mkinds</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> - An <code>mkinds</code> object. + An <code><a href='mkinds.html'>mkinds</a></code> object. </dd> <dt>&#8230;</dt> <dd> Not used. </dd> </dl> - </div> - <div class="col-md-3"> + + + </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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 38663f8f..edc9cde7 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>print.mkinmod. mkin</title> +<title> + — print.mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p> @@ -84,24 +86,38 @@ <pre><span class='co'># S3 method for mkinmod</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>x</dt> <dd> - An <code>mkinmod</code> object. + An <code><a href='mkinmod.html'>mkinmod</a></code> object. </dd> <dt>&#8230;</dt> <dd> Not used. </dd> </dl> - </div> - <div class="col-md-3"> + + + </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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 12776c74..1cd71697 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>schaefer07_complex_case. mkin</title> +<title> + — schaefer07_complex_case • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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). @@ -85,10 +87,9 @@ <pre><span class='fu'>data</span>(<span class='no'>schaefer07_complex_case</span>)</pre> - <div class="Format"> - <h2>Format</h2> + <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>The data set is a data frame with 8 observations on the following 6 variables. <dl class='dl-horizontal'> <dt><code>time</code></dt><dd>a numeric vector</dd> <dt><code>parent</code></dt><dd>a numeric vector</dd> @@ -97,33 +98,51 @@ <dt><code>C1</code></dt><dd>a numeric vector</dd> <dt><code>A2</code></dt><dd>a numeric vector</dd> </dl></p> - <p>The results are a data frame with 14 results for different parameter values</p> - </div> - - <div class="References"> - <h2>References</h2> + <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 + <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'>mkin_wide_to_long</span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) -<span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + + <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>) +<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'>list</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='fu'>c</span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</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'>"A2"</span>), <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> </div> - <div class="col-md-3"> + <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> + </div> </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index acbf36dc..1e1a0e2f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>summary.mkinfit. mkin</title> +<title> + — summary.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <p>Lists model equations, the summary as returned by <code>summary.modFit</code>, the chi2 error levels calculated according to FOCUS guidance (2006) as far @@ -89,11 +91,11 @@ <span class='co'># S3 method for summary.mkinfit</span> <span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> - <h2>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>object</dt> <dd> - an object of class <code>mkinfit</code>. + an object of class <code><a href='mkinfit.html'>mkinfit</a></code>. </dd> <dt>x</dt> <dd> @@ -121,36 +123,36 @@ </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The summary function returns a list derived from + <p>The summary function returns a list derived from <code>summary.modFit</code>, with components, among others</p> - <p>The print method is called for its side effect, i.e. printing the summary.</p> - </div> - - <div class="References"> - <h2>References</h2> + <p>The print method is called for its side effect, i.e. printing the summary.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + <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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000 + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'> <span class='fu'>summary</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:44 2016 -#> Date of summary: Thu Oct 6 10:47:44 2016 +#> Date of fit: Wed Oct 26 23:16:57 2016 +#> Date of summary: Wed Oct 26 23:16:57 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.079 s +#> Fitted with method Port using 35 model solutions performed in 0.089 s #> #> Weighting: none #> @@ -212,7 +214,18 @@ #> 118 parent 0.39 1.351 -0.9613 #> </div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -221,7 +234,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 04550199..b45c07fc 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>synthetic_data_for_UBA_2014. mkin</title> +<title> + — synthetic_data_for_UBA_2014 • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,16 +68,17 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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 @@ -99,28 +101,28 @@ <pre><span class='no'>synthetic_data_for_UBA_2014</span></pre> - <div class="Format"> - <h2>Format</h2> + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>A list containing datasets in the form internally used by the 'gmkin' package. + <p>A list containing datasets in the form internally used by the 'gmkin' package. The list has twelfe components. Each of the components is one dataset that has, among others, the following components <dl class='dl-horizontal'> <dt><code>title</code></dt><dd>The name of the dataset, e.g. <code>SFO_lin_a</code></dd> - <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code>mkinfit</code></dd> + <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></dd> </dl></p> - </div> - - <div class="Source"> - <h2>Source</h2> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + <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 + <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - </div> - <h2 id="examples">Examples</h2> + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> <span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> <span class='co'># M1 = list(type = "SFO", to = "M2"),</span> @@ -144,12 +146,29 @@ <span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <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> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 66253bba..a07be0a0 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,14 +6,14 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>transform_odeparms. mkin</title> +<title> + — transform_odeparms • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> - <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -22,6 +22,7 @@ <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> @@ -34,10 +35,9 @@ </head> <body> - <div class="container"> + <div class="container template-reference-topic"> <header> - -<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -56,6 +56,7 @@ <a href="../reference/index.html">Reference</a> </li> </ul> + <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin"> @@ -67,27 +68,28 @@ </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> + </header> - <div class="page-header"> - <h1> + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> </h1> -</div> + </div> -<div class="row"> - <div class="col-md-9"> <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>ilr</code> transformation is used.</p> + 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>mkinfit</code>.</p> + This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p> <pre><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, @@ -95,7 +97,7 @@ <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>Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <dt>parms</dt> <dd> @@ -107,9 +109,9 @@ </dd> <dt>mkinmod</dt> <dd> - The kinetic model of class <code>mkinmod</code>, containing the names of + 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>ilr</code> transformation, the parameter names and + 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. </dd> <dt>transform_rates</dt> @@ -128,27 +130,29 @@ 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>ilr</code> + transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code> transformation. </dd> </dl> - <div class="Value"> - <h2>Value</h2> + <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 + <p>A vector of transformed or backtransformed parameters with the same names as the original parameters.</p> - </div> - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + + <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'>list</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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'>mkinfit</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='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='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 10:47:45 2016 -#> Date of summary: Thu Oct 6 10:47:45 2016 +#> Date of fit: Wed Oct 26 23:16:59 2016 +#> Date of summary: Wed Oct 26 23:16:59 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -156,7 +160,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.638 s +#> Fitted with method Port using 153 model solutions performed in 0.721 s #> #> Weighting: none #> @@ -259,7 +263,16 @@ <span class='co'># summary(fit.ff.2, data = FALSE)</span> <span class='co'>## ---------------------------------------------</span></div></pre> </div> - <div class="col-md-3"> + <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> + <h2>Author</h2> Johannes Ranke @@ -268,7 +281,14 @@ </div> <footer> - <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + </footer> </div> |
