Update static docs

1 files changed, 48 insertions, 19 deletions

diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 6d816366..17ecdfe4 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -21,7 +21,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -95,70 +95,99 @@ values.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span>
-<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="co"># S3 method for summary.mkinfit</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for summary.mkinfit</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>object</dt>
 <dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
+
+
 <dt>data</dt>
 <dd><p>logical, indicating whether the data should be included in the
 summary.</p></dd>
+
+
 <dt>distimes</dt>
 <dd><p>logical, indicating whether DT50 and DT90 values should be
 included.</p></dd>
+
+
 <dt>alpha</dt>
 <dd><p>error level for confidence interval estimation from t
 distribution</p></dd>
+
+
 <dt>...</dt>
 <dd><p>optional arguments passed to methods like <code>print</code>.</p></dd>
+
+
 <dt>x</dt>
 <dd><p>an object of class <code>summary.mkinfit</code>.</p></dd>
+
+
 <dt>digits</dt>
 <dd><p>Number of digits to use for printing</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>The summary function returns a list with components, among others</p>
+    
+
+<p>The summary function returns a list with components, among others</p>
 <dl><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>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>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>
+
 </dl><p>The print method is called for its side effect, i.e. printing the summary.</p>
     </div>
     <div id="references">
@@ -176,19 +205,19 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:42:00 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:42:00 2022 </span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Fri Jul 22 11:39:29 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Jul 22 11:39:29 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.027 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.028 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -220,9 +249,9 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Parameter correlation:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               parent_0 log_k_parent     sigma</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     1.000e+00    5.428e-01 1.648e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent 5.428e-01    1.000e+00 2.514e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sigma        1.648e-07    2.514e-07 1.000e+00</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     1.000e+00    5.428e-01 1.642e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent 5.428e-01    1.000e+00 2.507e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma        1.642e-07    2.507e-07 1.000e+00</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Confidence intervals for internally transformed parameters are asymmetric.</span>
@@ -252,7 +281,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 <span class="r-out co"><span class="r-pr">#&gt;</span>    62   parent     5.98    10.862  -4.8818</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    90   parent     1.54     3.831  -2.2911</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   118   parent     0.39     1.351  -0.9613</span>
-<span class="r-in"></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -267,7 +296,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
 </div>
 
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