Merge branch 'v1.2.3_pkgdown'

1 files changed, 35 insertions, 18 deletions

diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 1e294eaf..d446a2a2 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -19,13 +19,13 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
       </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">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released 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">
@@ -36,6 +36,8 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
   <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>
@@ -43,22 +45,29 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
       <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>
@@ -66,6 +75,14 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
     <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>
@@ -239,7 +256,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             Model df      AIC      BIC    logLik   Test  L.Ratio p-value</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_sfo      1  5 625.0539 637.5529 -307.5269                        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop     2  9 495.1270 517.6253 -238.5635 1 vs 2 137.9269  &lt;.0001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop     2  9 495.1270 517.6253 -238.5635 1 vs 2 137.9268  &lt;.0001</span>
 <span class="r-in"><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">f_nlme_dfop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -270,7 +287,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            DT50     DT90 DT50back  DT50_k1  DT50_k2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent 10.79857 100.7937 30.34193 4.193938 43.85443</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="va">ds_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -321,12 +338,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   parent_A1 parent_sink </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   0.2768574   0.7231426 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   0.2768575   0.7231425 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             DT50     DT90 DT50back  DT50_k1  DT50_k2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent  11.07091 104.6320 31.49737 4.462383 46.20825</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> A1     162.30519 539.1662       NA       NA       NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent  11.07091 104.6320 31.49737 4.462384 46.20825</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> A1     162.30507 539.1658       NA       NA       NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span></span>
@@ -354,7 +371,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-out co"><span class="r-pr">#&gt;</span> Fixed effects:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_0   log_k1   log_k2 g_qlogis </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 94.04774 -1.82340 -4.16716  0.05686 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 94.04773 -1.82340 -4.16716  0.05686 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Random effects:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span>
@@ -368,7 +385,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: ~fitted(.) </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Parameter estimates:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      const       prop </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2.23223147 0.01262395 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2.23223593 0.01262367 </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="va">f_2_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
@@ -401,7 +418,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: ~1 | name </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Parameter estimates:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    parent        A1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1.0000000 0.2049995 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1.0000000 0.2049994 </span>
 <span class="r-in"><span>  <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span>
 <span class="r-in"><span>    control <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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -413,7 +430,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                     Model df      AIC      BIC    logLik   Test  L.Ratio</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo         1 13 843.8547 884.6201 -408.9274                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs     2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs     2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                     p-value</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo            </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs  &lt;.0001</span>
@@ -433,7 +450,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 </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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