Update online docs, fix bug that surfaced

1 files changed, 67 insertions, 49 deletions

diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html
index 87d4ca4a..1095dd28 100644
--- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html
@@ -34,14 +34,14 @@
       </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">
@@ -53,6 +53,9 @@
 <li>
       <a href="../../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    </li>
+<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>
@@ -60,22 +63,31 @@
       <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>
+<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>
+<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>
@@ -83,6 +95,15 @@
     <li>
       <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    </li>
+<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>
@@ -115,7 +136,7 @@ residue data on cyantraniliprole</h1>
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change on 6 January
-2023, last compiled on 28 Januar 2023</h4>
+2023, last compiled on 17 Februar 2023</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small>
       <div class="hidden name"><code>2022_cyan_pathway.rmd</code></div>
@@ -135,7 +156,7 @@ be fitted with the mkin package.</p>
 173340 (Application of nonlinear hierarchical models to the kinetic
 evaluation of chemical degradation data) of the German Environment
 Agency carried out in 2022 and 2023.</p>
-<p>The mkin package is used in version 1.2.2 which is currently under
+<p>The mkin package is used in version 1.2.3 which is currently under
 development. The newly introduced functionality that is used here is a
 simplification of excluding random effects for a set of fits based on a
 related set of fits with a reduced model, and the documentation of the
@@ -2185,7 +2206,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:07:38 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2313,7 +2334,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:08:17 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2443,7 +2464,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:09:12 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2588,7 +2609,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:09:18 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2726,7 +2747,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:10:30 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2872,7 +2893,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:16:28 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3018,7 +3039,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:10:49 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3183,7 +3204,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:17:00 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3348,7 +3369,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:11:04 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ifelse(time &lt;= tb, k1, k2) * cyan
@@ -3490,7 +3511,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:11:24 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ifelse(time &lt;= tb, k1, k2) * cyan
@@ -3638,7 +3659,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:34:28 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3802,7 +3823,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:37:36 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3948,7 +3969,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:38:34 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4139,7 +4160,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:45:32 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4330,7 +4351,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:38:37 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4526,7 +4547,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 10:46:02 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4727,7 +4748,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 11:18:41 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -4870,7 +4891,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 11:16:32 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -5036,7 +5057,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 11:22:28 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -5202,7 +5223,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 11:17:37 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5373,7 +5394,7 @@ saemix version used for fitting:      3.2
 mkin version used for pre-fitting:  1.2.2 
 R version used for fitting:         4.2.2 
 Date of fit:     Sat Jan 28 11:21:01 2023 
-Date of summary: Sat Jan 28 11:22:29 2023 
+Date of summary: Fri Feb 17 22:24:33 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5561,26 +5582,23 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.41 mkin_1.2.2
+[1] saemix_3.2 npde_3.3   knitr_1.41 mkin_1.2.3
 
 loaded via a namespace (and not attached):
- [1] mclust_6.0.0      lattice_0.20-45   prettyunits_1.1.1 ps_1.7.2         
- [5] zoo_1.8-11        assertthat_0.2.1  rprojroot_2.0.3   digest_0.6.31    
- [9] lmtest_0.9-40     utf8_1.2.2        R6_2.5.1          cellranger_1.1.0 
-[13] evaluate_0.19     ggplot2_3.4.0     highr_0.9         pillar_1.8.1     
-[17] rlang_1.0.6       readxl_1.4.1      callr_3.7.3       jquerylib_0.1.4  
-[21] rmarkdown_2.19    pkgdown_2.0.7     textshaping_0.3.6 desc_1.4.2       
-[25] stringr_1.5.0     munsell_0.5.0     compiler_4.2.2    xfun_0.35        
-[29] pkgconfig_2.0.3   systemfonts_1.0.4 pkgbuild_1.4.0    htmltools_0.5.4  
-[33] tidyselect_1.2.0  tibble_3.1.8      gridExtra_2.3     codetools_0.2-18 
-[37] fansi_1.0.3       crayon_1.5.2      dplyr_1.0.10      grid_4.2.2       
-[41] nlme_3.1-161      jsonlite_1.8.4    gtable_0.3.1      lifecycle_1.0.3  
-[45] DBI_1.1.3         magrittr_2.0.3    scales_1.2.1      cli_3.5.0        
-[49] stringi_1.7.8     cachem_1.0.6      fs_1.5.2          bslib_0.4.2      
-[53] ragg_1.2.4        generics_0.1.3    vctrs_0.5.1       deSolve_1.34     
-[57] tools_4.2.2       glue_1.6.2        purrr_1.0.0       processx_3.8.0   
-[61] fastmap_1.1.0     yaml_2.3.6        inline_0.3.19     colorspace_2.0-3 
-[65] memoise_2.0.1     sass_0.4.4       </code></pre>
+ [1] pillar_1.8.1      bslib_0.4.2       compiler_4.2.2    jquerylib_0.1.4  
+ [5] tools_4.2.2       mclust_6.0.0      digest_0.6.31     tibble_3.1.8     
+ [9] jsonlite_1.8.4    evaluate_0.19     memoise_2.0.1     lifecycle_1.0.3  
+[13] nlme_3.1-162      gtable_0.3.1      lattice_0.20-45   pkgconfig_2.0.3  
+[17] rlang_1.0.6       DBI_1.1.3         cli_3.5.0         yaml_2.3.6       
+[21] pkgdown_2.0.7     xfun_0.35         fastmap_1.1.0     gridExtra_2.3    
+[25] dplyr_1.0.10      stringr_1.5.0     generics_0.1.3    desc_1.4.2       
+[29] fs_1.5.2          vctrs_0.5.1       sass_0.4.4        systemfonts_1.0.4
+[33] tidyselect_1.2.0  rprojroot_2.0.3   lmtest_0.9-40     grid_4.2.2       
+[37] inline_0.3.19     glue_1.6.2        R6_2.5.1          textshaping_0.3.6
+[41] fansi_1.0.3       rmarkdown_2.19    purrr_1.0.0       ggplot2_3.4.0    
+[45] magrittr_2.0.3    scales_1.2.1      htmltools_0.5.4   assertthat_0.2.1 
+[49] colorspace_2.0-3  ragg_1.2.4        utf8_1.2.2        stringi_1.7.8    
+[53] munsell_0.5.0     cachem_1.0.6      zoo_1.8-11       </code></pre>
 </div>
 <div class="section level3">
 <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>