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_dmta_parent.html | 140 ++++++++++++----------- 1 file changed, 71 insertions(+), 69 deletions(-) (limited to 'docs/dev/articles/prebuilt/2022_dmta_parent.html') 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

 

 
   
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