From 34ec60f1b140d788880d84b70cb62b344f7d74b9 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sun, 16 Apr 2023 13:42:23 +0200
Subject: Complete rebuild of static docs

---
 docs/dev/reference/summary.nlme.mmkin.html | 60 +++++++++++++++++++-----------
 1 file changed, 38 insertions(+), 22 deletions(-)

(limited to 'docs/dev/reference/summary.nlme.mmkin.html')

diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html
index dcf2bd3d..cb2c20bd 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -21,13 +21,13 @@ endpoints such as formation fractions and DT50 values. Optionally
       </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">
@@ -38,6 +38,8 @@ endpoints such as formation fractions and DT50 values. Optionally
   <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>
@@ -45,22 +47,29 @@ endpoints such as formation fractions and DT50 values. Optionally
       <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>
@@ -68,6 +77,14 @@ endpoints such as formation fractions and DT50 values. Optionally
     <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>
@@ -233,13 +250,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> iteration limit reached without convergence (10)</span>
 <span class="r-in"><span><span class="va">f_nlme</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_mmkin</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span>
 <span class="r-in"><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">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> nlme version used for fitting:      3.1.160 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Nov 24 08:11:11 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 24 08:11:11 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> nlme version used for fitting:      3.1.162 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Sun Apr 16 08:34:41 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Sun Apr 16 08:34:41 2023 </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>
@@ -249,7 +265,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <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 in 0.542 s using 4 iterations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.194 s using 4 iterations</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -278,15 +294,15 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Level: ds</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Structure: Diagonal</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>          parent_0 log_k_parent Residual</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> StdDev: 6.924e-05       0.5863        1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>         parent_0 log_k_parent Residual</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> StdDev: 6.92e-05       0.5863        1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance function:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Structure: Constant plus proportion of variance covariate</span>
 <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> 0.0001208853 0.0789968036 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.0001208154 0.0789968021 </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 with asymmetric confidence intervals:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>              lower      est.     upper</span>
@@ -365,8 +381,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   14    104.8    95.234   9.56590 7.5232     1.271521</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   28     85.0    89.274  -4.27372 7.0523    -0.606001</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   28     77.2    89.274 -12.07372 7.0523    -1.712017</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   60     82.2    77.013   5.18661 6.0838     0.852526</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   60     86.1    77.013   9.08661 6.0838     1.493571</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   60     82.2    77.013   5.18660 6.0838     0.852526</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   60     86.1    77.013   9.08660 6.0838     1.493571</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   90     70.5    67.053   3.44692 5.2970     0.650733</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent   90     61.7    67.053  -5.35308 5.2970    -1.010591</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 4 parent  120     60.0    58.381   1.61905 4.6119     0.351058</span>
@@ -376,7 +392,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    1    108.0    99.914   8.08560 7.8929     1.024413</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    1    104.9    99.914   4.98560 7.8929     0.631655</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    3    100.5    96.641   3.85898 7.6343     0.505477</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935382</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935383</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    7     91.7    90.412   1.28752 7.1423     0.180267</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent    7     95.1    90.412   4.68752 7.1423     0.656304</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273295</span>
@@ -405,7 +421,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</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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