Fix link to mesotrione vignette in static docsHEADmain

7 files changed, 54 insertions, 53 deletions

diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt.html b/vignettes/web_only/mesotrione_parent_2023.html
index c9cd9cd9..fc9b0009 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt.html
+++ b/vignettes/web_only/mesotrione_parent_2023.html
@@ -1587,7 +1587,7 @@ div.tocify {
 <h1 class="title toc-ignore">Testing covariate modelling in hierarchical
 parent degradation kinetics with residue data on mesotrione</h1>
 <h4 class="author">Johannes Ranke</h4>
-<h4 class="date">Last change 13 May 2025 (rebuilt 2025-05-13)</h4>
+<h4 class="date">Last change 13 May 2025 (rebuilt 2025-05-14)</h4>
 
 </div>
 
@@ -3916,8 +3916,8 @@ Hierarchical SFO fit with constant variance
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:35 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:13 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - k_meso * meso
@@ -3993,8 +3993,8 @@ Hierarchical FOMC fit with constant variance
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:36 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:13 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - (alpha/beta) * 1/((time/beta) + 1) * meso
@@ -4004,7 +4004,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 0.832 s
+Fitted in 0.831 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4076,8 +4076,8 @@ Hierarchical DFOP fit with constant variance
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:36 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:14 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4089,7 +4089,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.483 s
+Fitted in 1.498 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4167,8 +4167,8 @@ Hierarchical SFORB fit with constant variance
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:37 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:14 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso_free/dt = - k_meso_free * meso_free - k_meso_free_bound *
@@ -4181,7 +4181,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.563 s
+Fitted in 1.548 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4274,8 +4274,8 @@ Hierarchical HS fit with constant variance
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:37 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:14 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ifelse(time &lt;= tb, k1, k2) * meso
@@ -4285,7 +4285,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.457 s
+Fitted in 1.422 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4366,8 +4366,8 @@ Hierarchichal SFO fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:52 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:30 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - k_meso * meso
@@ -4377,7 +4377,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.802 s
+Fitted in 1.865 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4447,8 +4447,8 @@ Hierarchichal FOMC fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:54 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:32 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - (alpha/beta) * 1/((time/beta) + 1) * meso
@@ -4458,7 +4458,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.512 s
+Fitted in 1.54 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4534,8 +4534,8 @@ Refined hierarchichal FOMC fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:54:57 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:35 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - (alpha/beta) * 1/((time/beta) + 1) * meso
@@ -4545,7 +4545,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.52 s
+Fitted in 2.583 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4619,8 +4619,8 @@ Hierarchichal DFOP fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:00 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:38 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4632,7 +4632,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.218 s
+Fitted in 2.231 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4714,8 +4714,8 @@ Refined hierarchical DFOP fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:05 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:43 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4727,7 +4727,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 4.711 s
+Fitted in 4.778 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4807,8 +4807,8 @@ Further refined hierarchical DFOP fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:12 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:50 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4820,7 +4820,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 3.202 s
+Fitted in 3.265 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -4898,8 +4898,8 @@ Hierarchichal SFORB fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:16 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:54 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso_free/dt = - k_meso_free * meso_free - k_meso_free_bound *
@@ -4912,7 +4912,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 3.153 s
+Fitted in 2.795 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -5009,8 +5009,8 @@ Refined hierarchichal SFORB fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:19 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:57 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso_free/dt = - k_meso_free * meso_free - k_meso_free_bound *
@@ -5023,7 +5023,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.832 s
+Fitted in 2.449 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -5116,8 +5116,8 @@ Hierarchichal HS fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:21 2025 
-Date of summary: Tue May 13 07:05:04 2025 
+Date of fit:     Wed May 14 05:10:59 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ifelse(time &lt;= tb, k1, k2) * meso
@@ -5127,7 +5127,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.397 s
+Fitted in 1.891 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -5213,8 +5213,8 @@ Refined hierarchichal HS fit with pH influence
 saemix version used for fitting:      3.3 
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.5.0 
-Date of fit:     Tue May 13 06:55:23 2025 
-Date of summary: Tue May 13 07:05:05 2025 
+Date of fit:     Wed May 14 05:11:01 2025 
+Date of summary: Wed May 14 05:11:02 2025 
 
 Equations:
 d_meso/dt = - ifelse(time &lt;= tb, k1, k2) * meso
@@ -5224,7 +5224,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.404 s
+Fitted in 1.417 s
 Using 300, 100 iterations and 3 chains
 
 Variance model: Constant variance 
@@ -5335,14 +5335,15 @@ other attached packages:
 loaded via a namespace (and not attached):
  [1] gtable_0.3.6      jsonlite_1.9.0    dplyr_1.1.4       compiler_4.5.0   
  [5] tidyselect_1.2.1  colorout_1.3-2    gridExtra_2.3     jquerylib_0.1.4  
- [9] scales_1.3.0      yaml_2.3.10       fastmap_1.2.0     lattice_0.22-6   
-[13] ggplot2_3.5.1     R6_2.6.1          generics_0.1.3    lmtest_0.9-40    
-[17] MASS_7.3-65       tibble_3.2.1      munsell_0.5.1     bslib_0.9.0      
-[21] pillar_1.10.1     rlang_1.1.5       cachem_1.1.0      xfun_0.51        
-[25] sass_0.4.9        cli_3.6.4         magrittr_2.0.3    digest_0.6.37    
-[29] grid_4.5.0        mclust_6.1.1      lifecycle_1.0.4   nlme_3.1-168     
-[33] vctrs_0.6.5       evaluate_1.0.3    glue_1.8.0        zoo_1.8-13       
-[37] colorspace_2.1-1  tools_4.5.0       pkgconfig_2.0.3   htmltools_0.5.8.1</code></pre>
+ [9] scales_1.3.0      readxl_1.4.4      yaml_2.3.10       fastmap_1.2.0    
+[13] lattice_0.22-6    ggplot2_3.5.1     R6_2.6.1          generics_0.1.3   
+[17] lmtest_0.9-40     MASS_7.3-65       tibble_3.2.1      munsell_0.5.1    
+[21] bslib_0.9.0       pillar_1.10.1     rlang_1.1.5       cachem_1.1.0     
+[25] xfun_0.51         sass_0.4.9        cli_3.6.4         magrittr_2.0.3   
+[29] digest_0.6.37     grid_4.5.0        mclust_6.1.1      lifecycle_1.0.4  
+[33] nlme_3.1-168      vctrs_0.6.5       evaluate_1.0.3    glue_1.8.0       
+[37] cellranger_1.1.0  codetools_0.2-20  zoo_1.8-13        colorspace_2.1-1 
+[41] tools_4.5.0       pkgconfig_2.0.3   htmltools_0.5.8.1</code></pre>
 </div>
 <div id="hardware-info" class="section level2">
 <h2>Hardware info</h2>
diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt.rmd b/vignettes/web_only/mesotrione_parent_2023.rmd
index 153c22ab..153c22ab 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt.rmd
+++ b/vignettes/web_only/mesotrione_parent_2023.rmd
diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-14-1.png b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-14-1.png
index 67fa91dc..67fa91dc 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-14-1.png
+++ b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-14-1.png
diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-19-1.png b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-19-1.png
index 41e087b6..41e087b6 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-19-1.png
+++ b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-19-1.png
diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-25-1.png b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-25-1.png
index afae6556..afae6556 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-25-1.png
+++ b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-25-1.png
diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-30-1.png b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-30-1.png
index 02e31e43..02e31e43 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-30-1.png
+++ b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-30-1.png
diff --git a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-8-1.png b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-8-1.png
index 2379b895..2379b895 100644
--- a/vignettes/web_only/mesotrione_parent_2023_prebuilt_files/figure-html/unnamed-chunk-8-1.png
+++ b/vignettes/web_only/mesotrione_parent_2023_files/figure-html/unnamed-chunk-8-1.png