From a01fe8923ff50dcc76c34fb09ad500f5f5433063 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 22:35:52 +0200 Subject: Release date, update pkgdown development docs --- docs/dev/articles/prebuilt/2022_cyan_pathway.html | 263 +++++++++++----------- docs/dev/articles/prebuilt/2022_dmta_parent.html | 140 ++++++------ docs/dev/articles/prebuilt/2022_dmta_pathway.html | 51 +++-- 3 files changed, 231 insertions(+), 223 deletions(-) (limited to 'docs/dev/articles/prebuilt') diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html index 7bb0fa5b..2359969e 100644 --- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html @@ -34,7 +34,7 @@ mkin - 1.2.4 + 1.2.5 @@ -136,7 +136,7 @@ residue data on cyantraniliprole Ranke

Last change on 20 April 2023, -last compiled on 20 April 2023

+last compiled on 19 Mai 2023 Source: vignettes/prebuilt/2022_cyan_pathway.rmd @@ -156,7 +156,7 @@ be fitted with the mkin package.

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.

-

The mkin package is used in version 1.2.4 which is currently under +

The mkin package is used in version 1.2.5 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 @@ -2220,10 +2220,10 @@ Hierarchical SFO path 1 fit with constant variance 


 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:33:05 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:42:02 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2236,7 +2236,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 438.011 s
+Fitted in 443.997 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2348,10 +2348,10 @@ Hierarchical SFO path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:32:55 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:42:01 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2364,7 +2364,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 427.249 s
+Fitted in 442.545 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -2478,10 +2478,10 @@ Hierarchical FOMC path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:33:49 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:42:38 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2496,7 +2496,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 481.497 s
+Fitted in 479.463 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2623,10 +2623,10 @@ Hierarchical FOMC path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:33:59 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:42:53 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2641,7 +2641,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 491.071 s
+Fitted in 494.121 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -2761,10 +2761,10 @@ Hierarchical DFOP path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:34:33 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:43:22 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2783,7 +2783,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 525.551 s
+Fitted in 523.691 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2907,10 +2907,10 @@ Hierarchical DFOP path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:37:03 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:46:08 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2929,7 +2929,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 675.804 s
+Fitted in 689.217 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3053,10 +3053,10 @@ Hierarchical SFORB path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:34:43 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:43:37 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3074,7 +3074,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 535.818 s
+Fitted in 538.025 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3218,10 +3218,10 @@ Hierarchical SFORB path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:37:02 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:45:51 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3239,7 +3239,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 674.859 s
+Fitted in 672.309 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3383,10 +3383,10 @@ Hierarchical HS path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:34:41 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:43:26 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan
@@ -3401,7 +3401,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 533.787 s
+Fitted in 526.974 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3525,10 +3525,10 @@ Hierarchical HS path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:34:39 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:43:29 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan
@@ -3543,7 +3543,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 531.084 s
+Fitted in 529.515 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3673,10 +3673,10 @@ Hierarchical FOMC path 2 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:45:51 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:54:58 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3691,7 +3691,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 517.002 s
+Fitted in 519.639 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3837,10 +3837,10 @@ Hierarchical FOMC path 2 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:45:39 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:54:41 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3855,7 +3855,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 505.619 s
+Fitted in 503.222 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3983,10 +3983,10 @@ Hierarchical DFOP path 2 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:46:46 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:55:53 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4006,7 +4006,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 572.382 s
+Fitted in 574.8 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4174,10 +4174,10 @@ Hierarchical DFOP path 2 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:49:18 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:58:32 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4197,7 +4197,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 724.515 s
+Fitted in 733.398 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4365,10 +4365,10 @@ Hierarchical SFORB path 2 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:46:33 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:55:51 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4386,7 +4386,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 559.097 s
+Fitted in 572.747 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4561,10 +4561,10 @@ Hierarchical SFORB path 2 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 20:49:20 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 17:58:21 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4582,7 +4582,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 726.293 s
+Fitted in 722.847 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4762,10 +4762,10 @@ error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 21:02:39 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:12:10 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -4780,7 +4780,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 796.615 s
+Fitted in 816.454 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4905,10 +4905,10 @@ variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 21:04:15 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:13:38 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4928,7 +4928,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 893.328 s
+Fitted in 904.25 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -5071,10 +5071,10 @@ error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 21:04:33 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:00 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -5094,7 +5094,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 910.788 s
+Fitted in 926.094 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -5237,10 +5237,10 @@ variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 21:04:09 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:13:34 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5258,7 +5258,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 887.369 s
+Fitted in 900.859 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -5408,10 +5408,10 @@ error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.4 
-R version used for fitting:         4.2.3 
-Date of fit:     Thu Apr 20 21:04:32 2023 
-Date of summary: Thu Apr 20 21:04:34 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:13:37 2023 
+Date of summary: Fri May 19 18:14:01 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5429,7 +5429,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 910.017 s
+Fitted in 903.326 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -5578,13 +5578,13 @@ JSE76  26.89  89.33       NA           NA           NA
 

 
Session info
 

-
R version 4.2.3 (2023-03-15)
+
R version 4.3.0 (2023-04-21)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so;  LAPACK version 3.11.0
 
 locale:
  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
@@ -5594,37 +5594,40 @@ locale:
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
 attached base packages:
 [1] parallel  stats     graphics  grDevices utils     datasets  methods  
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.4
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.5
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.35      zoo_1.8-12        tidyselect_1.2.0  xfun_0.38        
- [5] bslib_0.4.2       purrr_1.0.1       lattice_0.21-8    colorspace_2.1-0 
- [9] vctrs_0.6.1       generics_0.1.3    htmltools_0.5.5   yaml_2.3.7       
-[13] utf8_1.2.3        rlang_1.1.0       pkgbuild_1.4.0    pkgdown_2.0.7    
-[17] jquerylib_0.1.4   pillar_1.9.0      glue_1.6.2        DBI_1.1.3        
-[21] readxl_1.4.2      lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0    
-[25] gtable_0.3.3      cellranger_1.1.0  ragg_1.2.5        codetools_0.2-19 
-[29] memoise_2.0.1     evaluate_0.20     inline_0.3.19     callr_3.7.3      
-[33] fastmap_1.1.1     ps_1.7.4          lmtest_0.9-40     fansi_1.0.4      
-[37] highr_0.10        scales_1.2.1      cachem_1.0.7      desc_1.4.2       
-[41] jsonlite_1.8.4    systemfonts_1.0.4 fs_1.6.1          textshaping_0.3.6
-[45] gridExtra_2.3     ggplot2_3.4.2     digest_0.6.31     stringi_1.7.12   
-[49] processx_3.8.0    dplyr_1.1.1       grid_4.2.3        rprojroot_2.0.3  
-[53] cli_3.6.1         tools_4.2.3       magrittr_2.0.3    sass_0.4.5       
-[57] tibble_3.2.1      crayon_1.5.2      pkgconfig_2.0.3   prettyunits_1.1.1
-[61] rmarkdown_2.21    R6_2.5.1          mclust_6.0.0      nlme_3.1-162     
-[65] compiler_4.2.3   

+ [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_4.3.0        fastmap_1.1.1     cellranger_1.1.0  rprojroot_2.0.3  
+[13] jsonlite_1.8.4    processx_3.8.1    pkgbuild_1.4.0    deSolve_1.35     
+[17] DBI_1.1.3         mclust_6.0.0      ps_1.7.5          gridExtra_2.3    
+[21] purrr_1.0.1       fansi_1.0.4       scales_1.2.1      codetools_0.2-19 
+[25] textshaping_0.3.6 jquerylib_0.1.4   cli_3.6.1         crayon_1.5.2     
+[29] rlang_1.1.1       munsell_0.5.0     cachem_1.0.8      yaml_2.3.7       
+[33] inline_0.3.19     tools_4.3.0       memoise_2.0.1     dplyr_1.1.2      
+[37] colorspace_2.1-0  ggplot2_3.4.2     vctrs_0.6.2       R6_2.5.1         
+[41] zoo_1.8-12        lifecycle_1.0.3   stringr_1.5.0     fs_1.6.2         
+[45] ragg_1.2.5        callr_3.7.3       pkgconfig_2.0.3   desc_1.4.2       
+[49] pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0      gtable_0.3.3     
+[53] glue_1.6.2        systemfonts_1.0.4 highr_0.10        xfun_0.39        
+[57] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  htmltools_0.5.5  
+[61] nlme_3.1-162      rmarkdown_2.21    compiler_4.3.0    prettyunits_1.1.1
+[65] readxl_1.4.2     

 

 

 
Hardware info
 

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

-
MemTotal:       64936316 kB

+
MemTotal:       64925476 kB

 

 
   
diff --git a/docs/dev/articles/prebuilt/2022_dmta_parent.html b/docs/dev/articles/prebuilt/2022_dmta_parent.html
index 92259add..45a925b3 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_parent.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_parent.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.3
+        1.2.5
       
     
 
@@ -136,7 +136,7 @@ with residue data on dimethenamid and dimethenamid-P
 Ranke
             
             
Last change on 5 January
-2023, last compiled on 16 April 2023

+2023, last compiled on 19 Mai 2023
       
       Source: vignettes/prebuilt/2022_dmta_parent.rmd
       
@@ -155,7 +155,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.

 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.

-
The mkin package is used in version 1.2.3. It contains the test data
+
The mkin package is used in version 1.2.5. It contains the test data
 and the functions used in the evaluations. The saemix
 package is used as a backend for fitting the NLHM, but is also loaded to
 make the convergence plot function available.

@@ -1287,10 +1287,10 @@ Plot of the final NLHM DFOP fit
 
 summary(f_saem_dfop_tc_no_ranef_k2)

 
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 11:22:51 2023 
-Date of summary: Sat Jan 28 11:22:52 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:27 2023 
+Date of summary: Fri May 19 18:14:28 2023 
 
 Equations:
 d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1302,7 +1302,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 3.74 s
+Fitted in 4.477 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1463,10 +1463,10 @@ Hierarchical mkin fit of the SFO model with error model const
 
 

 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 11:22:44 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:19 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - k_DMTA * DMTA
@@ -1476,7 +1476,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 0.982 s
+Fitted in 1.091 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -1535,10 +1535,10 @@ Hierarchical mkin fit of the SFO model with error model tc
 
 

 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 11:22:46 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:21 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - k_DMTA * DMTA
@@ -1548,7 +1548,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.39 s
+Fitted in 2.517 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1609,10 +1609,10 @@ Hierarchical mkin fit of the FOMC model with error model const
 
 

 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 11:22:45 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:20 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1622,7 +1622,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.552 s
+Fitted in 1.25 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -1686,10 +1686,10 @@ Hierarchical mkin fit of the FOMC model with error model tc
 
 

 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 11:22:46 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:21 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1699,7 +1699,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.764 s
+Fitted in 2.666 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1765,10 +1765,10 @@ Hierarchical mkin fit of the DFOP model with error model const
 
 

 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 11:22:45 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:20 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1780,7 +1780,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.649 s
+Fitted in 1.639 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -1849,10 +1849,10 @@ Hierarchical mkin fit of the DFOP model with error model tc
 
 

 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 11:22:46 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:22 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1864,7 +1864,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 3.288 s
+Fitted in 3.435 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1935,10 +1935,10 @@ Hierarchical mkin fit of the HS model with error model const
 
 

 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 11:22:45 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:20 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA
@@ -1948,7 +1948,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.006 s
+Fitted in 1.946 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -2017,10 +2017,10 @@ Hierarchical mkin fit of the HS model with error model tc
 
 

 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 11:22:46 2023 
-Date of summary: Sat Jan 28 11:23:57 2023 
+mkin version used for pre-fitting:  1.2.5 
+R version used for fitting:         4.3.0 
+Date of fit:     Fri May 19 18:14:22 2023 
+Date of summary: Fri May 19 18:15:34 2023 
 
 Equations:
 d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA
@@ -2030,7 +2030,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 3.267 s
+Fitted in 3.626 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -2144,13 +2144,13 @@ Convergence plot for the NLHM HS fit with two-component error
 

 
Session info
 

-
R version 4.2.2 Patched (2022-11-10 r83330)
+
R version 4.3.0 (2023-04-21)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Debian GNU/Linux bookworm/sid
+Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so;  LAPACK version 3.11.0
 
 locale:
  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
@@ -2160,35 +2160,37 @@ locale:
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
 attached base packages:
 [1] parallel  stats     graphics  grDevices utils     datasets  methods  
 [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_1.42 mkin_1.2.5
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.34      zoo_1.8-11        tidyselect_1.2.0  xfun_0.35        
- [5] bslib_0.4.2       purrr_1.0.0       lattice_0.20-45   colorspace_2.0-3 
- [9] vctrs_0.5.1       generics_0.1.3    htmltools_0.5.4   yaml_2.3.6       
-[13] utf8_1.2.2        rlang_1.0.6       pkgdown_2.0.7     jquerylib_0.1.4  
-[17] pillar_1.8.1      glue_1.6.2        DBI_1.1.3         lifecycle_1.0.3  
-[21] stringr_1.5.0     munsell_0.5.0     gtable_0.3.1      ragg_1.2.4       
-[25] codetools_0.2-18  memoise_2.0.1     evaluate_0.19     fastmap_1.1.0    
-[29] lmtest_0.9-40     fansi_1.0.3       highr_0.9         scales_1.2.1     
-[33] cachem_1.0.6      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
-[37] fs_1.5.2          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.0    
-[41] digest_0.6.31     stringi_1.7.8     dplyr_1.0.10      grid_4.2.2       
-[45] rprojroot_2.0.3   cli_3.5.0         tools_4.2.2       magrittr_2.0.3   
-[49] sass_0.4.4        tibble_3.1.8      pkgconfig_2.0.3   assertthat_0.2.1 
-[53] rmarkdown_2.19    R6_2.5.1          mclust_6.0.0      nlme_3.1-161     
-[57] compiler_4.2.2   

+ [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_4.3.0        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_4.3.0       memoise_2.0.1    
+[29] dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2     vctrs_0.6.2      
+[33] R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3   stringr_1.5.0    
+[37] fs_1.6.2          ragg_1.2.5        pkgconfig_2.0.3   desc_1.4.2       
+[41] pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0      gtable_0.3.3     
+[45] glue_1.6.2        systemfonts_1.0.4 highr_0.10        xfun_0.39        
+[49] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  htmltools_0.5.5  
+[53] nlme_3.1-162      rmarkdown_2.21    compiler_4.3.0   

 

 

 
Hardware info
 

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

-
MemTotal:       64940452 kB

+
MemTotal:       64925476 kB

 

 
   
diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
index 959f3429..1861db06 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.4
+        1.2.5
       
     
 
@@ -136,7 +136,7 @@ residue data on dimethenamid and dimethenamid-P
 Ranke
             
             
Last change on 20 April 2023,
-last compiled on 20 April 2023

+last compiled on 19 Mai 2023
       
       Source: vignettes/prebuilt/2022_dmta_pathway.rmd
       
@@ -156,7 +156,7 @@ can be fitted with the mkin package.

 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.

-
The mkin package is used in version 1.2.4, which is currently under
+
The mkin package is used in version 1.2.5, which is currently under
 development. It contains the test data, and the functions used in the
 evaluations. The saemix package is used as a backend for
 fitting the NLHM, but is also loaded to make the convergence plot
@@ -1972,13 +1972,13 @@ error
 
Session info
 

-
R version 4.2.3 (2023-03-15)
+
R version 4.3.0 (2023-04-21)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so;  LAPACK version 3.11.0
 
 locale:
  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
@@ -1988,36 +1988,39 @@ locale:
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
 attached base packages:
 [1] parallel  stats     graphics  grDevices utils     datasets  methods  
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.4
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.5
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.35      zoo_1.8-12        tidyselect_1.2.0  xfun_0.38        
- [5] bslib_0.4.2       purrr_1.0.1       lattice_0.21-8    colorspace_2.1-0 
- [9] vctrs_0.6.1       generics_0.1.3    htmltools_0.5.5   yaml_2.3.7       
-[13] utf8_1.2.3        rlang_1.1.0       pkgbuild_1.4.0    pkgdown_2.0.7    
-[17] jquerylib_0.1.4   pillar_1.9.0      glue_1.6.2        DBI_1.1.3        
-[21] lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0     gtable_0.3.3     
-[25] ragg_1.2.5        codetools_0.2-19  memoise_2.0.1     evaluate_0.20    
-[29] inline_0.3.19     callr_3.7.3       fastmap_1.1.1     ps_1.7.4         
-[33] lmtest_0.9-40     fansi_1.0.4       highr_0.10        scales_1.2.1     
-[37] cachem_1.0.7      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
-[41] fs_1.6.1          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.2    
-[45] digest_0.6.31     stringi_1.7.12    processx_3.8.0    dplyr_1.1.1      
-[49] grid_4.2.3        rprojroot_2.0.3   cli_3.6.1         tools_4.2.3      
-[53] magrittr_2.0.3    sass_0.4.5        tibble_3.2.1      crayon_1.5.2     
-[57] pkgconfig_2.0.3   prettyunits_1.1.1 rmarkdown_2.21    R6_2.5.1         
-[61] mclust_6.0.0      nlme_3.1-162      compiler_4.2.3   

+ [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_4.3.0        fastmap_1.1.1     rprojroot_2.0.3   jsonlite_1.8.4   
+[13] processx_3.8.1    pkgbuild_1.4.0    deSolve_1.35      DBI_1.1.3        
+[17] mclust_6.0.0      ps_1.7.5          gridExtra_2.3     purrr_1.0.1      
+[21] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  textshaping_0.3.6
+[25] jquerylib_0.1.4   cli_3.6.1         crayon_1.5.2      rlang_1.1.1      
+[29] munsell_0.5.0     cachem_1.0.8      yaml_2.3.7        inline_0.3.19    
+[33] tools_4.3.0       memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0 
+[37] ggplot2_3.4.2     vctrs_0.6.2       R6_2.5.1          zoo_1.8-12       
+[41] lifecycle_1.0.3   stringr_1.5.0     fs_1.6.2          ragg_1.2.5       
+[45] callr_3.7.3       pkgconfig_2.0.3   desc_1.4.2        pkgdown_2.0.7    
+[49] bslib_0.4.2       pillar_1.9.0      gtable_0.3.3      glue_1.6.2       
+[53] systemfonts_1.0.4 highr_0.10        xfun_0.39         tibble_3.2.1     
+[57] lmtest_0.9-40     tidyselect_1.2.0  htmltools_0.5.5   nlme_3.1-162     
+[61] rmarkdown_2.21    compiler_4.3.0    prettyunits_1.1.1

 
 

 
Hardware info
 

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

-
MemTotal:       64936316 kB

+
MemTotal:       64925476 kB

 

 
   
-- 
cgit v1.2.1