Static documentation rebuilt by pkgdown

1 files changed, 65 insertions, 59 deletions

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>