Complete rebuild of static docs

1 files changed, 51 insertions, 13 deletions

diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 4bd170a1..3d902b77 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -17,13 +17,13 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav"><li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -34,6 +34,8 @@
   <ul class="dropdown-menu" role="menu"><li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
     <li>
       <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
     </li>
@@ -41,22 +43,29 @@
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
     <li>
-      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
     </li>
     <li>
-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
     </li>
     <li>
-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li class="divider">
+    <li class="dropdown-header">Performance</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/benchmarks.html">Benchmark timings for mkin</a>
@@ -64,6 +73,14 @@
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Miscellaneous</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>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
@@ -99,10 +116,12 @@
 <span>  i <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mmkin</span><span class="op">)</span>,</span>
 <span>  obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span>
 <span>  standardized <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  covariate_quantiles <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">0.05</span>, <span class="fl">0.95</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="st">"Time"</span>,</span>
 <span>  xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,</span>
 <span>  resplot <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">"predicted"</span>, <span class="st">"time"</span><span class="op">)</span>,</span>
-<span>  pop_curve <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  pop_curves <span class="op">=</span> <span class="st">"auto"</span>,</span>
 <span>  pred_over <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
@@ -143,6 +162,20 @@ variables in the model.</p></dd>
 <code>resplot = "time"</code>.</p></dd>
 
 
+<dt>covariates</dt>
+<dd><p>Data frame with covariate values for all variables in
+any covariate models in the object. If given, it overrides 'covariate_quantiles'.
+Each line in the data frame will result in a line drawn for the population.
+Rownames are used in the legend to label the lines.</p></dd>
+
+
+<dt>covariate_quantiles</dt>
+<dd><p>This argument only has an effect if the fitted
+object has covariate models. If so, the default is to show three population
+curves, for the 5th percentile, the 50th percentile and the 95th percentile
+of the covariate values used for fitting the model.</p></dd>
+
+
 <dt>xlab</dt>
 <dd><p>Label for the x axis.</p></dd>
 
@@ -156,10 +189,11 @@ variables in the model.</p></dd>
 predicted values?</p></dd>
 
 
-<dt>pop_curve</dt>
-<dd><p>Per default, a population curve is drawn in case
+<dt>pop_curves</dt>
+<dd><p>Per default, one population curve is drawn in case
 population parameters are fitted by the model, e.g. for saem objects.
-In case there is a covariate model, no population curve is currently shown.</p></dd>
+In case there is a covariate model, the behaviour depends on the value
+of 'covariates'</p></dd>
 
 
 <dt>pred_over</dt>
@@ -234,6 +268,10 @@ corresponding model prediction lines for the different datasets.</p></dd>
 
 <p>The function is called for its side effect.</p>
     </div>
+    <div id="note">
+    <h2>Note</h2>
+    <p>Covariate models are currently only supported for saem.mmkin objects.</p>
+    </div>
     <div id="author">
     <h2>Author</h2>
     <p>Johannes Ranke</p>
@@ -290,7 +328,7 @@ corresponding model prediction lines for the different datasets.</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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