Example evaluation of D24_2014, improve docs

1 files changed, 32 insertions, 33 deletions

diff --git a/docs/articles/web_only/mesotrione_parent_2023.html b/docs/articles/web_only/mesotrione_parent_2023.html
index c9409d05..2fda7b31 100644
--- a/docs/articles/web_only/mesotrione_parent_2023.html
+++ b/docs/articles/web_only/mesotrione_parent_2023.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../../index.html">mkin</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.11</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.10</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,7 @@
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change 12 September 2025
-(rebuilt 2025-09-12)</h4>
+(rebuilt 2025-11-28)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/mesotrione_parent_2023.rmd" class="external-link"><code>vignettes/web_only/mesotrione_parent_2023.rmd</code></a></small>
       <div class="d-none name"><code>mesotrione_parent_2023.rmd</code></div>
@@ -103,7 +103,7 @@ parameters. Because in some other case studies, the SFORB
 parameterisation of biexponential decline has shown some advantages over
 the DFOP parameterisation, SFORB was included in the list of tested
 models as well.</p>
-<p>The mkin package is used in version 1.2.11, which is contains the
+<p>The mkin package is used in version 1.2.10, which is contains the
 functions that were used for the evaluations. The <code>saemix</code>
 package is used as a backend for fitting the NLHM, but is also loaded to
 make the convergence plot function available.</p>
@@ -2429,7 +2429,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:01 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - k_meso * meso
@@ -2506,7 +2506,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:02 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - (alpha/beta) * 1/((time/beta) + 1) * meso
@@ -2589,7 +2589,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:02 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2680,7 +2680,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:02 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso_free/dt = - k_meso_free * meso_free - k_meso_free_bound *
@@ -2787,7 +2787,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:03 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - ifelse(time &lt;= tb, k1, k2) * meso
@@ -2880,7 +2880,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:15 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - k_meso * meso
@@ -2961,7 +2961,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:18 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - (alpha/beta) * 1/((time/beta) + 1) * meso
@@ -3048,7 +3048,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:21 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - (alpha/beta) * 1/((time/beta) + 1) * meso
@@ -3133,7 +3133,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:25 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3228,7 +3228,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:30 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3321,7 +3321,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:37 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3412,7 +3412,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:41 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso_free/dt = - k_meso_free * meso_free - k_meso_free_bound *
@@ -3523,7 +3523,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:44 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:24 2025 
 
 Equations:
 d_meso_free/dt = - k_meso_free * meso_free - k_meso_free_bound *
@@ -3630,7 +3630,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:48 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:25 2025 
 
 Equations:
 d_meso/dt = - ifelse(time &lt;= tb, k1, k2) * meso
@@ -3727,7 +3727,7 @@ saemix version used for fitting:      3.4
 mkin version used for pre-fitting:  1.2.11 
 R version used for fitting:         4.5.1 
 Date of fit:     Fri Sep 12 22:15:50 2025 
-Date of summary: Fri Sep 12 22:15:50 2025 
+Date of summary: Fri Nov 28 09:15:25 2025 
 
 Equations:
 d_meso/dt = - ifelse(time &lt;= tb, k1, k2) * meso
@@ -3819,7 +3819,7 @@ meso 14.69 82.45    24.82   14.69   29.29
 <div class="section level3">
 <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h3>
-<pre><code>R version 4.5.1 (2025-06-13)
+<pre><code>R version 4.5.2 (2025-10-31)
 Platform: x86_64-pc-linux-gnu
 Running under: Debian GNU/Linux 13 (trixie)
 
@@ -3843,23 +3843,22 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] rmarkdown_2.29  nvimcom_0.9-167 saemix_3.4      npde_3.5       
-[5] knitr_1.50      mkin_1.2.11    
+[1] saemix_3.4  npde_3.5    knitr_1.50  mkin_1.2.10
 
 loaded via a namespace (and not attached):
- [1] gtable_0.3.6       jsonlite_2.0.0     dplyr_1.1.4        compiler_4.5.1    
+ [1] gtable_0.3.6       jsonlite_2.0.0     dplyr_1.1.4        compiler_4.5.2    
  [5] tidyselect_1.2.1   dichromat_2.0-0.1  gridExtra_2.3      jquerylib_0.1.4   
- [9] systemfonts_1.2.3  scales_1.4.0       textshaping_1.0.1  readxl_1.4.5      
-[13] yaml_2.3.10        fastmap_1.2.0      lattice_0.22-7     ggplot2_3.5.2     
-[17] R6_2.6.1           generics_0.1.4     lmtest_0.9-40      MASS_7.3-65       
-[21] htmlwidgets_1.6.4  tibble_3.3.0       desc_1.4.3         bslib_0.9.0       
-[25] pillar_1.10.2      RColorBrewer_1.1-3 rlang_1.1.6        cachem_1.1.0      
-[29] xfun_0.52          fs_1.6.6           sass_0.4.10        cli_3.6.5         
-[33] pkgdown_2.1.3      magrittr_2.0.3     digest_0.6.37      grid_4.5.1        
-[37] mclust_6.1.1       lifecycle_1.0.4    nlme_3.1-168       vctrs_0.6.5       
-[41] evaluate_1.0.3     glue_1.8.0         cellranger_1.1.0   farver_2.1.2      
-[45] codetools_0.2-20   ragg_1.4.0         zoo_1.8-14         colorspace_2.1-1  
-[49] tools_4.5.1        pkgconfig_2.0.3    htmltools_0.5.8.1 </code></pre>
+ [9] systemfonts_1.2.3  scales_1.4.0       textshaping_1.0.1  yaml_2.3.10       
+[13] fastmap_1.2.0      lattice_0.22-7     ggplot2_3.5.2      R6_2.6.1          
+[17] generics_0.1.4     lmtest_0.9-40      MASS_7.3-65        htmlwidgets_1.6.4 
+[21] tibble_3.3.0       desc_1.4.3         bslib_0.9.0        pillar_1.10.2     
+[25] RColorBrewer_1.1-3 rlang_1.1.6        cachem_1.1.0       xfun_0.52         
+[29] fs_1.6.6           sass_0.4.10        cli_3.6.5          pkgdown_2.1.3     
+[33] magrittr_2.0.3     digest_0.6.37      grid_4.5.2         mclust_6.1.1      
+[37] lifecycle_1.0.4    nlme_3.1-168       vctrs_0.6.5        evaluate_1.0.3    
+[41] glue_1.8.0         farver_2.1.2       ragg_1.4.0         zoo_1.8-14        
+[45] colorspace_2.1-1   rmarkdown_2.29     tools_4.5.2        pkgconfig_2.0.3   
+[49] htmltools_0.5.8.1 </code></pre>
 </div>
 <div class="section level3">
 <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>