From 8b7edd4eaf0d196e674a085f744d1a69260a6c91 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2023 06:02:05 +0100 Subject: Update pkgdown docs to bootstrap 5 with search --- docs/articles/web_only/FOCUS_Z.html | 195 ++++++-------- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 66689 -> 67444 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 105896 -> 107009 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 104799 -> 106098 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 75224 -> 76831 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 36301 -> 37494 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 66689 -> 67444 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 66448 -> 67259 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 80380 -> 81751 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 105172 -> 106406 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 104538 -> 105359 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 88806 -> 89110 bytes docs/articles/web_only/NAFTA_examples.html | 196 ++++++-------- .../NAFTA_examples_files/figure-html/p10-1.png | Bin 79758 -> 81542 bytes .../NAFTA_examples_files/figure-html/p11-1.png | Bin 76315 -> 77600 bytes .../NAFTA_examples_files/figure-html/p12a-1.png | Bin 81697 -> 83512 bytes .../NAFTA_examples_files/figure-html/p12b-1.png | Bin 70800 -> 71409 bytes .../NAFTA_examples_files/figure-html/p13-1.png | Bin 78121 -> 78613 bytes .../NAFTA_examples_files/figure-html/p14-1.png | Bin 80656 -> 81557 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 76974 -> 77580 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 78970 -> 79748 bytes .../NAFTA_examples_files/figure-html/p16-1.png | Bin 93950 -> 94540 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 82665 -> 83061 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 80721 -> 81186 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 83052 -> 83142 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 102570 -> 102934 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 92407 -> 93632 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 78605 -> 78782 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 76240 -> 76883 bytes docs/articles/web_only/benchmarks.html | 217 ++++++--------- docs/articles/web_only/compiled_models.html | 216 ++++++--------- docs/articles/web_only/dimethenamid_2018.html | 295 +++++++++------------ docs/articles/web_only/multistart.html | 193 ++++++-------- .../figure-html/unnamed-chunk-3-1.png | Bin 64334 -> 65359 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 52775 -> 53645 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 22131 -> 22804 bytes docs/articles/web_only/saem_benchmarks.html | 219 ++++++--------- 37 files changed, 596 insertions(+), 935 deletions(-) (limited to 'docs/articles/web_only') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index f19f59ad..7fd597d2 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -4,144 +4,104 @@ - + + Example evaluation of FOCUS dataset Z • mkin - - - + + + - - + - + + Skip to contents -
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Example evaluation of FOCUS dataset Z

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Example evaluation of FOCUS dataset Z

Johannes Ranke

Last change 16 January 2018 -(rebuilt 2023-10-30)

+(rebuilt 2023-11-16) Source: vignettes/web_only/FOCUS_Z.rmd - - +
FOCUS_Z.rmd
@@ -472,34 +432,27 @@ Studies on Pesticides in EU Registration. 1.1 ed. - - +
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Evaluation of example datasets from Attachment 1 -to the US EPA SOP for the NAFTA guidance

+ +
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+

Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

Johannes Ranke

26 February 2019 (rebuilt -2023-10-30)

+2023-11-16) Source: vignettes/web_only/NAFTA_examples.rmd - - +
NAFTA_examples.rmd
@@ -1079,34 +1038,27 @@ Pesticide Degradation.” - - +
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Benchmark timings for mkin

+
+
+

Benchmark timings for mkin

Johannes Ranke

Last change 17 February 2023 -(rebuilt 2023-11-02)

+(rebuilt 2023-11-16) Source: vignettes/web_only/benchmarks.rmd - - +
benchmarks.rmd
@@ -465,8 +425,8 @@ models fitted to two datasets, i.e. eight fits for each test.

Ryzen 9 7950X 4.3.2 1.2.6 -1.400 -2.012 +1.408 +2.041 @@ -736,9 +696,9 @@ for each test.

Ryzen 9 7950X 4.3.2 1.2.6 -0.790 -2.212 -1.173 +0.795 +2.228 +1.178 @@ -1092,45 +1052,38 @@ dataset, i.e. one fit for each test.

Ryzen 9 7950X 4.3.2 1.2.6 -0.432 -0.551 -0.580 -1.322 -0.746 -0.996 +0.439 +0.557 +0.585 +1.338 +0.749 +0.999
-
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Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 1aa88e05..210ddaf7 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -4,144 +4,103 @@ - + + Performance benefit by using compiled model definitions in mkin • mkin - - - + + + - - + - + + Skip to contents -
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Performance benefit by using compiled model -definitions in mkin

+
+
+

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2023-10-30

+

2023-11-16

Source: vignettes/web_only/compiled_models.rmd - - +
compiled_models.rmd
@@ -216,10 +175,10 @@ solution is also implemented, which is included in the tests below.

print("R package rbenchmark is not available") }
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.213
-## 3     deSolve, compiled            1    1.418   0.302
-## 2      Eigenvalue based            1    2.000   0.426
-## 1 deSolve, not compiled            1   23.535   5.013
+## 4 analytical 1 1.000 0.109 +## 3 deSolve, compiled 1 1.284 0.140 +## 2 Eigenvalue based 1 1.670 0.182 +## 1 deSolve, not compiled 1 21.927 2.390

We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

@@ -250,44 +209,37 @@ compiled code is available.

}
## Temporary DLL for differentials generated and loaded
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.492
-## 1 deSolve, not compiled            1   20.398  10.036
-

Here we get a performance benefit of a factor of 20 using the version +## 2 deSolve, compiled 1 1.000 0.181 +## 1 deSolve, not compiled 1 23.646 4.280 +

Here we get a performance benefit of a factor of 24 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 1.2.6 on

-
## R version 4.3.1 (2023-06-16)
+
## R version 4.3.2 (2023-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Ubuntu 22.04.3 LTS

-
## CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz

-
-
- - - +
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+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 1cffd561..4221ba07 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -4,145 +4,104 @@ - + + Example evaluations of the dimethenamid data from 2018 • mkin - - - + + + - - + - + + Skip to contents -
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Example evaluations of the dimethenamid data -from 2018

+ +
+
+

Example evaluations of the dimethenamid data from 2018

Johannes Ranke

Last change 1 July 2022, -built on 30 Oct 2023

+built on 16 Nov 2023 Source: vignettes/web_only/dimethenamid_2018.rmd - - +
dimethenamid_2018.rmd
@@ -225,12 +184,12 @@ least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):

-plot(mixed(f_parent_mkin_const["SFO", ]))
+plot(mixed(f_parent_mkin_const["SFO", ]))

Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:

-plot(mixed(f_parent_mkin_const["DFOP", ]))
+plot(mixed(f_parent_mkin_const["DFOP", ]))

The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 @@ -242,7 +201,7 @@ dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:

-plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)
+plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)

While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -254,7 +213,7 @@ degradation model and the error model (see below).

predicted residues is reduced by using the two-component error model:

-plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)
+plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)

However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -344,7 +303,7 @@ effects does not improve the fits.

The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.

-plot(f_parent_nlme_dfop_tc)
+plot(f_parent_nlme_dfop_tc)

@@ -361,17 +320,8 @@ implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.

-library(saemix)
-
Loading required package: npde
-
Package saemix, version 3.2
-  please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
-

-Attaching package: 'saemix'
-
The following objects are masked from 'package:npde':
-
-    kurtosis, skewness
-
-saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
+library(saemix)
+saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
 saemix_control_moreiter <- saemixControl(nbiter.saemix = c(1600, 300), nb.chains = 15,
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
@@ -379,7 +329,7 @@ Attaching package: 'saemix'
print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)

The convergence plot for the SFO model using constant variance is shown below.

-
+
 f_parent_saemix_sfo_const <- mkin::saem(f_parent_mkin_const["SFO", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_sfo_const$so, plot.type = "convergence")

@@ -387,19 +337,19 @@ shown below.

 
Obviously the selected number of iterations is sufficient to reach
 convergence. This can also be said for the SFO fit using the
 two-component error model.

-
+
 f_parent_saemix_sfo_tc <- mkin::saem(f_parent_mkin_tc["SFO", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_sfo_tc$so, plot.type = "convergence")

 

 
When fitting the DFOP model with constant variance (see below),
 parameter convergence is not as unambiguous.

-
+
 f_parent_saemix_dfop_const <- mkin::saem(f_parent_mkin_const["DFOP", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_dfop_const$so, plot.type = "convergence")

 

-
+
 print(f_parent_saemix_dfop_const)

 
Kinetic nonlinear mixed-effects model fit by SAEM
 Structural model:
@@ -435,14 +385,14 @@ this model.

 also observe that the estimated variance of k2 becomes very small, while
 being ill-defined, as illustrated by the excessive confidence interval
 of SD.k2.

-
+
 f_parent_saemix_dfop_tc <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 f_parent_saemix_dfop_tc_moreiter <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
   control = saemix_control_moreiter, transformations = "saemix")
 plot(f_parent_saemix_dfop_tc$so, plot.type = "convergence")

 

-
+
 print(f_parent_saemix_dfop_tc)

 
Kinetic nonlinear mixed-effects model fit by SAEM
 Structural model:
@@ -484,7 +434,7 @@ message.

 
The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and
 the version with increased iterations can be compared using the model
 comparison function of the saemix package:

-
+
 AIC_parent_saemix <- saemix::compare.saemix(
   f_parent_saemix_sfo_const$so,
   f_parent_saemix_sfo_tc$so,
@@ -492,7 +442,7 @@ comparison function of the saemix package:

   f_parent_saemix_dfop_tc$so,
   f_parent_saemix_dfop_tc_moreiter$so)

 
Likelihoods calculated by importance sampling

-
+
 rownames(AIC_parent_saemix) <- c(
   "SFO const", "SFO tc", "DFOP const", "DFOP tc", "DFOP tc more iterations")
 print(AIC_parent_saemix)

@@ -506,7 +456,7 @@ DFOP tc more iterations 665.85 663.76

 algorithms implemented in saemix, the likelihood from Gaussian
 quadrature is added to the best fit, and the AIC values obtained from
 the three methods are compared.

-
+
 f_parent_saemix_dfop_tc$so <-
   saemix::llgq.saemix(f_parent_saemix_dfop_tc$so)
 AIC_parent_saemix_methods <- c(
@@ -530,7 +480,7 @@ iterations makes a lot of difference. When using the LAPACK version
 coming with Debian Bullseye, the AIC based on Gaussian quadrature is
 almost the same as the one obtained with the other methods, also when
 using defaults for the fit.

-
+
 f_parent_saemix_dfop_tc_defaults <- mkin::saem(f_parent_mkin_tc["DFOP", ])
 f_parent_saemix_dfop_tc_defaults$so <-
   saemix::llgq.saemix(f_parent_saemix_dfop_tc_defaults$so)
@@ -550,7 +500,7 @@ using defaults for the fit.

 
The following table gives the AIC values obtained with both backend
 packages using the same control parameters (800 iterations burn-in, 300
 iterations second phase, 15 chains).

-
+
 AIC_all <- data.frame(
   check.names = FALSE,
   "Degradation model" = c("SFO", "SFO", "DFOP", "DFOP"),
@@ -561,7 +511,7 @@ iterations second phase, 15 chains).

   saemix_is = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so,
     f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC, method = "is")
 )
-kable(AIC_all)

+kable(AIC_all)

 
@@ -624,48 +574,48 @@ satisfactory precision.

 
Session Info
 

-
+
-
R version 4.3.1 (2023-06-16)
+
R version 4.3.2 (2023-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Ubuntu 22.04.3 LTS
+Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
-LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
+BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
 
 locale:
- [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
- [3] LC_TIME=C                  LC_COLLATE=en_US.UTF-8    
- [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
- [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
+ [3] LC_TIME=C                  LC_COLLATE=de_DE.UTF-8    
+ [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
+ [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
-[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
-time zone: Europe/Zurich
+time zone: Europe/Berlin
 tzcode source: system (glibc)
 
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.2   npde_3.3     nlme_3.1-163 mkin_1.2.6   knitr_1.44  
+[1] saemix_3.2   npde_3.3     nlme_3.1-163 mkin_1.2.6   knitr_1.42  
 
 loaded via a namespace (and not attached):
- [1] sass_0.4.7        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
- [5] lattice_0.21-9    digest_0.6.33     magrittr_2.0.3    evaluate_0.22    
- [9] grid_4.3.1        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.7   
-[13] mclust_6.0.0      gridExtra_2.3     purrr_1.0.1       fansi_1.0.4      
-[17] scales_1.2.1      codetools_0.2-19  textshaping_0.3.6 jquerylib_0.1.4  
-[21] cli_3.6.1         rlang_1.1.1       munsell_0.5.0     cachem_1.0.8     
-[25] yaml_2.3.7        tools_4.3.1       parallel_4.3.1    memoise_2.0.1    
-[29] dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2     vctrs_0.6.3      
-[33] R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3   stringr_1.5.0    
-[37] fs_1.6.3          MASS_7.3-60       ragg_1.2.5        pkgconfig_2.0.3  
-[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.5.1       pillar_1.9.0     
-[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 xfun_0.40        
-[49] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  rstudioapi_0.15.0
-[53] htmltools_0.5.6.1 rmarkdown_2.23    compiler_4.3.1   

+ [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
+ [5] lattice_0.21-8    digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
+ [9] grid_4.3.2        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.4   
+[13] DBI_1.1.3         mclust_6.0.0      gridExtra_2.3     purrr_1.0.1      
+[17] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  textshaping_0.3.6
+[21] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       munsell_0.5.0    
+[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.2       parallel_4.3.2   
+[29] memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2    
+[33] vctrs_0.6.2       R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3  
+[37] stringr_1.5.0     fs_1.6.2          MASS_7.3-60       ragg_1.2.5       
+[41] pkgconfig_2.0.3   desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2      
+[45] pillar_1.9.0      gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4
+[49] highr_0.10        xfun_0.39         tibble_3.2.1      lmtest_0.9-40    
+[53] tidyselect_1.2.0  htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.2   

 

 

 
References
@@ -690,34 +640,27 @@ November 2017.” 
-
-        
-

-
+  
 

 
 
 
-      
 
   
 
-
   
 
   
diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html
index dff087e4..4438adc3 100644
--- a/docs/articles/web_only/multistart.html
+++ b/docs/articles/web_only/multistart.html
@@ -4,144 +4,104 @@
 
-
+
+Short demo of the multistart method • mkin
-
-
-
+
+
+
-
-
+
-
+
+    Skip to contents
     
 
-    

-      

-  

-    

-      
Short demo of the multistart method

+

+  

+      
Short demo of the multistart method

                         
Johannes
 Ranke

             
             
Last change 20 April 2023
-(rebuilt 2023-10-30)

+(rebuilt 2023-11-16)
       
       Source: vignettes/web_only/multistart.rmd
-      
-
+      
multistart.rmd

     

 
     
@@ -207,32 +167,27 @@ improvement in case of the full model, because it is less well-defined,
 which impedes convergence. For the reduced model, using multiple
 starting values only results in a small improvement of the model
 fit.

-  

-
-  
-
+  
 

 
 
 
-      

+    

   

 
Developed by Johannes Ranke.

 

 
-

+

   

 
Site built with pkgdown 2.0.7.

 

 
-      

+    

 

 
   
 
-
   
 
   
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index 8be6ba61..f41dc889 100644
Binary files a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png differ
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index bc518c0c..9e206791 100644
Binary files a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
index 9ecdf4c9..c8e918cd 100644
Binary files a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/docs/articles/web_only/saem_benchmarks.html b/docs/articles/web_only/saem_benchmarks.html
index 9180773e..91e41a5b 100644
--- a/docs/articles/web_only/saem_benchmarks.html
+++ b/docs/articles/web_only/saem_benchmarks.html
@@ -4,144 +4,104 @@
 
 
 
-
+
+
 Benchmark timings for saem.mmkin • mkin
-
-
-
+
+
+
 
-
-
+
 
 
 
-
+
+    Skip to contents
     
 
-    

-      

-  

-    

-      
Benchmark timings for saem.mmkin

+
+

+  

+      
Benchmark timings for saem.mmkin

                         
Johannes
 Ranke

             
             
Last change 17 February 2023
-(rebuilt 2023-11-02)

+(rebuilt 2023-11-16)
       
       Source: vignettes/web_only/saem_benchmarks.rmd
-      
-
+      
saem_benchmarks.rmd

     

 
     
@@ -193,7 +153,7 @@ explanation of the following preprocessing.

 
 anova(
   sfo_const, dfop_const, sforb_const, hs_const,
-  sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1)

+  sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1)

 

 

 Degradation model
 
 
 
 
 
 
 
 
 

@@ -440,10 +400,10 @@ systems. All trademarks belong to their respective owners.

-
-
-
-
+
+
+
+

 

 
 Linux
 1.2.6
 3.21.1261.9712.3592.4241.1352.0252.4062.478
 

 
 

@@ -555,10 +515,10 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.6
 3.2
-2.116
-3.246
-3.602
-3.036
+2.161
+3.325
+3.669
+3.153
 
 
 
@@ -654,8 +614,8 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.6
 3.2
-11.712
-290.532
+12.007
+286.757
 
 
 
@@ -741,40 +701,33 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.6
 3.2
-479.161
+480.577
 
 
 
 

 

-  

-
-  
 
-

 
 
-
-      

+    

   

 
Developed by Johannes Ranke.

 

 
-

+

   

 
Site built with pkgdown 2.0.7.

 

 
-      

+    

 

 
   
 
-
   
 
   
-- 
cgit v1.2.1


From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001
From: Johannes Ranke 
Date: Thu, 13 Feb 2025 16:30:31 +0100
Subject: Axis legend formatting, update vignettes

---
 docs/articles/web_only/FOCUS_Z.html                | 128 ++++++-------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 .../FOCUS_Z_files/header-attrs-2.6/header-attrs.js |  12 --
 .../FOCUS_Z_files/header-attrs-2.7/header-attrs.js |  12 --
 docs/articles/web_only/NAFTA_examples.html         | 211 ++++++++++-----------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 .../header-attrs-2.6/header-attrs.js               |  12 --
 .../header-attrs-2.7/header-attrs.js               |  12 --
 docs/articles/web_only/benchmarks.html             | 149 ++++++++-------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 .../header-attrs-2.6/header-attrs.js               |  12 --
 .../header-attrs-2.7/header-attrs.js               |  12 --
 docs/articles/web_only/compiled_models.html        | 138 ++++++--------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 .../header-attrs-2.6/header-attrs.js               |  12 --
 docs/articles/web_only/dimethenamid_2018.html      | 210 ++++++++++----------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 .../figure-html/f_parent_mkin_dfop_const-1.png     | Bin 57786 -> 57786 bytes
 .../f_parent_mkin_dfop_const_test-1.png            | Bin 57786 -> 57786 bytes
 .../figure-html/f_parent_mkin_dfop_tc_test-1.png   | Bin 59396 -> 59146 bytes
 .../f_parent_nlmixr_saem_dfop_const-1.png          | Bin 94264 -> 0 bytes
 .../figure-html/f_parent_nlmixr_saem_dfop_tc-1.png | Bin 82238 -> 0 bytes
 .../f_parent_nlmixr_saem_dfop_tc_10k-1.png         | Bin 81793 -> 0 bytes
 .../f_parent_nlmixr_saem_dfop_tc_1k-1.png          | Bin 84973 -> 0 bytes
 .../f_parent_nlmixr_saem_sfo_const-1.png           | Bin 71898 -> 0 bytes
 .../figure-html/f_parent_nlmixr_saem_sfo_tc-1.png  | Bin 77093 -> 0 bytes
 .../figure-html/f_parent_saemix_dfop_tc-1.png      | Bin 29299 -> 29343 bytes
 .../figure-html/plot_parent_nlme-1.png             | Bin 59192 -> 59209 bytes
 docs/articles/web_only/mkin_benchmarks.rda         | Bin 1273 -> 0 bytes
 docs/articles/web_only/multistart.html             | 120 +++++-------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 .../figure-html/unnamed-chunk-3-1.png              | Bin 65359 -> 62571 bytes
 .../figure-html/unnamed-chunk-4-1.png              | Bin 53645 -> 53560 bytes
 .../figure-html/unnamed-chunk-6-1.png              | Bin 53020 -> 0 bytes
 docs/articles/web_only/saem_benchmarks.html        | 157 ++++++++-------
 .../accessible-code-block-0.0.1/empty-anchor.js    |  15 --
 36 files changed, 537 insertions(+), 765 deletions(-)
 delete mode 100644 docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js
 delete mode 100644 docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js
 delete mode 100644 docs/articles/web_only/FOCUS_Z_files/header-attrs-2.7/header-attrs.js
 delete mode 100644 docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
 delete mode 100644 docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
 delete mode 100644 docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
 delete mode 100644 docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
 delete mode 100644 docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
 delete mode 100644 docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
 delete mode 100644 docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
 delete mode 100644 docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/accessible-code-block-0.0.1/empty-anchor.js
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/figure-html/f_parent_nlmixr_saem_dfop_const-1.png
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/figure-html/f_parent_nlmixr_saem_dfop_tc-1.png
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/figure-html/f_parent_nlmixr_saem_dfop_tc_10k-1.png
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/figure-html/f_parent_nlmixr_saem_dfop_tc_1k-1.png
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/figure-html/f_parent_nlmixr_saem_sfo_const-1.png
 delete mode 100644 docs/articles/web_only/dimethenamid_2018_files/figure-html/f_parent_nlmixr_saem_sfo_tc-1.png
 delete mode 100644 docs/articles/web_only/mkin_benchmarks.rda
 delete mode 100644 docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js
 delete mode 100644 docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png
 delete mode 100644 docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js

(limited to 'docs/articles/web_only')

diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 7fd597d2..e91942ce 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -5,86 +5,71 @@
 
 
 
-
 Example evaluation of FOCUS dataset Z • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 

 
 print(p5a)

@@ -184,7 +170,7 @@ same.

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

 
-plot(p5b)

+plot(p5b)

 

 
 print(p5b)

@@ -235,7 +221,7 @@ same.

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

 
-plot(p6)

+plot(p6)

 

 
 print(p6)

@@ -286,7 +272,7 @@ same.

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

 
-plot(p7)

+plot(p7)

 

 
 print(p7)

@@ -345,7 +331,7 @@ lower value for the rate constant is used here.

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

 
-plot(p8)

+plot(p8)

 

 
 print(p8)

@@ -400,7 +386,7 @@ lower value for the rate constant is used here.

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

 
-plot(p9a)

+plot(p9a)

 

 
 print(p9a)

@@ -454,7 +440,7 @@ suggest a simple exponential decline.

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

 
-plot(p9b)

+plot(p9b)

 print(p9b)
@@ -512,7 +498,7 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p10)
+plot(p10)

 print(p10)
@@ -572,7 +558,7 @@ difference in IORE model parameters between PestDF and mkin.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p11)
+plot(p11)

 print(p11)
@@ -638,7 +624,7 @@ overparameterisation.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p12a)
+plot(p12a) 

 print(p12a)
@@ -690,15 +676,14 @@ overparameterisation.

## Warning in qt(alpha/2, rdf): NaNs produced
## Warning in qt(1 - alpha/2, rdf): NaNs produced
## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced
-
## Warning in sqrt(1/diag(V)): NaNs produced
-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful
+
## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the
+## non-finite result may be dubious
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-
-plot(p12b)
+
+plot(p12b)

-
+
 print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -742,14 +727,14 @@ overparameterisation.

 

 
Example on page 13
 

-
+
 p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p13)

+
+plot(p13)

 

-
+
 print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -794,18 +779,17 @@ overparameterisation.

 

 
DT50 not observed in the study and DFOP problems in PestDF
 

-
+
 p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

 
## Warning in sqrt(diag(covar)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

+
## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the
+## non-finite result may be dubious

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p14)

+
+plot(p14)

 

-
+
 print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -852,18 +836,17 @@ same results in mkin and PestDF.

 

 
N is less than 1 and DFOP fraction parameter is below zero
 

-
+
 p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

 
## Warning in sqrt(diag(covar)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

+
## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the
+## non-finite result may be dubious

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p15a)

+
+plot(p15a)

 

-
+
 print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -903,16 +886,16 @@ same results in mkin and PestDF.

 ## 
 ## Representative half-life:
 ## [1] 41.33

-
+
 p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

 
## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p15b)

+
+plot(p15b)

 

-
+
 print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -960,16 +943,16 @@ mkin and PestDF.

 

 
The DFOP fraction parameter is greater than 1
 

-
+
 p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The representative half-life of the IORE model is longer than the one corresponding

 
## to the terminal degradation rate found with the DFOP model.

 
## The representative half-life obtained from the DFOP model may be used

-
-plot(p16)

+
+plot(p16)

 

-
+
 print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -1010,10 +993,12 @@ mkin and PestDF.

 ## Representative half-life:
 ## [1] 8.93

 
In PestDF, the DFOP fit seems to have stuck in a local minimum, as
-mkin finds a solution with a much lower \(\chi^2\) error level. As the half-life from
-the slower rate constant of the DFOP model is larger than the IORE
-derived half-life, the NAFTA recommendation obtained with mkin is to use
-the DFOP representative half-life of 8.9 days.

+mkin finds a solution with a much lower
+χ2\chi^2
+error level. As the half-life from the slower rate constant of the DFOP
+model is larger than the IORE derived half-life, the NAFTA
+recommendation obtained with mkin is to use the DFOP representative
+half-life of 8.9 days.

 

 

 
Conclusions
@@ -1038,28 +1023,26 @@ Pesticide Degradation.” 

 
 
 
     
 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.7/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 17c2f8d8..3566be42 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -5,86 +5,71 @@
 
 
 
-
 Benchmark timings for mkin • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 
 
 
     

-  

-
Developed by Johannes Ranke.

+  
Developed by Johannes Ranke.

 

 
 

-  

-
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.1.1.

 

 
     

 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/benchmarks_files/header-attrs-2.7/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 210ddaf7..bbf6e897 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -5,86 +5,71 @@
 
 
 
-
 Performance benefit by using compiled model definitions in mkin • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.109
-## 3     deSolve, compiled            1    1.284   0.140
-## 2      Eigenvalue based            1    1.670   0.182
-## 1 deSolve, not compiled            1   21.927   2.390

+## 4            analytical            1    1.000   0.105
+## 3     deSolve, compiled            1    1.333   0.140
+## 2      Eigenvalue based            1    1.667   0.175
+## 1 deSolve, not compiled            1   22.486   2.361

 
We see that using the compiled model is by more than a factor of 10
 faster than using deSolve without compiled code.

 

@@ -209,38 +195,36 @@ compiled code is available.

 }

 
## Temporary DLL for differentials generated and loaded

 
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.181
-## 1 deSolve, not compiled            1   23.646   4.280

+## 2     deSolve, compiled            1    1.000   0.175
+## 1 deSolve, not compiled            1   23.937   4.189

 
Here we get a performance benefit of a factor of 24 using the version
 of the differential equation model compiled from C code!

-
This vignette was built with mkin 1.2.6 on

-
## R version 4.3.2 (2023-10-31)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
This vignette was built with mkin 1.2.9 on

+
## R version 4.4.2 (2024-10-31)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Debian GNU/Linux 12 (bookworm)

 
## CPU model: AMD Ryzen 9 7950X 16-Core Processor

 

-  

 
 
 
     

-  

-
Developed by Johannes Ranke.

+  
Developed by Johannes Ranke.

 

 
 

-  

-
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.1.1.

 

 
     

 

 
-  
 
-  
+
+
 
   
 
diff --git a/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
deleted file mode 100644
index ca349fd6..00000000
--- a/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
+++ /dev/null
@@ -1,15 +0,0 @@
-// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});
diff --git a/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
deleted file mode 100644
index dd57d92e..00000000
--- a/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
+++ /dev/null
@@ -1,12 +0,0 @@
-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});
diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html
index 4221ba07..5d39704d 100644
--- a/docs/articles/web_only/dimethenamid_2018.html
+++ b/docs/articles/web_only/dimethenamid_2018.html
@@ -5,86 +5,71 @@
 
 
 
-
 Example evaluations of the dimethenamid data from 2018 • mkin
 
-
-
-
-
-
-
+
+
+
+
 
 
     Skip to contents
-    
 
-    

 

 
Using biexponential decline (DFOP) results in a slightly more random
 scatter of the residuals:

 
-plot(mixed(f_parent_mkin_const["DFOP", ]))

+plot(mixed(f_parent_mkin_const["DFOP", ]))

 

 
The population curve (bold line) in the above plot results from
 taking the mean of the individual transformed parameters, i.e. of log k1
@@ -201,7 +187,7 @@ dominates the average. This is alleviated if only rate constants that
 pass the t-test for significant difference from zero (on the
 untransformed scale) are considered in the averaging:

 
-plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)

+plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)

While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -213,7 +199,7 @@ degradation model and the error model (see below).

predicted residues is reduced by using the two-component error model:

-plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)
+plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)

However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -303,7 +289,7 @@ effects does not improve the fits.

The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.

-plot(f_parent_nlme_dfop_tc)
+plot(f_parent_nlme_dfop_tc)

@@ -320,8 +306,17 @@ implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.

-library(saemix)
-saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
+library(saemix)
+
Loading required package: npde
+
Package saemix, version 3.3, March 2024
+  please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
+

+Attaching package: 'saemix'
+
The following objects are masked from 'package:npde':
+
+    kurtosis, skewness
+
+saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15,
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
 saemix_control_moreiter <- saemixControl(nbiter.saemix = c(1600, 300), nb.chains = 15,
     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)
@@ -329,7 +324,7 @@ well for all the parent data fits shown in this vignette.

     print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE)

The convergence plot for the SFO model using constant variance is shown below.

-
+
 f_parent_saemix_sfo_const <- mkin::saem(f_parent_mkin_const["SFO", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_sfo_const$so, plot.type = "convergence")

@@ -337,19 +332,19 @@ shown below.

 
Obviously the selected number of iterations is sufficient to reach
 convergence. This can also be said for the SFO fit using the
 two-component error model.

-
+
 f_parent_saemix_sfo_tc <- mkin::saem(f_parent_mkin_tc["SFO", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_sfo_tc$so, plot.type = "convergence")

 

 
When fitting the DFOP model with constant variance (see below),
 parameter convergence is not as unambiguous.

-
+
 f_parent_saemix_dfop_const <- mkin::saem(f_parent_mkin_const["DFOP", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 plot(f_parent_saemix_dfop_const$so, plot.type = "convergence")

 

-
+
 print(f_parent_saemix_dfop_const)

 
Kinetic nonlinear mixed-effects model fit by SAEM
 Structural model:
@@ -385,14 +380,14 @@ this model.

 also observe that the estimated variance of k2 becomes very small, while
 being ill-defined, as illustrated by the excessive confidence interval
 of SD.k2.

-
+
 f_parent_saemix_dfop_tc <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
   control = saemix_control, transformations = "saemix")
 f_parent_saemix_dfop_tc_moreiter <- mkin::saem(f_parent_mkin_tc["DFOP", ], quiet = TRUE,
   control = saemix_control_moreiter, transformations = "saemix")
 plot(f_parent_saemix_dfop_tc$so, plot.type = "convergence")

 

-
+
 print(f_parent_saemix_dfop_tc)

 
Kinetic nonlinear mixed-effects model fit by SAEM
 Structural model:
@@ -413,11 +408,11 @@ DMTA_0    98.24165  96.29190 100.1914
 k1         0.06421   0.03352   0.0949
 k2         0.00866   0.00617   0.0111
 g          0.95340   0.91218   0.9946
-a.1        1.06463   0.86503   1.2642
-b.1        0.02964   0.02259   0.0367
-SD.DMTA_0  2.03611   0.40416   3.6681
+a.1        1.06463   0.87979   1.2495
+b.1        0.02964   0.02266   0.0366
+SD.DMTA_0  2.03611   0.40361   3.6686
 SD.k1      0.59534   0.25692   0.9338
-SD.k2      0.00042 -73.01372  73.0146
+SD.k2      0.00042 -73.00540  73.0062
 SD.g       1.04234   0.37189   1.7128

 
Doubling the number of iterations in the first phase of the algorithm
 leads to a slightly lower likelihood, and therefore to slightly higher
@@ -434,7 +429,7 @@ message.

 
The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and
 the version with increased iterations can be compared using the model
 comparison function of the saemix package:

-
+
 AIC_parent_saemix <- saemix::compare.saemix(
   f_parent_saemix_sfo_const$so,
   f_parent_saemix_sfo_tc$so,
@@ -442,7 +437,7 @@ comparison function of the saemix package:

   f_parent_saemix_dfop_tc$so,
   f_parent_saemix_dfop_tc_moreiter$so)

 
Likelihoods calculated by importance sampling

-
+
 rownames(AIC_parent_saemix) <- c(
   "SFO const", "SFO tc", "DFOP const", "DFOP tc", "DFOP tc more iterations")
 print(AIC_parent_saemix)

@@ -456,7 +451,7 @@ DFOP tc more iterations 665.85 663.76

 algorithms implemented in saemix, the likelihood from Gaussian
 quadrature is added to the best fit, and the AIC values obtained from
 the three methods are compared.

-
+
 f_parent_saemix_dfop_tc$so <-
   saemix::llgq.saemix(f_parent_saemix_dfop_tc$so)
 AIC_parent_saemix_methods <- c(
@@ -480,7 +475,7 @@ iterations makes a lot of difference. When using the LAPACK version
 coming with Debian Bullseye, the AIC based on Gaussian quadrature is
 almost the same as the one obtained with the other methods, also when
 using defaults for the fit.

-
+
 f_parent_saemix_dfop_tc_defaults <- mkin::saem(f_parent_mkin_tc["DFOP", ])
 f_parent_saemix_dfop_tc_defaults$so <-
   saemix::llgq.saemix(f_parent_saemix_dfop_tc_defaults$so)
@@ -500,7 +495,7 @@ using defaults for the fit.

 
The following table gives the AIC values obtained with both backend
 packages using the same control parameters (800 iterations burn-in, 300
 iterations second phase, 15 chains).

-
+
 AIC_all <- data.frame(
   check.names = FALSE,
   "Degradation model" = c("SFO", "SFO", "DFOP", "DFOP"),
@@ -511,7 +506,7 @@ iterations second phase, 15 chains).

   saemix_is = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so,
     f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC, method = "is")
 )
-kable(AIC_all)

+kable(AIC_all)

 
@@ -574,10 +569,10 @@ satisfactory precision.

 
Session Info
 

-
+
-
R version 4.3.2 (2023-10-31)
-Platform: x86_64-pc-linux-gnu (64-bit)
+
R version 4.4.2 (2024-10-31)
+Platform: x86_64-pc-linux-gnu
 Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
@@ -599,23 +594,22 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.2   npde_3.3     nlme_3.1-163 mkin_1.2.6   knitr_1.42  
+[1] saemix_3.3   npde_3.5     nlme_3.1-166 mkin_1.2.9   knitr_1.49  
 
 loaded via a namespace (and not attached):
- [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
- [5] lattice_0.21-8    digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
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-[13] DBI_1.1.3         mclust_6.0.0      gridExtra_2.3     purrr_1.0.1      
-[17] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  textshaping_0.3.6
-[21] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       munsell_0.5.0    
-[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.2       parallel_4.3.2   
-[29] memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2    
-[33] vctrs_0.6.2       R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3  
-[37] stringr_1.5.0     fs_1.6.2          MASS_7.3-60       ragg_1.2.5       
-[41] pkgconfig_2.0.3   desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2      
-[45] pillar_1.9.0      gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4
-[49] highr_0.10        xfun_0.39         tibble_3.2.1      lmtest_0.9-40    
-[53] tidyselect_1.2.0  htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.2   

+ [1] gtable_0.3.6      jsonlite_1.8.9    dplyr_1.1.4       compiler_4.4.2   
+ [5] tidyselect_1.2.1  parallel_4.4.2    gridExtra_2.3     jquerylib_0.1.4  
+ [9] systemfonts_1.1.0 scales_1.3.0      textshaping_0.4.1 yaml_2.3.10      
+[13] fastmap_1.2.0     lattice_0.22-6    ggplot2_3.5.1     R6_2.5.1         
+[17] generics_0.1.3    lmtest_0.9-40     MASS_7.3-61       htmlwidgets_1.6.4
+[21] tibble_3.2.1      desc_1.4.3        munsell_0.5.1     bslib_0.8.0      
+[25] pillar_1.9.0      rlang_1.1.4       utf8_1.2.4        cachem_1.1.0     
+[29] xfun_0.49         fs_1.6.5          sass_0.4.9        cli_3.6.3        
+[33] pkgdown_2.1.1     magrittr_2.0.3    digest_0.6.37     grid_4.4.2       
+[37] mclust_6.1.1      lifecycle_1.0.4   vctrs_0.6.5       evaluate_1.0.1   
+[41] glue_1.8.0        codetools_0.2-20  ragg_1.3.3        zoo_1.8-12       
+[45] fansi_1.0.6       colorspace_2.1-1  rmarkdown_2.29    pkgconfig_2.0.3  
+[49] tools_4.4.2       htmltools_0.5.8.1

 

 

 
References
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Ryzen 9 7950XLinux1.2.93.31.0861.9911.9492.411

 
 

 
Two-component error fits for SFO, DFOP, SFORB and HS.

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