Complete update of online docs for v1.2.0

1 files changed, 81 insertions, 58 deletions

diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 3a129533..4332ba05 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -19,7 +19,7 @@ may depend on the predicted value and is specified as a standard deviation."><!-
       </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">1.2.0</span>
       </span>
     </div>
 
@@ -46,19 +46,25 @@ may depend on the predicted value and is specified as a standard deviation."><!-
       <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -91,16 +97,16 @@ may depend on the predicted value and is specified as a standard deviation.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">add_err</span><span class="op">(</span>
-  <span class="va">prediction</span>,
-  <span class="va">sdfunc</span>,
-  secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,
-  n <span class="op">=</span> <span class="fl">10</span>,
-  LOD <span class="op">=</span> <span class="fl">0.1</span>,
-  reps <span class="op">=</span> <span class="fl">2</span>,
-  digits <span class="op">=</span> <span class="fl">1</span>,
-  seed <span class="op">=</span> <span class="cn">NA</span>
-<span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span>
+<span>  <span class="va">prediction</span>,</span>
+<span>  <span class="va">sdfunc</span>,</span>
+<span>  secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">10</span>,</span>
+<span>  LOD <span class="op">=</span> <span class="fl">0.1</span>,</span>
+<span>  reps <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>  digits <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  seed <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -108,29 +114,46 @@ may depend on the predicted value and is specified as a standard deviation.</p>
     <dl><dt>prediction</dt>
 <dd><p>A prediction from a kinetic model as produced by
 <code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd>
+
+
 <dt>sdfunc</dt>
 <dd><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></dd>
+
+
 <dt>secondary</dt>
 <dd><p>The names of state variables that should have an initial
 value of zero</p></dd>
+
+
 <dt>n</dt>
 <dd><p>The number of datasets to be generated.</p></dd>
+
+
 <dt>LOD</dt>
 <dd><p>The limit of detection (LOD). Values that are below the LOD after
 adding the random error will be set to NA.</p></dd>
+
+
 <dt>reps</dt>
 <dd><p>The number of replicates to be generated within the datasets.</p></dd>
+
+
 <dt>digits</dt>
 <dd><p>The number of digits to which the values will be rounded.</p></dd>
+
+
 <dt>seed</dt>
 <dd><p>The seed used for the generation of random numbers. If NA, the
 seed is not set.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the
+    
+
+<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>
     </div>
     <div id="references">
@@ -147,53 +170,53 @@ https://jrwb.de/posters/piacenza_2015.pdf</p>
 
     <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="co"># The kinetic model</span></span>
-<span class="r-in"><span class="va">m_SFO_SFO</span> <span class="op">&lt;-</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="st">"M1"</span><span class="op">)</span>,</span>
-<span class="r-in">                     M1 <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>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The kinetic model</span></span></span>
+<span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op">&lt;-</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="st">"M1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                     M1 <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>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Generate a prediction for a specific set of parameters</span></span>
-<span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span>
-<span class="r-in"><span class="co"># from 2015</span></span>
-<span class="r-in"><span class="va">d_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span>
-<span class="r-in">                         <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span>
-<span class="r-in">                           k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span>
-<span class="r-in">                         <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
-<span class="r-in">                         <span class="va">sampling_times</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span>
-<span class="r-in"><span class="co"># of 10, and generate three datasets</span></span>
-<span class="r-in"><span class="va">d_SFO_SFO_err</span> <span class="op">&lt;-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Name the datasets for nicer plotting</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span>
-<span class="r-in"><span class="co"># nicer plotting later on.  Be quiet and use only one core not to offend CRAN</span></span>
-<span class="r-in"><span class="co"># checks</span></span>
-<span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"><span class="va">f_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span>
-<span class="r-in">                   <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span>
-<span class="r-in">                   quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span>
+<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span>
+<span class="r-in"><span><span class="co"># from 2015</span></span></span>
+<span class="r-in"><span><span class="va">d_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span></span>
+<span class="r-in"><span>                         <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
+<span class="r-in"><span>                           k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                         <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                         <span class="va">sampling_times</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span>
+<span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span>
+<span class="r-in"><span><span class="va">d_SFO_SFO_err</span> <span class="op">&lt;-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span>
+<span class="r-in"><span><span class="co"># nicer plotting later on.  Be quiet and use only one core not to offend CRAN</span></span></span>
+<span class="r-in"><span><span class="co"># checks</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">f_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                   <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span>
+<span class="r-in"><span>                   quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span>
-<span class="r-in"><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span>
-<span class="r-in"><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span>
+<span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span>
+<span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span>
-<span class="r-in"><span class="co"># and plot.mmkin is used</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span>
+<span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="co"># }</span></span>
-<span class="r-in"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -208,7 +231,7 @@ https://jrwb.de/posters/piacenza_2015.pdf</p>
 </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> 2.0.6.</p>
 </div>
 
       </footer></div>