Fix and rebuild documentation, see NEWS

I had to fix the two pathway vignettes, as they did not work with
the released version any more. So they and the multistart vignette
which got some small fixes as well were rebuilt.

Complete rebuild of the online docs with the released version. The
documentation of the 'hierarchial_kinetics' format had to be fixed
as well.

1 files changed, 63 insertions, 22 deletions

diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html
index 6d8c0157..0581830c 100644
--- a/docs/reference/dimethenamid_2018.html
+++ b/docs/reference/dimethenamid_2018.html
@@ -22,13 +22,13 @@ constrained by data protection regulations."><!-- mathjax --><script src="https:
       </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">
@@ -39,6 +39,8 @@ constrained by data protection regulations."><!-- mathjax --><script src="https:
   <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>
@@ -46,22 +48,29 @@ constrained by data protection regulations."><!-- mathjax --><script src="https:
       <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>
@@ -69,6 +78,14 @@ constrained by data protection regulations."><!-- mathjax --><script src="https:
     <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>
@@ -205,10 +222,10 @@ specific pieces of information in the comments.</p>
 <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</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="va">f_dmta_saem_tc</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.0 </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 17 13:57:51 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 17 13:57:51 2022 </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:     Thu Apr 20 07:32:09 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Apr 20 07:32:09 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_DMTA/dt = - k_DMTA * DMTA</span>
@@ -221,12 +238,12 @@ specific pieces of information in the comments.</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 deSolve </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 802.957 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 301.026 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 9 chains</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>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Mean of starting values for individual parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for degradation parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       DMTA_0   log_k_DMTA    log_k_M23    log_k_M27    log_k_M31 f_DMTA_ilr_1 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      95.5662      -2.9048      -3.8130      -4.1600      -4.1486       0.1341 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2 f_DMTA_ilr_3 </span>
@@ -235,6 +252,30 @@ specific pieces of information in the comments.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Fixed degradation parameter values:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> None</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for random effects (square root of initial entries in omega):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>              DMTA_0 log_k_DMTA log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DMTA_0        4.802     0.0000    0.0000     0.000    0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_DMTA    0.000     0.9834    0.0000     0.000    0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M23     0.000     0.0000    0.6983     0.000    0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M27     0.000     0.0000    0.0000     1.028    0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M31     0.000     0.0000    0.0000     0.000    0.9841       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_1  0.000     0.0000    0.0000     0.000    0.0000       0.7185</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2  0.000     0.0000    0.0000     0.000    0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_3  0.000     0.0000    0.0000     0.000    0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>              f_DMTA_ilr_2 f_DMTA_ilr_3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DMTA_0             0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_DMTA         0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M23          0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M27          0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M31          0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_1       0.0000       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2       0.7378       0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_3       0.0000       0.4451</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for error model parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 b.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   1   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> Results:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
@@ -251,9 +292,9 @@ specific pieces of information in the comments.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_1     0.1346 -0.2150  0.4841</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2     0.1449 -0.2593  0.5491</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_3    -1.3882 -1.7011 -1.0753</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1              0.9156  0.8229  1.0084</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> b.1              0.1383  0.1215  0.1551</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0        3.7280 -0.6951  8.1511</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1              0.9156  0.8217  1.0095</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> b.1              0.1383  0.1216  0.1550</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0        3.7280 -0.6949  8.1508</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_DMTA    0.6431  0.2781  1.0080</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M23     1.0096  0.3782  1.6409</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M27     0.4583  0.1541  0.7625</span>
@@ -274,7 +315,7 @@ specific pieces of information in the comments.</p>
 <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>                   est.   lower  upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0       3.7280 -0.6951 8.1511</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0       3.7280 -0.6949 8.1508</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_DMTA   0.6431  0.2781 1.0080</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M23    1.0096  0.3782 1.6409</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M27    0.4583  0.1541 0.7625</span>
@@ -284,9 +325,9 @@ specific pieces of information in the comments.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_DMTA_ilr_3 0.3657  0.1383 0.5931</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:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       est.  lower  upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.9156 0.8229 1.0084</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.1383 0.1215 0.1551</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       est.  lower upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.9156 0.8217 1.009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.1383 0.1216 0.155</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>                   est.     lower    upper</span>
@@ -335,7 +376,7 @@ specific pieces of information in the comments.</p>
 </div>
 
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-  <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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