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-rw-r--r--docs/articles/mkin.html3
-rw-r--r--docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.pngbin113885 -> 113818 bytes
-rw-r--r--docs/news/index.html1
-rw-r--r--docs/reference/AIC.mmkin.html34
-rw-r--r--docs/reference/CAKE_export.html48
-rw-r--r--docs/reference/DFOP.solution.html39
-rw-r--r--docs/reference/Extract.mmkin.html33
-rw-r--r--docs/reference/FOMC.solution.html68
-rw-r--r--docs/reference/HS.solution.html37
-rw-r--r--docs/reference/IORE.solution.html51
-rw-r--r--docs/reference/SFO.solution.html27
-rw-r--r--docs/reference/SFORB.solution.html50
-rw-r--r--docs/reference/add_err-2.pngbin51024 -> 50582 bytes
-rw-r--r--docs/reference/add_err.html65
-rw-r--r--docs/reference/endpoints.html54
-rw-r--r--docs/reference/ilr.html49
-rw-r--r--docs/reference/index.html26
-rw-r--r--docs/reference/logLik.mkinfit.html51
-rw-r--r--docs/reference/logistic.solution-2.pngbin29139 -> 29336 bytes
-rw-r--r--docs/reference/logistic.solution.html44
-rw-r--r--docs/reference/max_twa_parent.html83
-rw-r--r--docs/reference/mkin_long_to_wide.html40
-rw-r--r--docs/reference/mkin_wide_to_long.html36
-rw-r--r--docs/reference/mkinds.html38
-rw-r--r--docs/reference/mkinerrmin.html57
-rw-r--r--docs/reference/mkinerrplot.html53
-rw-r--r--docs/reference/mkinfit.html441
-rw-r--r--docs/reference/mkinmod.html135
-rw-r--r--docs/reference/mkinparplot.html32
-rw-r--r--docs/reference/mkinplot.html22
-rw-r--r--docs/reference/mkinpredict.html107
-rw-r--r--docs/reference/mkinresplot.html72
-rw-r--r--docs/reference/mkinsub.html45
-rw-r--r--docs/reference/mmkin-4.pngbin62975 -> 62550 bytes
-rw-r--r--docs/reference/mmkin.html73
-rw-r--r--docs/reference/nafta.html81
-rw-r--r--docs/reference/plot.mkinfit-4.pngbin43670 -> 59080 bytes
-rw-r--r--docs/reference/plot.mkinfit-5.pngbin59080 -> 65273 bytes
-rw-r--r--docs/reference/plot.mkinfit.html126
-rw-r--r--docs/reference/plot.mmkin-4.pngbin38129 -> 37076 bytes
-rw-r--r--docs/reference/plot.mmkin.html76
-rw-r--r--docs/reference/plot.nafta.html36
-rw-r--r--docs/reference/print.mkinds.html14
-rw-r--r--docs/reference/print.mkinmod.html25
-rw-r--r--docs/reference/sigma_twocomp.html34
-rw-r--r--docs/reference/summary.mkinfit.html124
-rw-r--r--docs/reference/transform_odeparms.html119
-rw-r--r--docs/sitemap.xml3
48 files changed, 1275 insertions, 1277 deletions
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index ec138595..9caabec8 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -90,7 +90,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-09-19</h4>
+ <h4 class="date">2019-10-25</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
@@ -223,6 +223,7 @@
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+
<div id="tocnav">
<h2 class="hasAnchor">
<a href="#tocnav" class="anchor"></a>Contents</h2>
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index 751a79e1..e21b4233 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
Binary files differ
diff --git a/docs/news/index.html b/docs/news/index.html
index 20a71657..67f64150 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -136,7 +136,6 @@
<ul>
<li><p>Move long-running tests to tests/testthat/slow with a separate test log. They currently take around 7 minutes on my system</p></li>
<li><p>‘mkinfit’: Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals</p></li>
-<li><p>‘mkinfit’: The default algorithm for fitting the ‘obs’ error model is now IRLS</p></li>
<li><p>Vignette ‘twa.html’: Add the maximum time weighted average formulas for the hockey stick model</p></li>
<li><p>Support frameless plots (‘frame = FALSE’)</p></li>
<li><p>Support to suppress the chi2 error level (‘show_errmin = FALSE’) in ‘plot.mmkin’</p></li>
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index 2fe02c97..103bcb4a 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -8,11 +8,13 @@
<title>Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Calculated the AIC for a column of an mmkin object — AIC.mmkin" />
-<meta property="og:description" content="Provides a convenient way to compare different kineti models fitted to the
- same dataset." />
+<meta property="og:title" content="Calculated the AIC for a column of an mmkin object — AIC.mmkin" />
+<meta property="og:description" content="Provides a convenient way to compare different kinetic models fitted to the
+same dataset." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,21 +134,20 @@
</div>
<div class="ref-description">
-
- <p>Provides a convenient way to compare different kineti models fitted to the
- same dataset.</p>
-
+ <p>Provides a convenient way to compare different kinetic models fitted to the
+same dataset.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>object</th>
- <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, containing only one column.</p></td>
+ <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, containing only one
+column.</p></td>
</tr>
<tr>
<th>...</th>
@@ -157,15 +158,15 @@
<td><p>As in the generic method</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>As in the generic method (a numeric value for single fits, or a dataframe if
- there are several fits in the column).</p>
-
+ <p>As in the generic method (a numeric value for single fits, or a
+ dataframe if there are several fits in the column).</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># skip, as it takes &gt; 10 s on winbuilder</span>
+ <pre class="examples"><div class='input'>
+ <span class='co'># skip, as it takes &gt; 10 s on winbuilder</span>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>),
<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>,
<span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
@@ -184,15 +185,14 @@
#&gt; SFO 3 59.29336
#&gt; FOMC 4 44.68652
#&gt; DFOP 5 29.02372</div><div class='input'>
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index 52d00ac2..47536237 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -8,11 +8,13 @@
<title>Export a list of datasets format to a CAKE study file — CAKE_export • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Export a list of datasets format to a CAKE study file — CAKE_export" />
-<meta property="og:description" content="In addition to the datasets, the pathways in the degradation
- model can be specified as well." />
+<meta property="og:title" content="Export a list of datasets format to a CAKE study file — CAKE_export" />
+<meta property="og:description" content="In addition to the datasets, the pathways in the degradation model can be
+specified as well." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,46 +134,40 @@
</div>
<div class="ref-description">
-
- <p>In addition to the datasets, the pathways in the degradation
- model can be specified as well.</p>
-
+ <p>In addition to the datasets, the pathways in the degradation model can be
+specified as well.</p>
</div>
- <pre class="usage"><span class='fu'>CAKE_export</span>(<span class='no'>ds</span>, <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>),
- <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <pre class="usage"><span class='fu'>CAKE_export</span>(<span class='no'>ds</span>, <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
<span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"CAKE_export.csf"</span>, <span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>,
- <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>,
- <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>,
- <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>,
- <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>,
- <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(),
+ <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>, <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>,
+ <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>, <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>,
+ <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>, <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(),
<span class='kw'>optimiser</span> <span class='kw'>=</span> <span class='st'>"IRLS"</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>ds</th>
<td><p>A named list of datasets in long format as compatible with
- <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+<code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
</tr>
<tr>
<th>map</th>
<td><p>A character vector with CAKE compartment names (Parent, A1, ...),
- named with the names used in the list of datasets.</p></td>
+named with the names used in the list of datasets.</p></td>
</tr>
<tr>
<th>links</th>
<td><p>An optional character vector of target compartments, named with
- the names of the source compartments. In order to make this
- easier, the names are used as in the datasets supplied.</p></td>
+the names of the source compartments. In order to make this easier, the
+names are used as in the datasets supplied.</p></td>
</tr>
<tr>
<th>filename</th>
- <td><p>Where to write the result. Should end in .csf in order to be compatible
- with CAKE.</p></td>
+ <td><p>Where to write the result. Should end in .csf in order to be
+compatible with CAKE.</p></td>
</tr>
<tr>
<th>path</th>
@@ -210,20 +206,18 @@
<td><p>Can be OLS or IRLS.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The function is called for its side effect.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
<h2>Author</h2>
<p>Johannes Ranke</p>
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index b34d00a1..eef4f902 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -8,11 +8,13 @@
<title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" />
-<meta property="og:description" content="Function describing decline from a defined starting value using the sum
- of two exponential decline functions." />
+<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" />
+<meta property="og:description" content="Function describing decline from a defined starting value using the sum of
+two exponential decline functions." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,14 +134,12 @@
</div>
<div class="ref-description">
-
- <p>Function describing decline from a defined starting value using the sum
- of two exponential decline functions.</p>
-
+ <p>Function describing decline from a defined starting value using the sum of
+two exponential decline functions.</p>
</div>
<pre class="usage"><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -161,36 +161,33 @@
</tr>
<tr>
<th>g</th>
- <td><p>Fraction of the starting value declining according to the
- first kinetic constant.</p></td>
+ <td><p>Fraction of the starting value declining according to the first
+kinetic constant.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The value of the response variable at time <code>t</code>.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div></pre>
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index ae120587..879c1444 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -8,11 +8,13 @@
<title>Subsetting method for mmkin objects — [.mmkin • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,14 @@
-<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
+<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
<meta property="og:description" content="Subsetting method for mmkin objects." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +112,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,14 +133,12 @@
</div>
<div class="ref-description">
-
<p>Subsetting method for mmkin objects.</p>
-
</div>
<pre class="usage"># S3 method for mmkin
[(x, i, j, ..., drop = FALSE)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -160,32 +160,32 @@
</tr>
<tr>
<th>drop</th>
- <td><p>If FALSE, the method always returns an mmkin object, otherwise either
- a list of mkinfit objects or a single mkinfit object.</p></td>
+ <td><p>If FALSE, the method always returns an mmkin object, otherwise
+either a list of mkinfit objects or a single mkinfit object.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
+ <pre class="examples"><div class='input'>
+ <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
<span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>),
<span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt; dataset
#&gt; model B C
-#&gt; FOMC List,39 List,39
+#&gt; FOMC List,40 List,40
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,39
-#&gt; FOMC List,39
+#&gt; SFO List,40
+#&gt; FOMC List,40
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,39
+#&gt; SFO List,40
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(
@@ -210,15 +210,14 @@
#&gt;
#&gt; $message
#&gt; [1] "both X-convergence and relative convergence (5)"
-#&gt; </div></pre>
+#&gt; </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index df05afbd..f44ad713 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -8,11 +8,13 @@
<title>First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,17 +34,15 @@
-<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" />
-<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
- a decreasing rate constant.
-The form given here differs slightly from the original reference by Gustafson
- and Holden (1990). The parameter beta corresponds to 1/beta in the
- original equation." />
+<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" />
+<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+a decreasing rate constant." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -113,7 +113,6 @@ The form given here differs slightly from the original reference by Gustafson
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -135,17 +134,12 @@ The form given here differs slightly from the original reference by Gustafson
</div>
<div class="ref-description">
-
- <p>Function describing exponential decline from a defined starting value, with
- a decreasing rate constant.</p>
-<p>The form given here differs slightly from the original reference by Gustafson
- and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta in the
- original equation.</p>
-
+ <p>Function describing exponential decline from a defined starting value, with
+a decreasing rate constant.</p>
</div>
<pre class="usage"><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -159,52 +153,52 @@ The form given here differs slightly from the original reference by Gustafson
</tr>
<tr>
<th>alpha</th>
- <td><p>Shape parameter determined by coefficient of variation of rate constant
- values.</p></td>
+ <td><p>Shape parameter determined by coefficient of variation of rate
+constant values.</p></td>
</tr>
<tr>
<th>beta</th>
<td><p>Location parameter.</p></td>
</tr>
</table>
-
- <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The solution of the FOMC kinetic model reduces to the
- <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and
- <code>beta</code> with
- \(k = \frac{\beta}{\alpha}\).</p>
-
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The value of the response variable at time <code>t</code>.</p>
-
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The form given here differs slightly from the original reference by
+Gustafson and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta
+in the original equation.</p>
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The solution of the FOMC kinetic model reduces to the
+ <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and
+ <code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-<p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A
- new model based on spatial variability. <em>Environmental Science and
+<p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil:
+ A new model based on spatial variability. <em>Environmental Science and
Technology</em> <b>24</b>, 1032-1038</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div></pre>
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
- <li><a href="#note">Note</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#details">Details</a></li>
+ <li><a href="#note">Note</a></li>
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index b46902c5..82b9324c 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -8,11 +8,13 @@
<title>Hockey-Stick kinetics — HS.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" />
+<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" />
<meta property="og:description" content="Function describing two exponential decline functions with a break point
- between them." />
+between them." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,14 +134,12 @@
</div>
<div class="ref-description">
-
<p>Function describing two exponential decline functions with a break point
- between them.</p>
-
+between them.</p>
</div>
<pre class="usage"><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -161,37 +161,34 @@
</tr>
<tr>
<th>tb</th>
- <td><p>Break point. Before this time, exponential decline according
- to <code>k1</code> is calculated, after this time, exponential decline proceeds
- according to <code>k2</code>.</p></td>
+ <td><p>Break point. Before this time, exponential decline according to
+<code>k1</code> is calculated, after this time, exponential decline proceeds
+according to <code>k2</code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The value of the response variable at time <code>t</code>.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div></pre>
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 082c2f41..6af44ab8 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -8,11 +8,13 @@
<title>Indeterminate order rate equation kinetics — IORE.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" />
-<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
- a concentration dependent rate constant." />
+<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" />
+<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+a concentration dependent rate constant." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,14 +134,12 @@
</div>
<div class="ref-description">
-
- <p>Function describing exponential decline from a defined starting value, with
- a concentration dependent rate constant.</p>
-
+ <p>Function describing exponential decline from a defined starting value, with
+a concentration dependent rate constant.</p>
</div>
<pre class="usage"><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -153,34 +153,32 @@
</tr>
<tr>
<th>k__iore</th>
- <td><p>Rate constant. Note that this depends on the concentration units used.</p></td>
+ <td><p>Rate constant. Note that this depends on the concentration
+units used.</p></td>
</tr>
<tr>
<th>N</th>
<td><p>Exponent describing the nonlinearity of the rate equation</p></td>
</tr>
</table>
-
- <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The solution of the IORE kinetic model reduces to the
- <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1.
- The parameters of the IORE model can be transformed to equivalent parameters
- of the FOMC mode - see the NAFTA guidance for details.</p>
-
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The value of the response variable at time <code>t</code>.</p>
-
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The solution of the IORE kinetic model reduces to the
+ <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1. The parameters of the IORE model can
+ be transformed to equivalent parameters of the FOMC mode - see the NAFTA
+ guidance for details.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
- Evaluating and Calculating Degradation Kinetics in Environmental
- Media</p>
-
+ <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance
+ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># \dontrun{</span>
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># \dontrun{</span>
<span class='no'>fit.fomc</span> <span class='kw'>&lt;-</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'>&lt;-</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'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
@@ -195,19 +193,16 @@
#&gt; fomc 1.785233 15.1479 4.559973
#&gt; iore 1.785233 15.1479 4.559973
#&gt; iore.deS 1.785233 15.1479 4.559973</div><div class='input'> # }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
- <li><a href="#note">Note</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#note">Note</a></li>
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index cb0870a8..55fd61a4 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -8,11 +8,13 @@
<title>Single First-Order kinetics — SFO.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,14 @@
-<meta property="og:title" content="Single First-Order kinetics — SFO.solution" />
+<meta property="og:title" content="Single First-Order kinetics — SFO.solution" />
<meta property="og:description" content="Function describing exponential decline from a defined starting value." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +112,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,13 +133,11 @@
</div>
<div class="ref-description">
-
<p>Function describing exponential decline from a defined starting value.</p>
-
</div>
<pre class="usage"><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -154,32 +154,29 @@
<td><p>Kinetic constant.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The value of the response variable at time <code>t</code>.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div></pre>
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 398f787f..fbf067af 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -8,11 +8,13 @@
<title>Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,17 +34,18 @@
-<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" />
+<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" />
<meta property="og:description" content="Function describing the solution of the differential equations describing
- the kinetic model with first-order terms for a two-way transfer from a free
- to a bound fraction, and a first-order degradation term for the free
- fraction. The initial condition is a defined amount in the free fraction and
- no substance in the bound fraction." />
+the kinetic model with first-order terms for a two-way transfer from a free
+to a bound fraction, and a first-order degradation term for the free
+fraction. The initial condition is a defined amount in the free fraction
+and no substance in the bound fraction." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -113,7 +116,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -135,17 +137,15 @@
</div>
<div class="ref-description">
-
<p>Function describing the solution of the differential equations describing
- the kinetic model with first-order terms for a two-way transfer from a free
- to a bound fraction, and a first-order degradation term for the free
- fraction. The initial condition is a defined amount in the free fraction and
- no substance in the bound fraction.</p>
-
+the kinetic model with first-order terms for a two-way transfer from a free
+to a bound fraction, and a first-order degradation term for the free
+fraction. The initial condition is a defined amount in the free fraction
+and no substance in the bound fraction.</p>
</div>
<pre class="usage"><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -167,36 +167,34 @@
</tr>
<tr>
<th>k_1output</th>
- <td><p>Kinetic constant describing degradation of the free fraction.</p></td>
+ <td><p>Kinetic constant describing degradation of the free
+fraction.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>The value of the response variable, which is the sum of free and bound
- fractions at time <code>t</code>.</p>
-
+ <p>The value of the response variable, which is the sum of free and
+ bound fractions at time <code>t</code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div></pre>
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png
index df843300..d476bba1 100644
--- a/docs/reference/add_err-2.png
+++ b/docs/reference/add_err-2.png
Binary files differ
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index eeaf9e5b..67789694 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -8,11 +8,13 @@
<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,15 +34,16 @@
-<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" />
+<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" />
<meta property="og:description" content="Normally distributed errors are added to data predicted for a specific
- degradation model using mkinpredict. The variance of the error
- may depend on the predicted value and is specified as a standard deviation." />
+degradation model using mkinpredict. The variance of the error
+may depend on the predicted value and is specified as a standard deviation." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -111,7 +114,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -133,33 +135,32 @@
</div>
<div class="ref-description">
-
<p>Normally distributed errors are added to data predicted for a specific
- degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error
- may depend on the predicted value and is specified as a standard deviation.</p>
-
+degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error
+may depend on the predicted value and is specified as a standard deviation.</p>
</div>
- <pre class="usage"><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>, <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
- <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>,
- <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
-
+ <pre class="usage"><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>, <span class='kw'>secondary</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>,
+ <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>prediction</th>
- <td><p>A prediction from a kinetic model as produced by <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td>
+ <td><p>A prediction from a kinetic model as produced by
+<code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td>
</tr>
<tr>
<th>sdfunc</th>
- <td><p>A function taking the predicted value as its only argument and returning
- a standard deviation that should be used for generating the random error
- terms for this value.</p></td>
+ <td><p>A function taking the predicted value as its only argument and
+returning a standard deviation that should be used for generating the
+random error terms for this value.</p></td>
</tr>
<tr>
<th>secondary</th>
- <td><p>The names of state variables that should have an initial value of zero</p></td>
+ <td><p>The names of state variables that should have an initial
+value of zero</p></td>
</tr>
<tr>
<th>n</th>
@@ -167,8 +168,8 @@
</tr>
<tr>
<th>LOD</th>
- <td><p>The limit of detection (LOD). Values that are below the LOD after adding
- the random error will be set to NA.</p></td>
+ <td><p>The limit of detection (LOD). Values that are below the LOD after
+adding the random error will be set to NA.</p></td>
</tr>
<tr>
<th>reps</th>
@@ -180,25 +181,25 @@
</tr>
<tr>
<th>seed</th>
- <td><p>The seed used for the generation of random numbers. If NA, the seed
- is not set.</p></td>
+ <td><p>The seed used for the generation of random numbers. If NA, the
+seed is not set.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e.
- the components of the list are datasets compatible with
- <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
-
+ <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. the
+ components of the list are datasets compatible with <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy
- http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p>
-
+ <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is
+the question. XV Symposium on Pesticide Chemistry 2-4 September 2015,
+Piacenza, Italy
+http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># The kinetic model</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># The kinetic model</span>
<span class='no'>m_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='co'># Generate a prediction for a specific set of parameters</span>
@@ -235,17 +236,15 @@
<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span>
<span class='co'># and plot.mmkin is used</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index f0abb0b6..e81bdbb5 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -6,13 +6,16 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title>
+<title>Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit — endpoints • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,16 +35,19 @@
-<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" />
-<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
-fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites,
-the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but
-with the advantage that the SFORB model can also be used for metabolites." />
+<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit — endpoints" />
+<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions
+from kinetic models fitted with mkinfit. If the SFORB model was specified
+for one of the parents or metabolites, the Eigenvalues are returned. These
+are equivalent to the rate constantes of the DFOP model, but with the
+advantage that the SFORB model can also be used for metabolites." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -112,7 +118,6 @@ with the advantage that the SFORB model can also be used for metabolites." />
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -128,22 +133,22 @@ with the advantage that the SFORB model can also be used for metabolites." />
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1>
+ <h1>Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit</h1>
<div class="hidden name"><code>endpoints.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
-fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites,
-the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but
-with the advantage that the SFORB model can also be used for metabolites.</p>
-
+ <p>This function calculates DT50 and DT90 values as well as formation fractions
+from kinetic models fitted with mkinfit. If the SFORB model was specified
+for one of the parents or metabolites, the Eigenvalues are returned. These
+are equivalent to the rate constantes of the DFOP model, but with the
+advantage that the SFORB model can also be used for metabolites.</p>
</div>
<pre class="usage"><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -152,18 +157,17 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
<td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
</tr>
</table>
-
- <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
-
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list with the components mentioned above.</p>
-
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <pre class="examples"><div class='input'>
+ <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; logical(0)
#&gt;
@@ -173,17 +177,15 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
#&gt; $distimes
#&gt; DT50 DT90 DT50back
#&gt; parent 1.785233 15.1479 4.559973
-#&gt; </div></pre>
+#&gt; </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
- <li><a href="#note">Note</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#note">Note</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 925698d9..76ce2233 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -8,11 +8,13 @@
<title>Function to perform isometric log-ratio transformation — ilr • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,15 @@
-<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" />
-<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." />
+<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" />
+<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio
+transformations." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,40 +134,41 @@
</div>
<div class="ref-description">
-
- <p>This implementation is a special case of the class of isometric log-ratio transformations.</p>
-
+ <p>This implementation is a special case of the class of isometric log-ratio
+transformations.</p>
</div>
<pre class="usage"><span class='fu'>ilr</span>(<span class='no'>x</span>)
- <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre>
-
+
+<span class='fu'>invilr</span>(<span class='no'>x</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
- <td><p>A numeric vector. Naturally, the forward transformation is only sensible for
- vectors with all elements being greater than zero.</p></td>
+ <td><p>A numeric vector. Naturally, the forward transformation is only
+sensible for vectors with all elements being greater than zero.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>The result of the forward or backward transformation. The returned components always
- sum to 1 for the case of the inverse log-ratio transformation.</p>
-
+ <p>The result of the forward or backward transformation. The returned
+ components always sum to 1 for the case of the inverse log-ratio
+ transformation.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p>
-
+ <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for
+ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <div class='dont-index'><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div>
-
+ <div class='dont-index'><p>Another implementation can be found in R package
+ <code>robCompositions</code>.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># Order matters</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># Order matters</span>
<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#&gt; [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#&gt; [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span>
<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#&gt; [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span>
<span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#&gt; [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span>
@@ -173,19 +177,16 @@
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='fu'>invilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#&gt; [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>)
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#&gt; [1] 4</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#&gt; [1] 0.1 0.3 0.5</div></pre>
+<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#&gt; [1] 4</div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#&gt; [1] 0.1 0.3 0.5</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#see-also">See also</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 17a879a9..328f5aca 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -160,11 +160,12 @@
<td>
<p><code><a href="mmkin.html">mmkin()</a></code> </p>
</td>
- <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td>
+ <td><p>Fit one or more kinetic models with one or more state variables to one or
+more datasets</p></td>
</tr><tr>
<td>
- <p><code><a href="nafta.html">nafta()</a></code> </p>
+ <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i>&lt;nafta&gt;</i>)</a></code> </p>
</td>
<td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
</tr>
@@ -210,7 +211,8 @@
<td>
<p><code><a href="endpoints.html">endpoints()</a></code> </p>
</td>
- <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td>
+ <td><p>Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit</p></td>
</tr><tr>
<td>
@@ -242,7 +244,8 @@
<td>
<p><code><a href="plot.mmkin.html">plot(<i>&lt;mmkin&gt;</i>)</a></code> </p>
</td>
- <td><p>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</p></td>
+ <td><p>Plot model fits (observed and fitted) and the residuals for a row or column
+of an mmkin object</p></td>
</tr><tr>
<td>
@@ -352,23 +355,15 @@
<tr>
<td>
- <p><code><a href="nafta.html">nafta()</a></code> </p>
+ <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i>&lt;nafta&gt;</i>)</a></code> </p>
</td>
<td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
</tr><tr>
<td>
- <p><code><a href="print.nafta.html">print(<i>&lt;nafta&gt;</i>)</a></code> </p>
- </td>
- <td><p>Print nafta objects</p></td>
- </tr><tr>
-
- <td>
<p><code><a href="plot.nafta.html">plot(<i>&lt;nafta&gt;</i>)</a></code> </p>
</td>
- <td><p>Plot the results of the three models used in the NAFTA scheme. The plots
- are ordered with increasing complexity of the model in this function
- (SFO, then IORE, then DFOP).</p></td>
+ <td><p>Plot the results of the three models used in the NAFTA scheme.</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -388,7 +383,8 @@
<td>
<p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p>
</td>
- <td><p>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</p></td>
+ <td><p>Function to calculate maximum time weighted average concentrations from
+kinetic models fitted with mkinfit</p></td>
</tr><tr>
<td>
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index dbe0c116..c79146a9 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -8,11 +8,13 @@
<title>Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,19 +34,17 @@
-<meta property="og:title" content="Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit" />
+<meta property="og:title" content="Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit" />
<meta property="og:description" content="This function simply calculates the product of the likelihood densities
- calculated using dnorm, i.e. assuming normal distribution,
- with of the mean predicted by the degradation model, and the
- standard deviation predicted by the error model.
-The total number of estimated parameters returned with the value
- of the likelihood is calculated as the sum of fitted degradation
- model parameters and the fitted error model parameters." />
+calculated using dnorm, i.e. assuming normal distribution,
+with of the mean predicted by the degradation model, and the standard
+deviation predicted by the error model." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -115,7 +115,6 @@ The total number of estimated parameters returned with the value
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -137,20 +136,15 @@ The total number of estimated parameters returned with the value
</div>
<div class="ref-description">
-
<p>This function simply calculates the product of the likelihood densities
- calculated using <code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution,
- with of the mean predicted by the degradation model, and the
- standard deviation predicted by the error model.</p>
-<p>The total number of estimated parameters returned with the value
- of the likelihood is calculated as the sum of fitted degradation
- model parameters and the fitted error model parameters.</p>
-
+calculated using <code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution,
+with of the mean predicted by the degradation model, and the standard
+deviation predicted by the error model.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
<span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -163,21 +157,25 @@ The total number of estimated parameters returned with the value
<td><p>For compatibility with the generic method</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>An object of class <code><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></code> with the number of
- estimated parameters (degradation model parameters plus variance
- model parameters) as attribute.</p>
-
+ <p>An object of class <code><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></code> with the number of estimated
+ parameters (degradation model parameters plus variance model parameters)
+ as attribute.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The total number of estimated parameters returned with the value of the
+likelihood is calculated as the sum of fitted degradation model parameters
+and the fitted error model parameters.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Compare the AIC of columns of <code><a href='mmkin.html'>mmkin</a></code> objects using
<code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span>
+ <pre class="examples"><div class='input'>
+ <span class='co'># \dontrun{</span>
<span class='no'>sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)
@@ -186,17 +184,16 @@ The total number of estimated parameters returned with the value
#&gt; f_nw 5 204.4486
#&gt; f_obs 6 205.8727
#&gt; f_tc 6 141.9656</div><div class='input'> # }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#details">Details</a></li>
<li><a href="#see-also">See also</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png
index 752fd9d4..78a31f93 100644
--- a/docs/reference/logistic.solution-2.png
+++ b/docs/reference/logistic.solution-2.png
Binary files differ
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 91fe035e..b2f24d45 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -8,11 +8,13 @@
<title>Logistic kinetics — logistic.solution • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Logistic kinetics — logistic.solution" />
+<meta property="og:title" content="Logistic kinetics — logistic.solution" />
<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
- an increasing rate constant, supposedly caused by microbial growth" />
+an increasing rate constant, supposedly caused by microbial growth" />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,14 +134,12 @@
</div>
<div class="ref-description">
-
<p>Function describing exponential decline from a defined starting value, with
- an increasing rate constant, supposedly caused by microbial growth</p>
-
+an increasing rate constant, supposedly caused by microbial growth</p>
</div>
<pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -164,28 +164,25 @@
<td><p>Growth rate of the increase in the rate constant.</p></td>
</tr>
</table>
-
- <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The solution of the logistic model reduces to the
- <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to
- <code>kmax</code>.</p>
-
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The value of the response variable at time <code>t</code>.</p>
-
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The solution of the logistic model reduces to the
+ <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
Version 1.1, 18 December 2014
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
+ <pre class="examples"><div class='input'>
+ <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
<span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>),
<span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
@@ -221,19 +218,16 @@
#&gt; k0 0.4448750
#&gt; r 1.1821121
#&gt; sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; DT50 DT90 DT50_k0 DT50_kmax
-#&gt; parent 36.86533 62.41511 4297.854 10.83349</div></pre>
+#&gt; parent 36.86533 62.41511 4297.854 10.83349</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
- <li><a href="#note">Note</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#note">Note</a></li>
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index d1c2a805..ef2a55bf 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -6,13 +6,16 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent • mkin</title>
+<title>Function to calculate maximum time weighted average concentrations from
+kinetic models fitted with mkinfit — max_twa_parent • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,17 +35,19 @@
-<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" />
-<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations
-(TWAs) for kinetic models fitted with mkinfit. Currently, only
-calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
-using the analytical formulas given in the PEC soil section of the FOCUS
-guidance." />
+<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from
+kinetic models fitted with mkinfit — max_twa_parent" />
+<meta property="og:description" content="This function calculates maximum moving window time weighted average
+concentrations (TWAs) for kinetic models fitted with mkinfit.
+Currently, only calculations for the parent are implemented for the SFO,
+FOMC, DFOP and HS models, using the analytical formulas given in the PEC
+soil section of the FOCUS guidance." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -113,7 +118,6 @@ guidance." />
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -129,27 +133,30 @@ guidance." />
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</h1>
+ <h1>Function to calculate maximum time weighted average concentrations from
+kinetic models fitted with mkinfit</h1>
<div class="hidden name"><code>max_twa_parent.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>This function calculates maximum moving window time weighted average concentrations
-(TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. Currently, only
-calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
-using the analytical formulas given in the PEC soil section of the FOCUS
-guidance.</p>
-
+ <p>This function calculates maximum moving window time weighted average
+concentrations (TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>.
+Currently, only calculations for the parent are implemented for the SFO,
+FOMC, DFOP and HS models, using the analytical formulas given in the PEC
+soil section of the FOCUS guidance.</p>
</div>
<pre class="usage"><span class='fu'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='no'>windows</span>)
- <span class='fu'>max_twa_sfo</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k</span>, <span class='no'>t</span>)
- <span class='fu'>max_twa_fomc</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>, <span class='no'>t</span>)
- <span class='fu'>max_twa_dfop</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>, <span class='no'>t</span>)
- <span class='fu'>max_twa_hs</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>, <span class='no'>t</span>)</pre>
-
+
+<span class='fu'>max_twa_sfo</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k</span>, <span class='no'>t</span>)
+
+<span class='fu'>max_twa_fomc</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>, <span class='no'>t</span>)
+
+<span class='fu'>max_twa_dfop</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>, <span class='no'>t</span>)
+
+<span class='fu'>max_twa_hs</span>(<span class='kw'>M0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>, <span class='no'>t</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -159,14 +166,15 @@ guidance.</p>
</tr>
<tr>
<th>windows</th>
- <td><p>The width of the time windows for which the TWAs should be calculated.</p></td>
+ <td><p>The width of the time windows for which the TWAs should be
+calculated.</p></td>
</tr>
<tr>
<th>M0</th>
<td><p>The initial concentration for which the maximum time weighted
- average over the decline curve should be calculated. The default
- is to use a value of 1, which means that a relative maximum time
- weighted average factor (f_twa) is calculated.</p></td>
+average over the decline curve should be calculated. The default is to use
+a value of 1, which means that a relative maximum time weighted average
+factor (f_twa) is calculated.</p></td>
</tr>
<tr>
<th>k</th>
@@ -201,36 +209,33 @@ guidance.</p>
<td><p>Parameter of the HS model.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>For <code>max_twa_parent</code>, a numeric vector, named using the <code>windows</code> argument.
- For the other functions, a numeric vector of length one (also known as 'a
- number').</p>
-
+ <p>For <code>max_twa_parent</code>, a numeric vector, named using the
+ <code>windows</code> argument. For the other functions, a numeric vector of
+ length one (also known as 'a number').</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <pre class="examples"><div class='input'>
+ <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#&gt; 7 21
-#&gt; 34.71343 18.22124 </div></pre>
+#&gt; 34.71343 18.22124 </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 169aefd4..bb7c263a 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -8,11 +8,13 @@
<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,15 +34,16 @@
-<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" />
-<meta property="og:description" content="This function takes a dataframe in the long form, i.e. with a row
- for each observed value, and converts it into a dataframe with one
- independent variable and several dependent variables as columns." />
+<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" />
+<meta property="og:description" content="This function takes a dataframe in the long form, i.e. with a row for each
+observed value, and converts it into a dataframe with one independent
+variable and several dependent variables as columns." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -111,7 +114,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -133,23 +135,22 @@
</div>
<div class="ref-description">
-
- <p>This function takes a dataframe in the long form, i.e. with a row
- for each observed value, and converts it into a dataframe with one
- independent variable and several dependent variables as columns.</p>
-
+ <p>This function takes a dataframe in the long form, i.e. with a row for each
+observed value, and converts it into a dataframe with one independent
+variable and several dependent variables as columns.</p>
</div>
<pre class="usage"><span class='fu'>mkin_long_to_wide</span>(<span class='no'>long_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>outtime</span> <span class='kw'>=</span> <span class='st'>"time"</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>long_data</th>
- <td><p>The dataframe must contain one variable called "time" with the time values specified by the
- <code>time</code> argument, one column called "name" with the grouping of the observed values, and
- finally one column of observed values called "value".</p></td>
+ <td><p>The dataframe must contain one variable called "time" with
+the time values specified by the <code>time</code> argument, one column called
+"name" with the grouping of the observed values, and finally one column of
+observed values called "value".</p></td>
</tr>
<tr>
<th>time</th>
@@ -160,14 +161,14 @@
<td><p>The name of the time variable in the wide output data.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Dataframe in wide format.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; time parent m1
+ <pre class="examples"><div class='input'>
+<span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; time parent m1
#&gt; 1 0 99.46 0.00
#&gt; 2 0 102.04 0.00
#&gt; 3 1 93.50 4.84
@@ -189,15 +190,14 @@
#&gt; 19 100 NA 31.04
#&gt; 20 100 NA 33.13
#&gt; 21 120 NA 25.15
-#&gt; 22 120 NA 33.31</div></pre>
+#&gt; 22 120 NA 33.31</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index d8ae913f..523d45e1 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -8,11 +8,13 @@
<title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,16 @@
-<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" />
-<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several
- dependent variable and converts it into the long form as required by mkinfit." />
+<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" />
+<meta property="og:description" content="This function simply takes a dataframe with one independent variable and
+several dependent variable and converts it into the long form as required by
+mkinfit." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +114,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,50 +135,49 @@
</div>
<div class="ref-description">
-
- <p>This function simply takes a dataframe with one independent variable and several
- dependent variable and converts it into the long form as required by <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
-
+ <p>This function simply takes a dataframe with one independent variable and
+several dependent variable and converts it into the long form as required by
+<code><a href='mkinfit.html'>mkinfit</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>wide_data</th>
- <td><p>The dataframe must contain one variable with the time values specified by the
- <code>time</code> argument and usually more than one column of observed values.</p></td>
+ <td><p>The dataframe must contain one variable with the time
+values specified by the <code>time</code> argument and usually more than one
+column of observed values.</p></td>
</tr>
<tr>
<th>time</th>
<td><p>The name of the time variable.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Dataframe in long format as needed for <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>))
+ <pre class="examples"><div class='input'>
+<span class='no'>wide</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>))
<span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#&gt; name time value
#&gt; 1 x 1 1
#&gt; 2 x 2 4
#&gt; 3 x 3 7
#&gt; 4 y 1 3
#&gt; 5 y 2 4
-#&gt; 6 y 3 5</div></pre>
+#&gt; 6 y 3 5</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index e0f4fbb6..386c00d7 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -8,11 +8,13 @@
<title>A dataset class for mkin — mkinds • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,14 @@
-<meta property="og:title" content="A dataset class for mkin — mkinds" />
+<meta property="og:title" content="A dataset class for mkin — mkinds" />
<meta property="og:description" content="A dataset class for mkin" />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +112,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,51 +133,47 @@
</div>
<div class="ref-description">
-
<p>A dataset class for mkin</p>
-
</div>
<pre class="usage"><span class='no'>mkinds</span></pre>
-
+
+
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An <code>R6Class</code> generator object.</p>
-
<h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
-<dl class='dl-horizontal'>
-<dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd>
-<dt><code>sampling</code></dt><dd><p>times The sampling times</p></dd>
+<dl class='dl-horizontal'>
+<dt>list("title")</dt><dd><p>A full title for the dataset</p></dd>
-<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd>
+<dt>list("sampling")</dt><dd><p>times The sampling times</p></dd>
-<dt><code>observed</code></dt><dd><p>Names of the observed compounds</p></dd>
+<dt>list("time_unit")</dt><dd><p>The time unit</p></dd>
-<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd>
+<dt>list("observed")</dt><dd><p>Names of the observed compounds</p></dd>
-<dt><code>replicates</code></dt><dd><p>The number of replicates</p></dd>
+<dt>list("unit")</dt><dd><p>The unit of the observations</p></dd>
-<dt><code>data</code></dt><dd><p>A dataframe with at least the columns name, time and value
-in order to be compatible with mkinfit</p></dd>
+<dt>list("replicates")</dt><dd><p>The number of replicates</p></dd>
+<dt>list("data")</dt><dd><p>A dataframe with at least the columns name, time and
+value in order to be compatible with mkinfit</p></dd>
</dl>
-
+
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'>&lt;-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre>
+ <pre class="examples"><div class='input'>
+<span class='no'>mds</span> <span class='kw'>&lt;-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
-
<li><a href="#format">Format</a></li>
-
<li><a href="#fields">Fields</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 941e30f5..1a31bc60 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -8,11 +8,13 @@
<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" />
-<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the
-chi-squared test as defined in the FOCUS kinetics report from 2006." />
+<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" />
+<meta property="og:description" content="This function finds the smallest relative error still resulting in passing
+the chi-squared test as defined in the FOCUS kinetics report from 2006." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,14 +134,12 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
</div>
<div class="ref-description">
-
- <p>This function finds the smallest relative error still resulting in passing the
-chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
-
+ <p>This function finds the smallest relative error still resulting in passing
+the chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
</div>
<pre class="usage"><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -152,35 +152,33 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
<td><p>The confidence level chosen for the chi-squared test.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A dataframe with the following components:</p>
-<dt>err.min</dt><dd><p>The relative error, expressed as a fraction.</p></dd>
- <dt>n.optim</dt><dd><p>The number of optimised parameters attributed to the data series.</p></dd>
- <dt>df</dt><dd><p>The number of remaining degrees of freedom for the chi2 error level
- calculations. Note that mean values are used for the chi2 statistic and
- therefore every time point with observed values in the series only counts
- one time.</p></dd>
- The dataframe has one row for the total dataset and one further row for
- each observed state variable in the model.
+<dt>err.min</dt><dd><p>The
+relative error, expressed as a fraction.</p></dd> <dt>n.optim</dt><dd><p>The number of
+optimised parameters attributed to the data series.</p></dd> <dt>df</dt><dd><p>The number of
+remaining degrees of freedom for the chi2 error level calculations. Note
+that mean values are used for the chi2 statistic and therefore every time
+point with observed values in the series only counts one time.</p></dd> The
+dataframe has one row for the total dataset and one further row for each
+observed state variable in the model.
-
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
- EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics, EC
+Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+ <pre class="examples"><div class='input'>
+<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
@@ -192,19 +190,16 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
#&gt; All data 0.1544 4 13
#&gt; parent 0.1659 2 7
#&gt; m1 0.1095 2 6</div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#details">Details</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html
index 4386673c..079a6708 100644
--- a/docs/reference/mkinerrplot.html
+++ b/docs/reference/mkinerrplot.html
@@ -37,11 +37,10 @@
<meta property="og:title" content="Function to plot squared residuals and the error model for an mkin object — mkinerrplot" />
<meta property="og:description" content="This function plots the squared residuals for the specified subset of the
- observed variables from an mkinfit object. In addition, one or more
- dashed line(s) show the fitted error model.
- A combined plot of the fitted model and this error model plot can be
- obtained with plot.mkinfit
- using the argument show_errplot = TRUE." />
+observed variables from an mkinfit object. In addition, one or more dashed
+line(s) show the fitted error model. A combined plot of the fitted model
+and this error model plot can be obtained with plot.mkinfit
+using the argument show_errplot = TRUE." />
<meta name="twitter:card" content="summary" />
@@ -139,21 +138,17 @@
<div class="ref-description">
<p>This function plots the squared residuals for the specified subset of the
- observed variables from an mkinfit object. In addition, one or more
- dashed line(s) show the fitted error model.
- A combined plot of the fitted model and this error model plot can be
- obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
- using the argument <code>show_errplot = TRUE</code>.</p>
+observed variables from an mkinfit object. In addition, one or more dashed
+line(s) show the fitted error model. A combined plot of the fitted model
+and this error model plot can be obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
+using the argument <code>show_errplot = TRUE</code>.</p>
</div>
- <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>,
- <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
- <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)),
- <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>,
- <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span><span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
- <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
- <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='no'>...</span>)</pre>
+ <pre class="usage"><span class='fu'>mkinerrplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,
+ <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>predicted</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Predicted"</span>,
+ <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Squared residual"</span>, <span class='kw'>maxy</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -164,8 +159,9 @@
</tr>
<tr>
<th>obs_vars</th>
- <td><p>A character vector of names of the observed variables for which residuals
- should be plotted. Defaults to all observed variables in the model</p></td>
+ <td><p>A character vector of names of the observed variables for
+which residuals should be plotted. Defaults to all observed variables in
+the model</p></td>
</tr>
<tr>
<th>xlim</th>
@@ -182,7 +178,7 @@
<tr>
<th>maxy</th>
<td><p>Maximum value of the residuals. This is used for the scaling of
- the y axis and defaults to "auto".</p></td>
+the y axis and defaults to "auto".</p></td>
</tr>
<tr>
<th>legend</th>
@@ -190,8 +186,8 @@
</tr>
<tr>
<th>lpos</th>
- <td><p>Where should the legend be placed? Default is "topright". Will be passed on to
- <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td>
+ <td><p>Where should the legend be placed? Default is "topright". Will
+be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td>
</tr>
<tr>
<th>col_obs</th>
@@ -213,15 +209,18 @@
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p>
+ <p>Nothing is returned by this function, as it is called for its side
+ effect, namely to produce a plot.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the
- mkinfit object.</p></div>
+ <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted
+ lines of the mkinfit object.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># \dontrun{</span>
<span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index e07d1f13..6c98bc38 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -8,11 +8,13 @@
<title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,21 +34,20 @@
-<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" />
-<meta property="og:description" content="This function maximises the likelihood of the observed data using
- the Port algorithm nlminb, and the specified initial or fixed
- parameters and starting values. In each step of the optimsation, the kinetic
- model is solved using the function mkinpredict. The parameters
- of the selected error model are fitted simultaneously with the degradation
- model parameters, as both of them are arguments of the likelihood function.
-Per default, parameters in the kinetic models are internally transformed in
- order to better satisfy the assumption of a normal distribution of their
- estimators." />
+<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" />
+<meta property="og:description" content="This function maximises the likelihood of the observed data using the Port
+algorithm nlminb, and the specified initial or fixed
+parameters and starting values. In each step of the optimsation, the
+kinetic model is solved using the function mkinpredict. The
+parameters of the selected error model are fitted simultaneously with the
+degradation model parameters, as both of them are arguments of the
+likelihood function." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -117,7 +118,6 @@ Per default, parameters in the kinetic models are internally transformed in
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -139,135 +139,126 @@ Per default, parameters in the kinetic models are internally transformed in
</div>
<div class="ref-description">
-
- <p>This function maximises the likelihood of the observed data using
- the Port algorithm <code><a href='https://rdrr.io/r/stats/nlminb.html'>nlminb</a></code>, and the specified initial or fixed
- parameters and starting values. In each step of the optimsation, the kinetic
- model is solved using the function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The parameters
- of the selected error model are fitted simultaneously with the degradation
- model parameters, as both of them are arguments of the likelihood function.</p>
-<p>Per default, parameters in the kinetic models are internally transformed in
- order to better satisfy the assumption of a normal distribution of their
- estimators.</p>
-
+ <p>This function maximises the likelihood of the observed data using the Port
+algorithm <code><a href='https://rdrr.io/r/stats/nlminb.html'>nlminb</a></code>, and the specified initial or fixed
+parameters and starting values. In each step of the optimsation, the
+kinetic model is solved using the function <code><a href='mkinpredict.html'>mkinpredict</a></code>. The
+parameters of the selected error model are fitted simultaneously with the
+degradation model parameters, as both of them are arguments of the
+likelihood function.</p>
</div>
- <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>,
- <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
- <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
- <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
- <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>],
- <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>),
- <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
- <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
<span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>eval.max</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>iter.max</span> <span class='kw'>=</span> <span class='fl'>200</span>),
- <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+ <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>,
<span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>),
- <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>,
- <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>),
- <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>,
- <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-
+ <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>,
+ <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>mkinmod</th>
- <td><p>A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic model to be
- fitted to the data, or one of the shorthand names ("SFO", "FOMC", "DFOP",
- "HS", "SFORB", "IORE"). If a shorthand name is given, a parent only degradation
- model is generated for the variable with the highest value in
- <code>observed</code>.</p></td>
+ <td><p>A list of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the kinetic
+model to be fitted to the data, or one of the shorthand names ("SFO",
+"FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a
+parent only degradation model is generated for the variable with the
+highest value in <code>observed</code>.</p></td>
</tr>
<tr>
<th>observed</th>
- <td><p>A dataframe with the observed data. The first column called "name" must
- contain the name of the observed variable for each data point. The second
- column must contain the times of observation, named "time". The third
- column must be named "value" and contain the observed values. Zero values
- in the "value" column will be removed, with a warning, in order to
- avoid problems with fitting the two-component error model. This is not
- expected to be a problem, because in general, values of zero are not
- observed in degradation data, because there is a lower limit of detection.</p></td>
+ <td><p>A dataframe with the observed data. The first column called
+"name" must contain the name of the observed variable for each data point.
+The second column must contain the times of observation, named "time".
+The third column must be named "value" and contain the observed values.
+Zero values in the "value" column will be removed, with a warning, in
+order to avoid problems with fitting the two-component error model. This
+is not expected to be a problem, because in general, values of zero are
+not observed in degradation data, because there is a lower limit of
+detection.</p></td>
</tr>
<tr>
<th>parms.ini</th>
- <td><p>A named vector of initial values for the parameters, including parameters
- to be optimised and potentially also fixed parameters as indicated by
- <code>fixed_parms</code>. If set to "auto", initial values for rate constants
- are set to default values. Using parameter names that are not in the model
- gives an error.</p>
+ <td><p>A named vector of initial values for the parameters,
+ including parameters to be optimised and potentially also fixed parameters
+ as indicated by <code>fixed_parms</code>. If set to "auto", initial values for
+ rate constants are set to default values. Using parameter names that are
+ not in the model gives an error.</p>
<p>It is possible to only specify a subset of the parameters that the model
- needs. You can use the parameter lists "bparms.ode" from a previously
- fitted model, which contains the differential equation parameters from this
- model. This works nicely if the models are nested. An example is given
- below.</p></td>
+ needs. You can use the parameter lists "bparms.ode" from a previously
+ fitted model, which contains the differential equation parameters from
+ this model. This works nicely if the models are nested. An example is
+ given below.</p></td>
</tr>
<tr>
<th>state.ini</th>
- <td><p>A named vector of initial values for the state variables of the model. In
- case the observed variables are represented by more than one model
- variable, the names will differ from the names of the observed variables
- (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default is to set
- the initial value of the first model variable to the mean of the time zero
- values for the variable with the maximum observed value, and all others to 0.
- If this variable has no time zero observations, its initial value is set to 100.</p></td>
+ <td><p>A named vector of initial values for the state variables of
+the model. In case the observed variables are represented by more than one
+model variable, the names will differ from the names of the observed
+variables (see <code>map</code> component of <code><a href='mkinmod.html'>mkinmod</a></code>). The default
+is to set the initial value of the first model variable to the mean of the
+time zero values for the variable with the maximum observed value, and all
+others to 0. If this variable has no time zero observations, its initial
+value is set to 100.</p></td>
</tr>
<tr>
<th>err.ini</th>
- <td><p>A named vector of initial values for the error model parameters to be
- optimised. If set to "auto", initial values are set to default values.
- Otherwise, inital values for all error model parameters must be
- given.</p></td>
+ <td><p>A named vector of initial values for the error model
+parameters to be optimised. If set to "auto", initial values are set to
+default values. Otherwise, inital values for all error model parameters
+must be given.</p></td>
</tr>
<tr>
<th>fixed_parms</th>
- <td><p>The names of parameters that should not be optimised but rather kept at the
- values specified in <code>parms.ini</code>.</p></td>
+ <td><p>The names of parameters that should not be optimised but
+rather kept at the values specified in <code>parms.ini</code>.</p></td>
</tr>
<tr>
<th>fixed_initials</th>
- <td><p>The names of model variables for which the initial state at time 0 should
- be excluded from the optimisation. Defaults to all state variables except
- for the first one.</p></td>
+ <td><p>The names of model variables for which the initial
+state at time 0 should be excluded from the optimisation. Defaults to all
+state variables except for the first one.</p></td>
</tr>
<tr>
<th>from_max_mean</th>
- <td><p>If this is set to TRUE, and the model has only one observed variable, then
- data before the time of the maximum observed value (after averaging for each
- sampling time) are discarded, and this time is subtracted from all
- remaining time values, so the time of the maximum observed mean value is
- the new time zero.</p></td>
+ <td><p>If this is set to TRUE, and the model has only one
+observed variable, then data before the time of the maximum observed value
+(after averaging for each sampling time) are discarded, and this time is
+subtracted from all remaining time values, so the time of the maximum
+observed mean value is the new time zero.</p></td>
</tr>
<tr>
<th>solution_type</th>
- <td><p>If set to "eigen", the solution of the system of differential equations is
- based on the spectral decomposition of the coefficient matrix in cases that
- this is possible. If set to "deSolve", a numerical ode solver from package
- <code>deSolve</code> is used. If set to "analytical", an analytical
- solution of the model is used. This is only implemented for simple
- degradation experiments with only one state variable, i.e. with no
- metabolites. The default is "auto", which uses "analytical" if possible,
- otherwise "deSolve" if a compiler is present, and "eigen" if no
- compiler is present and the model can be expressed using eigenvalues and
- eigenvectors. This argument is passed on to the helper function
- <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td>
+ <td><p>If set to "eigen", the solution of the system of
+differential equations is based on the spectral decomposition of the
+coefficient matrix in cases that this is possible. If set to "deSolve", a
+numerical ode solver from package <code>deSolve</code> is used. If set to
+"analytical", an analytical solution of the model is used. This is only
+implemented for simple degradation experiments with only one state
+variable, i.e. with no metabolites. The default is "auto", which uses
+"analytical" if possible, otherwise "deSolve" if a compiler is present,
+and "eigen" if no compiler is present and the model can be expressed using
+eigenvalues and eigenvectors. This argument is passed on to the helper
+function <code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td>
</tr>
<tr>
<th>method.ode</th>
- <td><p>The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code> to
- <code>ode</code> in case the solution type is "deSolve". The default
- "lsoda" is performant, but sometimes fails to converge.</p></td>
+ <td><p>The solution method passed via <code><a href='mkinpredict.html'>mkinpredict</a></code>
+to <code>ode</code> in case the solution type is "deSolve". The default
+"lsoda" is performant, but sometimes fails to converge.</p></td>
</tr>
<tr>
<th>use_compiled</th>
- <td><p>If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code>
- model is used in the calls to <code><a href='mkinpredict.html'>mkinpredict</a></code> even if a compiled
- version is present.</p></td>
+ <td><p>If set to <code>FALSE</code>, no compiled version of the
+<code><a href='mkinmod.html'>mkinmod</a></code> model is used in the calls to
+<code><a href='mkinpredict.html'>mkinpredict</a></code> even if a compiled version is present.</p></td>
</tr>
<tr>
<th>control</th>
@@ -275,92 +266,90 @@ Per default, parameters in the kinetic models are internally transformed in
</tr>
<tr>
<th>transform_rates</th>
- <td><p>Boolean specifying if kinetic rate constants should be transformed in the
- model specification used in the fitting for better compliance with the
- assumption of normal distribution of the estimator. If TRUE, also
- alpha and beta parameters of the FOMC model are log-transformed, as well
- as k1 and k2 rate constants for the DFOP and HS models and the break point
- tb of the HS model. If FALSE, zero is used as a lower bound for the rates
- in the optimisation.</p></td>
+ <td><p>Boolean specifying if kinetic rate constants should
+be transformed in the model specification used in the fitting for better
+compliance with the assumption of normal distribution of the estimator. If
+TRUE, also alpha and beta parameters of the FOMC model are
+log-transformed, as well as k1 and k2 rate constants for the DFOP and HS
+models and the break point tb of the HS model. If FALSE, zero is used as
+a lower bound for the rates in the optimisation.</p></td>
</tr>
<tr>
<th>transform_fractions</th>
- <td><p>Boolean specifying if formation fractions constants should be transformed in the
- model specification used in the fitting for better compliance with the
- assumption of normal distribution of the estimator. The default (TRUE) is
- to do transformations. If TRUE, the g parameter of the DFOP and HS
- models are also transformed, as they can also be seen as compositional
- data. The transformation used for these transformations is the
- <code><a href='ilr.html'>ilr</a></code> transformation.</p></td>
+ <td><p>Boolean specifying if formation fractions
+constants should be transformed in the model specification used in the
+fitting for better compliance with the assumption of normal distribution
+of the estimator. The default (TRUE) is to do transformations. If TRUE,
+the g parameter of the DFOP and HS models are also transformed, as they
+can also be seen as compositional data. The transformation used for these
+transformations is the <code><a href='ilr.html'>ilr</a></code> transformation.</p></td>
</tr>
<tr>
<th>quiet</th>
- <td><p>Suppress printing out the current value of the negative log-likelihood
- after each improvement?</p></td>
+ <td><p>Suppress printing out the current value of the negative
+log-likelihood after each improvement?</p></td>
</tr>
<tr>
<th>atol</th>
- <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8,
- lower than in <code>lsoda</code>.</p></td>
+ <td><p>Absolute error tolerance, passed to <code>ode</code>. Default
+is 1e-8, lower than in <code>lsoda</code>.</p></td>
</tr>
<tr>
<th>rtol</th>
- <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10,
- much lower than in <code>lsoda</code>.</p></td>
+ <td><p>Absolute error tolerance, passed to <code>ode</code>. Default
+is 1e-10, much lower than in <code>lsoda</code>.</p></td>
</tr>
<tr>
<th>n.outtimes</th>
- <td><p>The length of the dataseries that is produced by the model prediction
- function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy of
- the numerical solver if that is used (see <code>solution_type</code> argument.
- The default value is 100.</p></td>
+ <td><p>The length of the dataseries that is produced by the model
+prediction function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy
+of the numerical solver if that is used (see <code>solution_type</code>
+argument. The default value is 100.</p></td>
</tr>
<tr>
<th>error_model</th>
- <td><p>If the error model is "const", a constant standard deviation
- is assumed.</p>
+ <td><p>If the error model is "const", a constant standard
+ deviation is assumed.</p>
<p>If the error model is "obs", each observed variable is assumed to have its
- own variance.</p>
+ own variance.</p>
<p>If the error model is "tc" (two-component error model), a two component
- error model similar to the one described by Rocke and Lorenzato (1995) is
- used for setting up the likelihood function. Note that this model deviates
- from the model by Rocke and Lorenzato, as their model implies that the
- errors follow a lognormal distribution for large values, not a normal
- distribution as assumed by this method.</p></td>
+ error model similar to the one described by Rocke and Lorenzato (1995) is
+ used for setting up the likelihood function. Note that this model
+ deviates from the model by Rocke and Lorenzato, as their model implies
+ that the errors follow a lognormal distribution for large values, not a
+ normal distribution as assumed by this method.</p></td>
</tr>
<tr>
<th>error_model_algorithm</th>
- <td><p>If "auto", the selected algorithm depends on the error model.
- If the error model is "const", nonlinear least squares fitting ("OLS") is
- selected. If the error model is "obs", iteratively reweighted least squares
- fitting ("IRLS") is selected. If the error model is "tc", the "d_3"
- algorithm is selected.</p>
-<p>The algorithm "d_3" will directly minimize the negative
- log-likelihood and - independently - also use the three step algorithm
- described below. The fit with the higher likelihood is returned.</p>
-<p>The algorithm "direct" will directly minimize the negative
- log-likelihood.</p>
-<p>The algorithm "twostep" will minimize the negative log-likelihood
- after an initial unweighted least squares optimisation step.</p>
-<p>The algorithm "threestep" starts with unweighted least squares,
- then optimizes only the error model using the degradation model
- parameters found, and then minimizes the negative log-likelihood
- with free degradation and error model parameters.</p>
-<p>The algorithm "fourstep" starts with unweighted least squares,
- then optimizes only the error model using the degradation model
- parameters found, then optimizes the degradation model again
- with fixed error model parameters, and finally minimizes the negative
- log-likelihood with free degradation and error model parameters.</p>
+ <td><p>If "auto", the selected algorithm depends on
+ the error model. If the error model is "const", unweighted nonlinear
+ least squares fitting ("OLS") is selected. If the error model is "obs", or
+ "tc", the "d_3" algorithm is selected.</p>
+<p>The algorithm "d_3" will directly minimize the negative log-likelihood and
+ - independently - also use the three step algorithm described below. The
+ fit with the higher likelihood is returned.</p>
+<p>The algorithm "direct" will directly minimize the negative log-likelihood.</p>
+<p>The algorithm "twostep" will minimize the negative log-likelihood after an
+ initial unweighted least squares optimisation step.</p>
+<p>The algorithm "threestep" starts with unweighted least squares, then
+ optimizes only the error model using the degradation model parameters
+ found, and then minimizes the negative log-likelihood with free
+ degradation and error model parameters.</p>
+<p>The algorithm "fourstep" starts with unweighted least squares, then
+ optimizes only the error model using the degradation model parameters
+ found, then optimizes the degradation model again with fixed error model
+ parameters, and finally minimizes the negative log-likelihood with free
+ degradation and error model parameters.</p>
<p>The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with
- unweighted least squares, and then iterates optimization of the error model
- parameters and subsequent
- optimization of the degradation model using those error model parameters,
- until the error model parameters converge.</p></td>
+ unweighted least squares, and then iterates optimization of the error
+ model parameters and subsequent optimization of the degradation model
+ using those error model parameters, until the error model parameters
+ converge.</p></td>
</tr>
<tr>
<th>reweight.tol</th>
- <td><p>Tolerance for the convergence criterion calculated from the error model
- parameters in IRLS fits.</p></td>
+ <td><p>Tolerance for the convergence criterion calculated from
+the error model parameters in IRLS fits.</p></td>
</tr>
<tr>
<th>reweight.max.iter</th>
@@ -372,50 +361,54 @@ Per default, parameters in the kinetic models are internally transformed in
</tr>
<tr>
<th>...</th>
- <td><p>Further arguments that will be passed on to <code>deSolve</code>.</p></td>
+ <td><p>Further arguments that will be passed on to
+<code>deSolve</code>.</p></td>
</tr>
</table>
-
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model
+ for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A list with "mkinfit" in the class attribute. A summary can be obtained by
- <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
-
- <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+ <p>A list with "mkinfit" in the class attribute. A summary can be
+ obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
- <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
-<p>Comparisons of models fitted to the same data can be made using <code><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></code>
- by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p>
-<p>Fitting of several models to several datasets in a single call to
- <code><a href='mmkin.html'>mmkin</a></code>.</p></div>
-
+ <p>Per default, parameters in the kinetic models are internally transformed in
+order to better satisfy the assumption of a normal distribution of their
+estimators.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>When using the "IORE" submodel for metabolites, fitting with
"transform_rates = TRUE" (the default) often leads to failures of the
numerical ODE solver. In this situation it may help to switch off the
internal rate transformation.</p>
-
- <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
- measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
-
+ <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
+ <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
+<p>Comparisons of models fitted to the same data can be made using
+ <code><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></code> by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p>
+<p>Fitting of several models to several datasets in a single call to
+ <code><a href='mmkin.html'>mmkin</a></code>.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Mon Oct 21 12:07:39 2019
-#&gt; Date of summary: Mon Oct 21 12:07:39 2019
+#&gt; Date of fit: Fri Oct 25 02:08:07 2019
+#&gt; Date of summary: Fri Oct 25 02:08:07 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 222 model solutions performed in 0.459 s
+#&gt; Fitted using 222 model solutions performed in 0.453 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -487,7 +480,7 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</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'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.462 0.000 1.463 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt; 1.447 0.000 1.448 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -560,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
#&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.04 0.00 1.04 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt; 1.032 0.000 1.032 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -596,8 +589,8 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Mon Oct 21 12:07:54 2019
-#&gt; Date of summary: Mon Oct 21 12:07:54 2019
+#&gt; Date of fit: Fri Oct 25 02:08:22 2019
+#&gt; Date of summary: Fri Oct 25 02:08:22 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -605,7 +598,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 421 model solutions performed in 1.07 s
+#&gt; Fitted using 421 model solutions performed in 1.062 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -713,8 +706,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 120 m1 25.15 28.78984 -3.640e+00
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Mon Oct 21 12:07:56 2019
-#&gt; Date of summary: Mon Oct 21 12:07:56 2019
+#&gt; Date of fit: Fri Oct 25 02:08:25 2019
+#&gt; Date of summary: Fri Oct 25 02:08:25 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -722,11 +715,12 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 897 model solutions performed in 2.363 s
+#&gt; Fitted using 978 model solutions performed in 2.523 s
#&gt;
#&gt; Error model: Variance unique to each observed variable
#&gt;
-#&gt; Error model algorithm: IRLS
+#&gt; Error model algorithm: d_3
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -761,16 +755,16 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent
-#&gt; parent_0 1.00000 0.51078 -0.19132 -0.59997 0.035676
-#&gt; log_k_parent 0.51078 1.00000 -0.37457 -0.59239 0.069834
-#&gt; log_k_m1 -0.19132 -0.37457 1.00000 0.74398 -0.026158
-#&gt; f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041371
-#&gt; sigma_parent 0.03568 0.06983 -0.02616 -0.04137 1.000000
-#&gt; sigma_m1 -0.03385 -0.06626 0.02482 0.03926 -0.004628
+#&gt; parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035670
+#&gt; log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069833
+#&gt; log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158
+#&gt; f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369
+#&gt; sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000
+#&gt; sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628
#&gt; sigma_m1
#&gt; parent_0 -0.033847
#&gt; log_k_parent -0.066265
-#&gt; log_k_m1 0.024824
+#&gt; log_k_m1 0.024823
#&gt; f_parent_ilr_1 0.039256
#&gt; sigma_parent -0.004628
#&gt; sigma_m1 1.000000
@@ -784,7 +778,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01
#&gt; k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03
#&gt; f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01
-#&gt; sigma_parent 3.401000 5.985 5.661e-07 2.244000 4.559e+00
+#&gt; sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00
#&gt; sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
@@ -805,47 +799,47 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 99.65420 -1.942e-01
-#&gt; 0 parent 102.04 99.65420 2.386e+00
-#&gt; 1 parent 93.50 90.26335 3.237e+00
-#&gt; 1 parent 92.50 90.26335 2.237e+00
-#&gt; 3 parent 63.23 74.05308 -1.082e+01
-#&gt; 3 parent 68.99 74.05308 -5.063e+00
-#&gt; 7 parent 52.32 49.84326 2.477e+00
-#&gt; 7 parent 55.13 49.84326 5.287e+00
+#&gt; 0 parent 99.46 99.65417 -1.942e-01
+#&gt; 0 parent 102.04 99.65417 2.386e+00
+#&gt; 1 parent 93.50 90.26332 3.237e+00
+#&gt; 1 parent 92.50 90.26332 2.237e+00
+#&gt; 3 parent 63.23 74.05306 -1.082e+01
+#&gt; 3 parent 68.99 74.05306 -5.063e+00
+#&gt; 7 parent 52.32 49.84325 2.477e+00
+#&gt; 7 parent 55.13 49.84325 5.287e+00
#&gt; 14 parent 27.27 24.92971 2.340e+00
#&gt; 14 parent 26.64 24.92971 1.710e+00
#&gt; 21 parent 11.50 12.46890 -9.689e-01
#&gt; 21 parent 11.64 12.46890 -8.289e-01
#&gt; 35 parent 2.85 3.11925 -2.692e-01
#&gt; 35 parent 2.91 3.11925 -2.092e-01
-#&gt; 50 parent 0.69 0.70678 -1.678e-02
-#&gt; 50 parent 0.63 0.70678 -7.678e-02
+#&gt; 50 parent 0.69 0.70679 -1.679e-02
+#&gt; 50 parent 0.63 0.70679 -7.679e-02
#&gt; 75 parent 0.05 0.05952 -9.523e-03
#&gt; 75 parent 0.06 0.05952 4.772e-04
#&gt; 1 m1 4.84 4.81075 2.925e-02
#&gt; 1 m1 5.64 4.81075 8.292e-01
-#&gt; 3 m1 12.91 13.04197 -1.320e-01
-#&gt; 3 m1 12.96 13.04197 -8.197e-02
-#&gt; 7 m1 22.97 25.06848 -2.098e+00
-#&gt; 7 m1 24.47 25.06848 -5.985e-01
+#&gt; 3 m1 12.91 13.04196 -1.320e-01
+#&gt; 3 m1 12.96 13.04196 -8.196e-02
+#&gt; 7 m1 22.97 25.06847 -2.098e+00
+#&gt; 7 m1 24.47 25.06847 -5.985e-01
#&gt; 14 m1 41.69 36.70308 4.987e+00
#&gt; 14 m1 33.21 36.70308 -3.493e+00
#&gt; 21 m1 44.37 41.65115 2.719e+00
#&gt; 21 m1 46.44 41.65115 4.789e+00
#&gt; 35 m1 41.22 43.29465 -2.075e+00
#&gt; 35 m1 37.95 43.29465 -5.345e+00
-#&gt; 50 m1 41.19 41.19948 -9.477e-03
+#&gt; 50 m1 41.19 41.19948 -9.479e-03
#&gt; 50 m1 40.01 41.19948 -1.189e+00
#&gt; 75 m1 40.09 36.44035 3.650e+00
#&gt; 75 m1 33.85 36.44035 -2.590e+00
-#&gt; 100 m1 31.04 31.98772 -9.477e-01
-#&gt; 100 m1 33.13 31.98772 1.142e+00
-#&gt; 120 m1 25.15 28.80428 -3.654e+00
-#&gt; 120 m1 33.31 28.80428 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
+#&gt; 100 m1 31.04 31.98773 -9.477e-01
+#&gt; 100 m1 33.13 31.98773 1.142e+00
+#&gt; 120 m1 25.15 28.80429 -3.654e+00
+#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Mon Oct 21 12:08:06 2019
-#&gt; Date of summary: Mon Oct 21 12:08:06 2019
+#&gt; Date of fit: Fri Oct 25 02:08:34 2019
+#&gt; Date of summary: Fri Oct 25 02:08:34 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -853,7 +847,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2289 model solutions performed in 9.175 s
+#&gt; Fitted using 2289 model solutions performed in 9.136 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
@@ -969,21 +963,18 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 120 m1 25.15 29.04130 -3.891304
#&gt; 120 m1 33.31 29.04130 4.268696</div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
+ <li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
-
- <li><a href="#see-also">See also</a></li>
-
+ <li><a href="#details">Details</a></li>
<li><a href="#note">Note</a></li>
-
- <li><a href="#source">Source</a></li>
-
+ <li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index f592af1c..2eefdc2e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -8,11 +8,13 @@
<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,18 +34,17 @@
-<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" />
-<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to
- a list, specifying the kinetic model type and reaction or transfer to other
- observed compartments. Instead of specifying several expressions, a list
- of lists can be given in the speclist argument.
-For the definition of model types and their parameters, the equations given
- in the FOCUS and NAFTA guidance documents are used." />
+<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" />
+<meta property="og:description" content="The function usually takes several expressions, each assigning a compound
+name to a list, specifying the kinetic model type and reaction or transfer
+to other observed compartments. Instead of specifying several expressions, a
+list of lists can be given in the speclist argument." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -114,7 +115,6 @@ For the definition of model types and their parameters, the equations given
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -136,49 +136,47 @@ For the definition of model types and their parameters, the equations given
</div>
<div class="ref-description">
-
- <p>The function usually takes several expressions, each assigning a compound name to
- a list, specifying the kinetic model type and reaction or transfer to other
- observed compartments. Instead of specifying several expressions, a list
- of lists can be given in the speclist argument.</p>
-<p>For the definition of model types and their parameters, the equations given
- in the FOCUS and NAFTA guidance documents are used.</p>
-
+ <p>The function usually takes several expressions, each assigning a compound
+name to a list, specifying the kinetic model type and reaction or transfer
+to other observed compartments. Instead of specifying several expressions, a
+list of lists can be given in the speclist argument.</p>
</div>
- <pre class="usage"><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-
+ <pre class="usage"><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>...</th>
- <td><p>For each observed variable, a list has to be specified as an argument, containing
- at least a component <code>type</code>, specifying the type of kinetics to use
- for the variable. Currently, single first order kinetics "SFO",
- indeterminate order rate equation kinetics "IORE", or
- single first order with reversible binding "SFORB" are implemented for all
- variables, while
- "FOMC", "DFOP" and "HS" can additionally be chosen for the first
- variable which is assumed to be the source compartment.
- Additionally, each component of the list can include a character vector <code>to</code>,
- specifying names of variables to which a transfer is to be assumed in the
- model.
- If the argument <code>use_of_ff</code> is set to "min" (default) and the model for
- the compartment is "SFO" or "SFORB", an additional component of the list
- can be "sink=FALSE" effectively fixing the flux to sink to zero.</p></td>
+ <td><p>For each observed variable, a list has to be specified as an
+argument, containing at least a component <code>type</code>, specifying the type
+of kinetics to use for the variable. Currently, single first order
+kinetics "SFO", indeterminate order rate equation kinetics "IORE", or
+single first order with reversible binding "SFORB" are implemented for all
+variables, while "FOMC", "DFOP" and "HS" can additionally be chosen for
+the first variable which is assumed to be the source compartment.
+Additionally, each component of the list can include a character vector
+<code>to</code>, specifying names of variables to which a transfer is to be
+assumed in the model. If the argument <code>use_of_ff</code> is set to "min"
+(default) and the model for the compartment is "SFO" or "SFORB", an
+additional component of the list can be "sink=FALSE" effectively fixing
+the flux to sink to zero.</p></td>
</tr>
<tr>
<th>use_of_ff</th>
- <td><p>Specification of the use of formation fractions in the model equations and, if
- applicable, the coefficient matrix. If "min", a minimum use of formation
- fractions is made in order to avoid fitting the product of formation fractions
- and rate constants. If "max", formation fractions are always used.</p></td>
+ <td><p>Specification of the use of formation fractions in the
+model equations and, if applicable, the coefficient matrix. If "min", a
+minimum use of formation fractions is made in order to avoid fitting the
+product of formation fractions and rate constants. If "max", formation
+fractions are always used.</p></td>
</tr>
<tr>
<th>speclist</th>
- <td><p>The specification of the observed variables and their submodel types and
- pathways can be given as a single list using this argument. Default is NULL.</p></td>
+ <td><p>The specification of the observed variables and their
+submodel types and pathways can be given as a single list using this
+argument. Default is NULL.</p></td>
</tr>
<tr>
<th>quiet</th>
@@ -186,44 +184,46 @@ For the definition of model types and their parameters, the equations given
</tr>
<tr>
<th>verbose</th>
- <td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give
- detailed information about the C function being built.</p></td>
+ <td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if
+applicable to give detailed information about the C function being built.</p></td>
</tr>
</table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing</p>
-<dt>diffs</dt><dd><p>A vector of string representations of differential equations,
- one for each modelling variable.</p></dd>
- <dt>parms</dt><dd><p>A vector of parameter names occurring in the differential equations.</p></dd>
- <dt>map</dt><dd><p>A list containing named character vectors for each observed variable, specifying
- the modelling variables by which it is represented.</p></dd>
- <dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd>
- <dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be
- represented by one.</p></dd>
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
+ <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>,
+ containing, among others,</p>
+<dt>diffs</dt><dd><p>A vector of string representations of differential equations, one for
+ each modelling variable.</p></dd>
+ <dt>map</dt><dd><p>A list containing named character vectors for each observed variable,
+ specifying the modelling variables by which it is represented.</p></dd>
+ <dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd>
+ <dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be
+ represented by one.</p></dd>
+ <dt>ll</dt><dd><p>The likelihood function, taking the parameter vector as the first argument.</p></dd>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>For the definition of model types and their parameters, the equations given
+in the FOCUS and NAFTA guidance documents are used.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The IORE submodel is not well tested (yet). When using this model for metabolites,
- you may want to read the second note in the help page to
- <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
-
+ <p>The IORE submodel is not well tested for metabolites. When using this
+ model for metabolites, you may want to read the second note in the help
+ page to <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
- Evaluating and Calculating Degradation Kinetics in Environmental
- Media</p>
-
+ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))
<span class='co'># One parent compound, one metabolite, both single first order</span>
@@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file663b71dc323f.c 2&gt; file663b71dc323f.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file59d942b9ac06.c 2&gt; file59d942b9ac06.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
@@ -260,7 +260,7 @@ For the definition of model types and their parameters, the equations given
#&gt; 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
#&gt; 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
#&gt; 19: }</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'># If we have several parallel metabolites </span>
+<span class='co'># If we have several parallel metabolites</span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
@@ -276,13 +276,10 @@ For the definition of model types and their parameters, the equations given
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#details">Details</a></li>
<li><a href="#note">Note</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 79a4cc2b..af936795 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -8,11 +8,13 @@
<title>Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" />
-<meta property="og:description" content="This function plots the confidence intervals for the parameters
- fitted using mkinfit." />
+<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" />
+<meta property="og:description" content="This function plots the confidence intervals for the parameters fitted using
+mkinfit." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,14 +134,12 @@
</div>
<div class="ref-description">
-
- <p>This function plots the confidence intervals for the parameters
- fitted using <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
-
+ <p>This function plots the confidence intervals for the parameters fitted using
+<code><a href='mkinfit.html'>mkinfit</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -148,26 +148,26 @@
<td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p>
-
+ <p>Nothing is returned by this function, as it is called for its side
+ effect, namely to produce a plot.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># \dontrun{</span>
<span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"anisole"</span>)),
- <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'># }</div></pre>
+ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'># }
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 33d69b6d..d078e239 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -8,11 +8,13 @@
<title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,15 @@
-<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" />
-<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." />
+<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" />
+<meta property="og:description" content="Deprecated function. It now only calls the plot method
+plot.mkinfit." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,13 +134,12 @@
</div>
<div class="ref-description">
-
- <p>Deprecated function. It now only calls the plot method <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p>
-
+ <p>Deprecated function. It now only calls the plot method
+<code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -150,20 +152,18 @@
<td><p>further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The function is called for its side effect.</p>
-
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ </ul>
<h2>Author</h2>
<p>Johannes Ranke</p>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 5faff3c7..f7d543ad 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -8,11 +8,13 @@
<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,15 +34,16 @@
-<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" />
+<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" />
<meta property="og:description" content="This function produces a time series for all the observed variables in a
- kinetic model as specified by mkinmod, using a specific set of
- kinetic parameters and initial values for the state variables." />
+kinetic model as specified by mkinmod, using a specific set of
+kinetic parameters and initial values for the state variables." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -111,7 +114,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -133,89 +135,105 @@
</div>
<div class="ref-description">
-
<p>This function produces a time series for all the observed variables in a
- kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of
- kinetic parameters and initial values for the state variables.</p>
-
+kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of
+kinetic parameters and initial values for the state variables.</p>
</div>
<pre class="usage"><span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
- <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for mkinmod</span>
+<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for mkinfit</span>
+<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>,
+ <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>, or a kinetic
- fit as fitted by <code><a href='mkinfit.html'>mkinfit</a></code>. In the latter case, the fitted
- parameters are used for the prediction.</p></td>
+fit as fitted by <code><a href='mkinfit.html'>mkinfit</a></code>. In the latter case, the fitted
+parameters are used for the prediction.</p></td>
</tr>
<tr>
<th>odeparms</th>
- <td><p>A numeric vector specifying the parameters used in the kinetic model, which
- is generally defined as a set of ordinary differential equations.</p></td>
+ <td><p>A numeric vector specifying the parameters used in the
+kinetic model, which is generally defined as a set of ordinary
+differential equations.</p></td>
</tr>
<tr>
<th>odeini</th>
- <td><p>A numeric vectory containing the initial values of the state variables of
- the model. Note that the state variables can differ from the observed
- variables, for example in the case of the SFORB model.</p></td>
+ <td><p>A numeric vectory containing the initial values of the state
+variables of the model. Note that the state variables can differ from the
+observed variables, for example in the case of the SFORB model.</p></td>
</tr>
<tr>
<th>outtimes</th>
- <td><p>A numeric vector specifying the time points for which model predictions
- should be generated.</p></td>
+ <td><p>A numeric vector specifying the time points for which model
+predictions should be generated.</p></td>
</tr>
<tr>
<th>solution_type</th>
- <td><p>The method that should be used for producing the predictions. This should
- generally be "analytical" if there is only one observed variable, and
- usually "deSolve" in the case of several observed variables. The third
- possibility "eigen" is faster but not applicable to some models e.g.
- using FOMC for the parent compound.</p></td>
+ <td><p>The method that should be used for producing the
+predictions. This should generally be "analytical" if there is only one
+observed variable, and usually "deSolve" in the case of several observed
+variables. The third possibility "eigen" is faster but not applicable to
+some models e.g. using FOMC for the parent compound.</p></td>
</tr>
<tr>
- <th>method.ode</th>
- <td><p>The solution method passed via <code>mkinpredict</code> to
- <code>ode</code> in case the solution type is "deSolve". The default
- "lsoda" is performant, but sometimes fails to converge.</p></td>
+ <th>use_compiled</th>
+ <td><p>If set to <code>FALSE</code>, no compiled version of the
+<code><a href='mkinmod.html'>mkinmod</a></code> model is used, even if is present.</p></td>
</tr>
<tr>
- <th>use_compiled</th>
- <td><p>If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code>
- model is used, even if is present.</p></td>
+ <th>method.ode</th>
+ <td><p>The solution method passed via <code>mkinpredict</code>
+to <code>ode</code> in case the solution type is "deSolve". The default
+"lsoda" is performant, but sometimes fails to converge.</p></td>
</tr>
<tr>
<th>atol</th>
- <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8,
- lower than in <code>lsoda</code>.</p></td>
+ <td><p>Absolute error tolerance, passed to <code>ode</code>. Default
+is 1e-8, lower than in <code>lsoda</code>.</p></td>
</tr>
<tr>
<th>rtol</th>
- <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10,
- much lower than in <code>lsoda</code>.</p></td>
+ <td><p>Absolute error tolerance, passed to <code>ode</code>. Default
+is 1e-10, much lower than in <code>lsoda</code>.</p></td>
</tr>
<tr>
<th>map_output</th>
- <td><p>Boolean to specify if the output should list values for the observed
- variables (default) or for all state variables (if set to FALSE).</p></td>
+ <td><p>Boolean to specify if the output should list values for
+the observed variables (default) or for all state variables (if set to
+FALSE).</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Further arguments passed to the ode solver in case such a solver is used.</p></td>
+ <td><p>Further arguments passed to the ode solver in case such a
+solver is used.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A matrix in the same format as the output of <code>ode</code>.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
+ <pre class="examples"><div class='input'>
+ <span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
<span class='co'># Compare solution types</span>
<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; time degradinol
@@ -342,7 +360,7 @@
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.022 0.000 0.021 </div><div class='input'>
+#&gt; 0.021 0.000 0.021 </div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># Predict from a fitted model</span>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
@@ -380,15 +398,14 @@
#&gt; 4 0.3 75.25515 3.399419
#&gt; 5 0.4 72.98675 4.441969
#&gt; 6 0.5 70.78673 5.441679</div><div class='input'> # }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index eea5b218..1ac2cdbe 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -8,11 +8,13 @@
<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,16 +34,17 @@
-<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" />
-<meta property="og:description" content="This function plots the residuals for the specified subset of the
- observed variables from an mkinfit object. A combined plot of the fitted
- model and the residuals can be obtained using plot.mkinfit
- using the argument show_residuals = TRUE." />
+<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" />
+<meta property="og:description" content="This function plots the residuals for the specified subset of the observed
+variables from an mkinfit object. A combined plot of the fitted model and
+the residuals can be obtained using plot.mkinfit using the
+argument show_residuals = TRUE." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -112,7 +115,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -134,23 +136,17 @@
</div>
<div class="ref-description">
-
- <p>This function plots the residuals for the specified subset of the
- observed variables from an mkinfit object. A combined plot of the fitted
- model and the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
- using the argument <code>show_residuals = TRUE</code>.</p>
-
+ <p>This function plots the residuals for the specified subset of the observed
+variables from an mkinfit object. A combined plot of the fitted model and
+the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the
+argument <code>show_residuals = TRUE</code>.</p>
</div>
- <pre class="usage"><span class='fu'>mkinresplot</span>(<span class='no'>object</span>,
- <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
- <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)),
- <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>,
- <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
- <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
- <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='no'>...</span>)</pre>
-
+ <pre class="usage"><span class='fu'>mkinresplot</span>(<span class='no'>object</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>,
+ <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>,
+ <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
+ <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -160,8 +156,9 @@
</tr>
<tr>
<th>obs_vars</th>
- <td><p>A character vector of names of the observed variables for which residuals
- should be plotted. Defaults to all observed variables in the model</p></td>
+ <td><p>A character vector of names of the observed variables for
+which residuals should be plotted. Defaults to all observed variables in
+the model</p></td>
</tr>
<tr>
<th>xlim</th>
@@ -173,12 +170,13 @@
</tr>
<tr>
<th>ylab</th>
- <td><p>Label for the y axis. Defaults to "Residual [% of applied radioactivity]".</p></td>
+ <td><p>Label for the y axis. Defaults to "Residual [% of applied
+radioactivity]".</p></td>
</tr>
<tr>
<th>maxabs</th>
- <td><p>Maximum absolute value of the residuals. This is used for the scaling of
- the y axis and defaults to "auto".</p></td>
+ <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
</tr>
<tr>
<th>legend</th>
@@ -186,8 +184,8 @@
</tr>
<tr>
<th>lpos</th>
- <td><p>Where should the legend be placed? Default is "topright". Will be passed on to
- <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td>
+ <td><p>Where should the legend be placed? Default is "topright". Will
+be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td>
</tr>
<tr>
<th>col_obs</th>
@@ -206,29 +204,27 @@
<td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p>
-
+ <p>Nothing is returned by this function, as it is called for its side
+ effect, namely to produce a plot.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted lines of the
- mkinfit object.</p></div>
-
+ <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted
+ lines of the mkinfit object.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div></pre>
+ <pre class="examples"><div class='input'>
+<span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#see-also">See also</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 1523138c..e38c153c 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -8,11 +8,13 @@
<title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +34,15 @@
-<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" />
+<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" />
<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for
- mkinmod." />
+mkinmod." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -132,48 +134,46 @@
</div>
<div class="ref-description">
-
<p>This is a convenience function to set up the lists used as arguments for
- <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
-
+<code><a href='mkinmod.html'>mkinmod</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>mkinsub</span>(<span class='no'>submodel</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>submodel</th>
- <td><p>Character vector of length one to specify the submodel type. See
- <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td>
+ <td><p>Character vector of length one to specify the submodel type.
+See <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td>
</tr>
<tr>
<th>to</th>
- <td><p>Vector of the names of the state variable to which a transformation
- shall be included in the model.</p></td>
+ <td><p>Vector of the names of the state variable to which a
+transformation shall be included in the model.</p></td>
</tr>
<tr>
<th>sink</th>
- <td><p>Should a pathway to sink be included in the model in addition to the
- pathways to other state variables?</p></td>
+ <td><p>Should a pathway to sink be included in the model in addition to
+the pathways to other state variables?</p></td>
</tr>
<tr>
<th>full_name</th>
- <td><p>An optional name to be used e.g. for plotting fits performed with the model.
- You can use non-ASCII characters here, but then your R code will not be
- portable, <em>i.e.</em> may produce unintended plot results on other
- operating systems or system configurations.</p></td>
+ <td><p>An optional name to be used e.g. for plotting fits
+performed with the model. You can use non-ASCII characters here, but then
+your R code will not be portable, <em>i.e.</em> may produce unintended plot
+results on other operating systems or system configurations.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># One parent compound, one metabolite, both single first order.</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
@@ -184,15 +184,14 @@
<span class='co'># Now supplying full names</span>
<span class='no'>SFO_SFO.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div></pre>
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png
index 9d8c0931..201ef0fd 100644
--- a/docs/reference/mmkin-4.png
+++ b/docs/reference/mmkin-4.png
Binary files differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 0f384062..8312c17c 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -6,13 +6,16 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title>
+<title>Fit one or more kinetic models with one or more state variables to one or
+more datasets — mmkin • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,14 +35,16 @@
-<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" />
-<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets
- specified in its first two arguments." />
+<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or
+more datasets — mmkin" />
+<meta property="og:description" content="This function calls mkinfit on all combinations of models and
+datasets specified in its first two arguments." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -110,7 +115,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -126,65 +130,64 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1>
+ <h1>Fit one or more kinetic models with one or more state variables to one or
+more datasets</h1>
<div class="hidden name"><code>mmkin.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and datasets
- specified in its first two arguments.</p>
-
+ <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and
+datasets specified in its first two arguments.</p>
</div>
- <pre class="usage"><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>,
- <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-
+ <pre class="usage"><span class='fu'>mmkin</span>(<span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>datasets</span>,
+ <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>models</th>
- <td><p>Either a character vector of shorthand names ("SFO", "FOMC", "DFOP",
- "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code>
- objects.</p></td>
+ <td><p>Either a character vector of shorthand names like
+<code><a href='https://rdrr.io/r/base/c.html'>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</a></code>, or an optionally named
+list of <code><a href='mkinmod.html'>mkinmod</a></code> objects.</p></td>
</tr>
<tr>
<th>datasets</th>
- <td><p>An optionally named list of datasets suitable as observed data for
- <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ <td><p>An optionally named list of datasets suitable as observed
+data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
</tr>
<tr>
<th>cores</th>
- <td><p>The number of cores to be used for multicore processing. This is only
- used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines,
- cores &gt; 1 is not supported, you need to use the <code>cluster</code> argument
- to use multiple logical processors.</p></td>
+ <td><p>The number of cores to be used for multicore processing. This
+is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows
+machines, cores &gt; 1 is not supported, you need to use the <code>cluster</code>
+argument to use multiple logical processors.</p></td>
</tr>
<tr>
<th>cluster</th>
- <td><p>A cluster as returned by <code>makeCluster</code> to be used for parallel
- execution.</p></td>
+ <td><p>A cluster as returned by <code>makeCluster</code> to be used
+for parallel execution.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model
- and dataset names as row and column indices.</p>
-
+ <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using
+ the model and dataset names as row and column indices.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p></div>
-
+ <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for
+ plotting.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># \dontrun{</span>
<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
@@ -199,8 +202,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.016 0.029 4.960 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 19.084 0.004 19.099 </div><div class='input'>
+#&gt; 0.011 0.032 4.774 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 18.676 0.000 18.687 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340481 0.2659519 0.7505684 0.2494316
@@ -221,17 +224,15 @@
<span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
<span class='co'># allow to plot the observed variables separately</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#see-also">See also</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index c5ea9a9a..60917ff4 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -8,11 +8,13 @@
<title>Evaluate parent kinetics using the NAFTA guidance — nafta • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,15 +34,18 @@
-<meta property="og:title" content="Evaluate parent kinetics using the NAFTA guidance — nafta" />
-<meta property="og:description" content="The function fits the SFO, IORE and DFOP models using
- mmkin and returns an object of class
- nafta that has methods for printing and plotting." />
+<meta property="og:title" content="Evaluate parent kinetics using the NAFTA guidance — nafta" />
+<meta property="og:description" content="The function fits the SFO, IORE and DFOP models using mmkin
+and returns an object of class nafta that has methods for printing
+and plotting.
+Print nafta objects. The results for the three models are printed in the
+order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -111,7 +116,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -133,24 +137,27 @@
</div>
<div class="ref-description">
-
- <p>The function fits the SFO, IORE and DFOP models using
- <code><a href='mmkin.html'>mmkin</a></code> and returns an object of class
- <code>nafta</code> that has methods for printing and plotting.</p>
-
+ <p>The function fits the SFO, IORE and DFOP models using <code><a href='mmkin.html'>mmkin</a></code>
+and returns an object of class <code>nafta</code> that has methods for printing
+and plotting.</p>
+<p>Print nafta objects. The results for the three models are printed in the
+order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</p>
</div>
- <pre class="usage"><span class='fu'>nafta</span>(<span class='no'>ds</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-
+ <pre class="usage"><span class='fu'>nafta</span>(<span class='no'>ds</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for nafta</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>ds</th>
- <td><p>A dataframe that must contain one variable called "time" with the time
- values specified by the <code>time</code> argument, one column called "name" with
- the grouping of the observed values, and finally one column of observed
- values called "value".</p></td>
+ <td><p>A dataframe that must contain one variable called "time" with the
+time values specified by the <code>time</code> argument, one column called
+"name" with the grouping of the observed values, and finally one column of
+observed values called "value".</p></td>
</tr>
<tr>
<th>title</th>
@@ -162,31 +169,41 @@
</tr>
<tr>
<th>...</th>
- <td><p>Further arguments passed to <code><a href='mmkin.html'>mmkin</a></code>.</p></td>
+ <td><p>Further arguments passed to <code><a href='mmkin.html'>mmkin</a></code> (not for the
+printing method).</p></td>
+ </tr>
+ <tr>
+ <th>x</th>
+ <td><p>An <code>nafta</code> object.</p></td>
+ </tr>
+ <tr>
+ <th>digits</th>
+ <td><p>Number of digits to be used for printing parameters and
+dissipation times.</p></td>
</tr>
</table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>An list of class <code>nafta</code>. The list element named "mmkin" is the
- <code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models.
- The list element named "title" contains the title of the dataset used.
- The list element "data" contains the dataset used in the fits.</p>
-
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
- <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
- in environmental media. NAFTA Technical Working Group on Pesticides
+ <p>NAFTA (2011) Guidance for evaluating and calculating degradation
+ kinetics in environmental media. NAFTA Technical Working Group on
+ Pesticides
<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
accessed 2019-02-22</p>
<p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
Calculate Representative Half-life Values and Characterizing Pesticide
Degradation
<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
-
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An list of class <code>nafta</code>. The list element named "mmkin" is the
+ <code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models. The
+ list element named "title" contains the title of the dataset used. The
+ list element "data" contains the dataset used in the fits.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
+ <pre class="examples"><div class='input'>
+ <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Sums of squares:
#&gt; SFO IORE DFOP
#&gt; 1378.6832 615.7730 517.8836
#&gt;
@@ -223,17 +240,15 @@
#&gt; DFOP 429 2380 841
#&gt;
#&gt; Representative half-life:
-#&gt; [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre>
+#&gt; [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
- <li><a href="#value">Value</a></li>
-
<li><a href="#source">Source</a></li>
-
+ <li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png
index 60203c3d..20f30221 100644
--- a/docs/reference/plot.mkinfit-4.png
+++ b/docs/reference/plot.mkinfit-4.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png
index 20f30221..ad2ffa8c 100644
--- a/docs/reference/plot.mkinfit-5.png
+++ b/docs/reference/plot.mkinfit-5.png
Binary files differ
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index df01a00b..04ef75e4 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -8,11 +8,13 @@
<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,18 +34,16 @@
-<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
+<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" />
<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters
- from a previous successful call to mkinfit and plots
- the observed data together with the solution of the fitted model.
-If the current plot device is a tikz device,
- then latex is being used for the formatting of the chi2 error level,
- if show_errmin = TRUE." />
+from a previous successful call to mkinfit and plots the
+observed data together with the solution of the fitted model." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -114,7 +114,6 @@ If the current plot device is a tikz device,
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -136,42 +135,34 @@ If the current plot device is a tikz device,
</div>
<div class="ref-description">
-
<p>Solves the differential equations with the optimised and fixed parameters
- from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots
- the observed data together with the solution of the fitted model.</p>
-<p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device,
- then latex is being used for the formatting of the chi2 error level,
- if <code>show_errmin = TRUE</code>.</p>
-
+from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the
+observed data together with the solution of the fitted model.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>,
- <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
- <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>,
- <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>),
- <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>,
- <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>,
- <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)),
- <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>,
- <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
- <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
- <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>),
- <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</span>, <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
+ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Observed"</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>),
+ <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>), <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>,
+ <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)), <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>,
+ <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+
<span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)
+
<span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
- <td><p>Alias for fit introduced for compatibility with the generic S3 method.</p></td>
+ <td><p>Alias for fit introduced for compatibility with the generic S3
+method.</p></td>
</tr>
<tr>
<th>fit</th>
@@ -179,9 +170,9 @@ If the current plot device is a tikz device,
</tr>
<tr>
<th>obs_vars</th>
- <td><p>A character vector of names of the observed variables for which the
- data and the model should be plotted. Defauls to all observed variables
- in the model.</p></td>
+ <td><p>A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.</p></td>
</tr>
<tr>
<th>xlab</th>
@@ -201,7 +192,8 @@ If the current plot device is a tikz device,
</tr>
<tr>
<th>col_obs</th>
- <td><p>Colors used for plotting the observed data and the corresponding model prediction lines.</p></td>
+ <td><p>Colors used for plotting the observed data and the
+corresponding model prediction lines.</p></td>
</tr>
<tr>
<th>pch_obs</th>
@@ -221,41 +213,44 @@ If the current plot device is a tikz device,
</tr>
<tr>
<th>show_residuals</th>
- <td><p>Should residuals be shown? If only one plot of the fits is shown, the
- residual plot is in the lower third of the plot. Otherwise, i.e. if
- "sep_obs" is given, the residual plots will be located to the right of
- the plots of the fitted curves.</p></td>
+ <td><p>Should residuals be shown? If only one plot of the
+fits is shown, the residual plot is in the lower third of the plot.
+Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
+to the right of the plots of the fitted curves.</p></td>
</tr>
<tr>
<th>show_errplot</th>
- <td><p>Should squared residuals and the error model be shown? If only one plot of
- the fits is shown, this plot is in the lower third of the plot.
- Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
- to the right of the plots of the fitted curves.</p></td>
+ <td><p>Should squared residuals and the error model be shown?
+If only one plot of the fits is shown, this plot is in the lower third of
+the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will
+be located to the right of the plots of the fitted curves.</p></td>
</tr>
<tr>
<th>maxabs</th>
- <td><p>Maximum absolute value of the residuals. This is used for the scaling of
- the y axis and defaults to "auto".</p></td>
+ <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
</tr>
<tr>
<th>sep_obs</th>
- <td><p>Should the observed variables be shown in separate subplots? If yes, residual plots
- requested by "show_residuals" will be shown next to, not below the plot of the fits.</p></td>
+ <td><p>Should the observed variables be shown in separate subplots?
+If yes, residual plots requested by "show_residuals" will be shown next
+to, not below the plot of the fits.</p></td>
</tr>
<tr>
<th>rel.height.middle</th>
- <td><p>The relative height of the middle plot, if more than two rows of plots are shown.</p></td>
+ <td><p>The relative height of the middle plot, if more
+than two rows of plots are shown.</p></td>
</tr>
<tr>
<th>row_layout</th>
- <td><p>Should we use a row layout where the residual plot or the error model plot is shown
- to the right?</p></td>
+ <td><p>Should we use a row layout where the residual plot or the
+error model plot is shown to the right?</p></td>
</tr>
<tr>
<th>lpos</th>
- <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as the first argument.
- If not length one, this should be of the same length as the obs_var argument.</p></td>
+ <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as
+the first argument. If not length one, this should be of the same length
+as the obs_var argument.</p></td>
</tr>
<tr>
<th>inset</th>
@@ -263,11 +258,13 @@ If the current plot device is a tikz device,
</tr>
<tr>
<th>show_errmin</th>
- <td><p>Should the FOCUS chi2 error value be shown in the upper margin of the plot?</p></td>
+ <td><p>Should the FOCUS chi2 error value be shown in the upper
+margin of the plot?</p></td>
</tr>
<tr>
<th>errmin_digits</th>
- <td><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></td>
+ <td><p>The number of significant digits for rounding the FOCUS
+chi2 error percentage.</p></td>
</tr>
<tr>
<th>frame</th>
@@ -278,38 +275,41 @@ If the current plot device is a tikz device,
<td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The function is called for its side effect.</p>
-
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then
+latex is being used for the formatting of the chi2 error level, if
+<code>show_errmin = TRUE</code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span>
+ <pre class="examples"><div class='input'>
+<span class='co'># One parent compound, one metabolite, both single first order, path from</span>
<span class='co'># parent to sink included</span>
<span class='co'># \dontrun{</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='co'># Show the observed variables separately</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Show the observed variables separately, with residuals</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
- <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span>
<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))
<span class='co'># Show the observed variables separately, with the error model</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
- <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'># }
+ <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
index 44037bb4..13d96256 100644
--- a/docs/reference/plot.mmkin-4.png
+++ b/docs/reference/plot.mmkin-4.png
Binary files differ
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 9a11108f..8b68cfae 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -6,13 +6,16 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin</title>
+<title>Plot model fits (observed and fitted) and the residuals for a row or column
+of an mmkin object — plot.mmkin • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,17 +35,17 @@
-<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" />
-<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model
- fitted for at least one dataset is shown. When it is a column, the fit of at least one model
- to the same dataset is shown.
-If the current plot device is a tikz device,
- then latex is being used for the formatting of the chi2 error level." />
+<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column
+of an mmkin object — plot.mmkin" />
+<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the
+same model fitted for at least one dataset is shown. When it is a column,
+the fit of at least one model to the same dataset is shown." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -113,7 +116,6 @@ If the current plot device is a tikz device,
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -129,32 +131,31 @@ If the current plot device is a tikz device,
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1>
+ <h1>Plot model fits (observed and fitted) and the residuals for a row or column
+of an mmkin object</h1>
<div class="hidden name"><code>plot.mmkin.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>When x is a row selected from an mmkin object (<code><a href='Extract.mmkin.html'>[.mmkin</a></code>), the same model
- fitted for at least one dataset is shown. When it is a column, the fit of at least one model
- to the same dataset is shown.</p>
-<p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device,
- then latex is being used for the formatting of the chi2 error level.</p>
-
+ <p>When x is a row selected from an mmkin object (<code><a href='Extract.mmkin.html'>[.mmkin</a></code>), the
+same model fitted for at least one dataset is shown. When it is a column,
+the fit of at least one model to the same dataset is shown.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>,
- <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre>
-
+ <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
+ <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
- <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one column.</p></td>
+ <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one
+column.</p></td>
</tr>
<tr>
<th>main</th>
@@ -166,21 +167,24 @@ If the current plot device is a tikz device,
</tr>
<tr>
<th>resplot</th>
- <td><p>Should the residuals plotted against time, using <code><a href='mkinresplot.html'>mkinresplot</a></code>,
- or as squared residuals against predicted values, with the error model,
- using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
+ <td><p>Should the residuals plotted against time, using
+<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
+values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
</tr>
<tr>
<th>show_errmin</th>
- <td><p>Should the chi2 error level be shown on top of the plots to the left?</p></td>
+ <td><p>Should the chi2 error level be shown on top of the plots
+to the left?</p></td>
</tr>
<tr>
<th>errmin_var</th>
- <td><p>The variable for which the FOCUS chi2 error value should be shown.</p></td>
+ <td><p>The variable for which the FOCUS chi2 error value should
+be shown.</p></td>
</tr>
<tr>
<th>errmin_digits</th>
- <td><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></td>
+ <td><p>The number of significant digits for rounding the FOCUS
+chi2 error percentage.</p></td>
</tr>
<tr>
<th>cex</th>
@@ -188,21 +192,27 @@ If the current plot device is a tikz device,
</tr>
<tr>
<th>rel.height.middle</th>
- <td><p>The relative height of the middle plot, if more than two rows of plots are shown.</p></td>
+ <td><p>The relative height of the middle plot, if more
+than two rows of plots are shown.</p></td>
</tr>
<tr>
<th>...</th>
- <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td>
+ <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
+<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The function is called for its side effect.</p>
-
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then
+latex is being used for the formatting of the chi2 error level.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span>
+ <pre class="examples"><div class='input'>
+ <span class='co'># \dontrun{</span>
<span class='co'># Only use one core not to offend CRAN checks</span>
<span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>),
<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</span>
@@ -214,15 +224,15 @@ If the current plot device is a tikz device,
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Show the error models</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> # }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index c5eed391..294a79a4 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -6,15 +6,15 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Plot the results of the three models used in the NAFTA scheme. The plots
- are ordered with increasing complexity of the model in this function
- (SFO, then IORE, then DFOP). — plot.nafta • mkin</title>
+<title>Plot the results of the three models used in the NAFTA scheme. — plot.nafta • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -34,15 +34,15 @@
-<meta property="og:title" content="Plot the results of the three models used in the NAFTA scheme. The plots
- are ordered with increasing complexity of the model in this function
- (SFO, then IORE, then DFOP). — plot.nafta" />
-<meta property="og:description" content="Calls plot.mmkin." />
+<meta property="og:title" content="Plot the results of the three models used in the NAFTA scheme. — plot.nafta" />
+<meta property="og:description" content="The plots are ordered with increasing complexity of the model in this
+function (SFO, then IORE, then DFOP)." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -113,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -129,22 +128,19 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Plot the results of the three models used in the NAFTA scheme. The plots
- are ordered with increasing complexity of the model in this function
- (SFO, then IORE, then DFOP).</h1>
+ <h1>Plot the results of the three models used in the NAFTA scheme.</h1>
<div class="hidden name"><code>plot.nafta.Rd</code></div>
</div>
<div class="ref-description">
-
- <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p>
-
+ <p>The plots are ordered with increasing complexity of the model in this
+function (SFO, then IORE, then DFOP).</p>
</div>
<pre class="usage"><span class='co'># S3 method for nafta</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -165,20 +161,22 @@
<td><p>Further arguments passed to <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The function is called for its side effect.</p>
-
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
- </ul>
+ <li><a href="#details">Details</a></li>
+ </ul>
<h2>Author</h2>
<p>Johannes Ranke</p>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 810123b8..d7ba94e1 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -8,11 +8,13 @@
<title>Print mkinds objects — print.mkinds • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,14 @@
-<meta property="og:title" content="Print mkinds objects — print.mkinds" />
+<meta property="og:title" content="Print mkinds objects — print.mkinds" />
<meta property="og:description" content="Print mkinds objects." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +112,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,14 +133,12 @@
</div>
<div class="ref-description">
-
<p>Print mkinds objects.</p>
-
</div>
<pre class="usage"><span class='co'># S3 method for mkinds</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -151,14 +151,14 @@
<td><p>Not used.</p></td>
</tr>
</table>
-
+
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
- </ul>
+ </ul>
</div>
</div>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 5a8feab8..03e73e29 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -8,11 +8,13 @@
<title>Print mkinmod objects — print.mkinmod • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,13 +34,15 @@
-<meta property="og:title" content="Print mkinmod objects — print.mkinmod" />
-<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." />
+<meta property="og:title" content="Print mkinmod objects — print.mkinmod" />
+<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its
+components." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -109,7 +113,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -131,14 +134,13 @@
</div>
<div class="ref-description">
-
- <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p>
-
+ <p>Print mkinmod objects in a way that the user finds his way to get to its
+components.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinmod</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -151,10 +153,11 @@
<td><p>Not used.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
+ <pre class="examples"><div class='input'>
+ <span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
@@ -171,13 +174,13 @@
#&gt; Differential equations:
#&gt; d_parent/dt = - k_parent * parent
#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
-#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div></pre>
+#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index ef62212a..d95e1c28 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -36,13 +36,8 @@
<meta property="og:title" content="Two component error model — sigma_twocomp" />
-<meta property="og:description" content="Function describing the standard deviation of the measurement error
- in dependence of the measured value \(y\):
-$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$
- sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)
-This is the error model used for example by Werner et al. (1978). The model
- proposed by Rocke and Lorenzato (1995) can be written in this form as well,
- but assumes approximate lognormal distribution of errors for high values of y." />
+<meta property="og:description" content="Function describing the standard deviation of the measurement error in
+dependence of the measured value \(y\):" />
<meta name="twitter:card" content="summary" />
@@ -139,13 +134,8 @@ This is the error model used for example by Werner et al. (1978). The model
</div>
<div class="ref-description">
- <p>Function describing the standard deviation of the measurement error
- in dependence of the measured value \(y\):</p>
-<p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$
- sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)</p>
-<p>This is the error model used for example by Werner et al. (1978). The model
- proposed by Rocke and Lorenzato (1995) can be written in this form as well,
- but assumes approximate lognormal distribution of errors for high values of y.</p>
+ <p>Function describing the standard deviation of the measurement error in
+dependence of the measured value \(y\):</p>
</div>
<pre class="usage"><span class='fu'>sigma_twocomp</span>(<span class='no'>y</span>, <span class='no'>sigma_low</span>, <span class='no'>rsd_high</span>)</pre>
@@ -159,18 +149,27 @@ This is the error model used for example by Werner et al. (1978). The model
</tr>
<tr>
<th>sigma_low</th>
- <td><p>The asymptotic minimum of the standard deviation for low observed values</p></td>
+ <td><p>The asymptotic minimum of the standard deviation for low
+observed values</p></td>
</tr>
<tr>
<th>rsd_high</th>
- <td><p>The coefficient describing the increase of the standard deviation with
- the magnitude of the observed value</p></td>
+ <td><p>The coefficient describing the increase of the standard
+deviation with the magnitude of the observed value</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The standard deviation of the response variable.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ sigma =
+sqrt(sigma_low^2 + y^2 * rsd_high^2)</p>
+<p>This is the error model used for example by Werner et al. (1978). The model
+proposed by Rocke and Lorenzato (1995) can be written in this form as well,
+but assumes approximate lognormal distribution of errors for high values of
+y.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978)
@@ -185,6 +184,7 @@ This is the error model used for example by Werner et al. (1978). The model
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
+ <li><a href="#details">Details</a></li>
<li><a href="#references">References</a></li>
</ul>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 73410181..65bc6326 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -8,11 +8,13 @@
<title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,16 +34,18 @@
-<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" />
-<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with some
- uncertainty statistics, the chi2 error levels calculated according to FOCUS
- guidance (2006) as defined therein, formation fractions, DT50 values and
- optionally the data, consisting of observed, predicted and residual values." />
+<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" />
+<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with
+some uncertainty statistics, the chi2 error levels calculated according to
+FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+and optionally the data, consisting of observed, predicted and residual
+values." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -112,7 +116,6 @@
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -134,19 +137,21 @@
</div>
<div class="ref-description">
-
- <p>Lists model equations, initial parameter values, optimised parameters with some
- uncertainty statistics, the chi2 error levels calculated according to FOCUS
- guidance (2006) as defined therein, formation fractions, DT50 values and
- optionally the data, consisting of observed, predicted and residual values.</p>
-
+ <p>Lists model equations, initial parameter values, optimised parameters with
+some uncertainty statistics, the chi2 error levels calculated according to
+FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+and optionally the data, consisting of observed, predicted and residual
+values.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>)
+
<span class='co'># S3 method for summary.mkinfit</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre>
-
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) -
+ <span class='fl'>3</span>), <span class='no'>...</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -155,91 +160,94 @@
<td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
</tr>
<tr>
- <th>x</th>
- <td><p>an object of class <code>summary.mkinfit</code>.</p></td>
- </tr>
- <tr>
<th>data</th>
- <td><p>logical, indicating whether the data should be included in the summary.</p></td>
+ <td><p>logical, indicating whether the data should be included in the
+summary.</p></td>
</tr>
<tr>
<th>distimes</th>
- <td><p>logical, indicating whether DT50 and DT90 values should be included.</p></td>
+ <td><p>logical, indicating whether DT50 and DT90 values should be
+included.</p></td>
</tr>
<tr>
<th>alpha</th>
- <td><p>error level for confidence interval estimation from t distribution</p></td>
- </tr>
- <tr>
- <th>digits</th>
- <td><p>Number of digits to use for printing</p></td>
+ <td><p>error level for confidence interval estimation from t
+distribution</p></td>
</tr>
<tr>
<th>...</th>
<td><p>optional arguments passed to methods like <code>print</code>.</p></td>
</tr>
+ <tr>
+ <th>x</th>
+ <td><p>an object of class <code>summary.mkinfit</code>.</p></td>
+ </tr>
+ <tr>
+ <th>digits</th>
+ <td><p>Number of digits to use for printing</p></td>
+ </tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The summary function returns a list with components, among others</p>
<dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd>
- <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were produced</p></dd>
+ <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were
+ produced</p></dd>
+ <dt>diffs</dt><dd><p>The differential equations used in the model</p></dd>
<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
- <dt>residuals, residualVariance, sigma, modVariance, df</dt><dd><p>As in summary.modFit</p></dd>
- <dt>cov.unscaled, cov.scaled, info, niter, stopmess, par</dt><dd><p>As in summary.modFit</p></dd>
- <dt>bpar</dt><dd><p>Optimised and backtransformed parameters</p></dd>
- <dt>diffs </dt><dd><p>The differential equations used in the model</p></dd>
- <dt>data </dt><dd><p>The data (see Description above).</p></dd>
- <dt>start </dt><dd><p>The starting values and bounds, if applicable, for optimised parameters.</p></dd>
- <dt>fixed </dt><dd><p>The values of fixed parameters.</p></dd>
- <dt>errmin </dt><dd><p>The chi2 error levels for each observed variable.</p></dd>
- <dt>bparms.ode </dt><dd><p>All backtransformed ODE parameters, for use as starting parameters for
- related models.</p></dd>
- <dt>errparms </dt><dd><p>Error model parameters.</p></dd>
- <dt>ff </dt><dd><p>The estimated formation fractions derived from the fitted model.</p></dd>
- <dt>distimes </dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+ <dt>bpar</dt><dd><p>Optimised and backtransformed
+ parameters</p></dd>
+ <dt>data</dt><dd><p>The data (see Description above).</p></dd>
+ <dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised
+ parameters.</p></dd>
+ <dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd>
+ <dt>errmin </dt><dd><p>The chi2 error levels for
+ each observed variable.</p></dd>
+ <dt>bparms.ode</dt><dd><p>All backtransformed ODE
+ parameters, for use as starting parameters for related models.</p></dd>
+ <dt>errparms</dt><dd><p>Error model parameters.</p></dd>
+ <dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
+ model.</p></dd>
+ <dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
The print method is called for its side effect, i.e. printing the summary.
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
+ <pre class="examples"><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Thu Sep 19 09:52:40 2019
-#&gt; Date of summary: Thu Sep 19 09:52:40 2019
+#&gt; Date of fit: Fri Oct 25 02:09:45 2019
+#&gt; Date of summary: Fri Oct 25 02:09:45 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 131 model solutions performed in 0.27 s
+#&gt; Fitted using 131 model solutions performed in 0.274 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
#&gt; Error model algorithm: OLS
#&gt;
#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 101.240000 state
-#&gt; k_parent_sink 0.100000 deparm
-#&gt; sigma 5.265546 error
+#&gt; value type
+#&gt; parent_0 101.24 state
+#&gt; k_parent_sink 0.10 deparm
#&gt;
#&gt; Starting values for the transformed parameters actually optimised:
#&gt; value lower upper
#&gt; parent_0 101.240000 -Inf Inf
#&gt; log_k_parent_sink -2.302585 -Inf Inf
-#&gt; sigma 5.265546 0 Inf
#&gt;
#&gt; Fixed parameter values:
#&gt; None
@@ -287,17 +295,15 @@
#&gt; 30 parent 29.71 35.738 -6.0283
#&gt; 62 parent 5.98 10.862 -4.8818
#&gt; 90 parent 1.54 3.831 -2.2911
-#&gt; 118 parent 0.39 1.351 -0.9613</div></pre>
+#&gt; 118 parent 0.39 1.351 -0.9613</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index b1a952d9..4d88a03e 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -8,11 +8,13 @@
<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title>
+
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
@@ -32,21 +34,19 @@
-<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" />
-<meta property="og:description" content="The transformations are intended to map parameters that should only take
- on restricted values to the full scale of real numbers. For kinetic rate
- constants and other paramters that can only take on positive values, a
- simple log transformation is used. For compositional parameters, such as
- the formations fractions that should always sum up to 1 and can not be
- negative, the ilr transformation is used.
-The transformation of sets of formation fractions is fragile, as it supposes
- the same ordering of the components in forward and backward transformation.
- This is no problem for the internal use in mkinfit." />
+<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" />
+<meta property="og:description" content="The transformations are intended to map parameters that should only take on
+restricted values to the full scale of real numbers. For kinetic rate
+constants and other paramters that can only take on positive values, a
+simple log transformation is used. For compositional parameters, such as the
+formations fractions that should always sum up to 1 and can not be negative,
+the ilr transformation is used." />
<meta name="twitter:card" content="summary" />
+
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -117,7 +117,6 @@ The transformation of sets of formation fractions is fragile, as it supposes
<a href="../news/index.html">News</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -139,71 +138,80 @@ The transformation of sets of formation fractions is fragile, as it supposes
</div>
<div class="ref-description">
-
- <p>The transformations are intended to map parameters that should only take
- on restricted values to the full scale of real numbers. For kinetic rate
- constants and other paramters that can only take on positive values, a
- simple log transformation is used. For compositional parameters, such as
- the formations fractions that should always sum up to 1 and can not be
- negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p>
-<p>The transformation of sets of formation fractions is fragile, as it supposes
- the same ordering of the components in forward and backward transformation.
- This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
-
+ <p>The transformations are intended to map parameters that should only take on
+restricted values to the full scale of real numbers. For kinetic rate
+constants and other paramters that can only take on positive values, a
+simple log transformation is used. For compositional parameters, such as the
+formations fractions that should always sum up to 1 and can not be negative,
+the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p>
</div>
- <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>,
- <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>,
- <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-
+ <pre class="usage"><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
+<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>parms</th>
- <td><p>Parameters of kinetic models as used in the differential equations.</p></td>
- </tr>
- <tr>
- <th>transparms</th>
- <td><p>Transformed parameters of kinetic models as used in the fitting procedure.</p></td>
+ <td><p>Parameters of kinetic models as used in the differential
+equations.</p></td>
</tr>
<tr>
<th>mkinmod</th>
- <td><p>The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of
- the model variables that are needed for grouping the formation fractions
- before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and
- the information if the pathway to sink is included in the model.</p></td>
+ <td><p>The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing
+the names of the model variables that are needed for grouping the
+formation fractions before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter
+names and the information if the pathway to sink is included in the model.</p></td>
</tr>
<tr>
<th>transform_rates</th>
- <td><p>Boolean specifying if kinetic rate constants should be transformed in the
- model specification used in the fitting for better compliance with the
- assumption of normal distribution of the estimator. If TRUE, also
- alpha and beta parameters of the FOMC model are log-transformed, as well
- as k1 and k2 rate constants for the DFOP and HS models and the break point tb
- of the HS model.</p></td>
+ <td><p>Boolean specifying if kinetic rate constants should
+be transformed in the model specification used in the fitting for better
+compliance with the assumption of normal distribution of the estimator. If
+TRUE, also alpha and beta parameters of the FOMC model are
+log-transformed, as well as k1 and k2 rate constants for the DFOP and HS
+models and the break point tb of the HS model.</p></td>
</tr>
<tr>
<th>transform_fractions</th>
- <td><p>Boolean specifying if formation fractions constants should be transformed in the
- model specification used in the fitting for better compliance with the
- assumption of normal distribution of the estimator. The default (TRUE) is
- to do transformations. The g parameter of the DFOP and HS models are also
- transformed, as they can also be seen as compositional data. The
- transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code>
- transformation.</p></td>
+ <td><p>Boolean specifying if formation fractions
+constants should be transformed in the model specification used in the
+fitting for better compliance with the assumption of normal distribution
+of the estimator. The default (TRUE) is to do transformations. The g
+parameter of the DFOP and HS models are also transformed, as they can also
+be seen as compositional data. The transformation used for these
+transformations is the <code><a href='ilr.html'>ilr</a></code> transformation.</p></td>
+ </tr>
+ <tr>
+ <th>transparms</th>
+ <td><p>Transformed parameters of kinetic models as used in the
+fitting procedure.</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>A vector of transformed or backtransformed parameters with the same names
- as the original parameters.</p>
+ <p>A vector of transformed or backtransformed parameters with the same
+ names as the original parameters.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The transformation of sets of formation fractions is fragile, as it supposes
+the same ordering of the components in forward and backward transformation.
+This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
+ <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
+
+<ul>
+<li><p><code>backtransform_odeparms</code>: Backtransform the set of transformed parameters</p></li>
+</ul>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
+ <pre class="examples"><div class='input'>
+<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.s</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)
@@ -278,15 +286,16 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt; k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075
#&gt; k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019
#&gt; sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div><div class='input'># }
+
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#value">Value</a></li>
-
+ <li><a href="#details">Details</a></li>
+ <li><a href="#functions">Functions</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 9d241510..b62b9a44 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -133,9 +133,6 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html</loc>
</url>
<url>
- <loc>https://pkgdown.jrwb.de/mkin/reference/print.nafta.html</loc>
- </url>
- <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc>
</url>
<url>

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