From 78d34a8918edcb91982a3886e4898a63898f52c3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 20 Apr 2023 21:40:08 +0200 Subject: Update vignettes in dev docs After the post-release fixes to the release version online docs --- docs/dev/articles/prebuilt/2022_dmta_pathway.html | 79 +++++++++++++---------- 1 file changed, 45 insertions(+), 34 deletions(-) (limited to 'docs/dev/articles/prebuilt/2022_dmta_pathway.html') diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html index 0285a193..959f3429 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.4 @@ -135,8 +135,8 @@ residue data on dimethenamid and dimethenamid-P

Johannes Ranke

-

Last change on 8 January -2023, last compiled on 16 April 2023

+

Last change on 20 April 2023, +last compiled on 20 April 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 1.2.3, which is currently under +

The mkin package is used in version 1.2.4, 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 @@ -171,10 +171,17 @@ processing, the parallel package is used.

library(saemix) library(parallel) n_cores <- detectCores() -if (Sys.info()["sysname"] == "Windows") { - cl <- makePSOCKcluster(n_cores) -} else { - cl <- makeForkCluster(n_cores) + +# We need to start a new cluster after defining a compiled model that is +# saved as a DLL to the user directory, therefore we define a function +# This is used again after defining the pathway model +start_cluster <- function(n_cores) { + if (Sys.info()["sysname"] == "Windows") { + ret <- makePSOCKcluster(n_cores) + } else { + ret <- makeForkCluster(n_cores) + } + return(ret) }
@@ -1441,6 +1448,8 @@ of parent models tested here.

unload = TRUE, overwrite = TRUE, quiet = TRUE ) +cl <- start_cluster(n_cores) + deg_mods_1 <- list( sfo_path_1 = m_sfo_path_1, fomc_path_1 = m_fomc_path_1, @@ -1883,6 +1892,8 @@ SFORB pathway fit with two-component error, reduced parameter model

Plots of the remaining fits and listings for all successful fits are shown in the Appendix.

+
+stopCluster(cl)

Conclusions @@ -1921,24 +1932,24 @@ Level with Nonlinear Mixed-Effects Models.” Environments

Plots of hierarchical fits not selected for refinement

-
+
 plot(saem_1[["sfo_path_1", "tc"]])

 

-SFO pathway fit with two-component error

+SFO pathway fit with two-component error

 SFO pathway fit with two-component error
 

 

-
+
 plot(saem_1[["fomc_path_1", "tc"]])

 

-FOMC pathway fit with two-component error

+FOMC pathway fit with two-component error

 FOMC pathway fit with two-component error
 

 

-
+
 plot(saem_1[["sforb_path_1", "tc"]])

 

-HS pathway fit with two-component error

+HS pathway fit with two-component error

 HS pathway fit with two-component error
 

 

@@ -1961,9 +1972,9 @@ error
 
Session info
 

-
R version 4.2.2 Patched (2022-11-10 r83330)
+
R version 4.2.3 (2023-03-15)
 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
@@ -1982,31 +1993,31 @@ attached base packages:
 [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_1.2.4
 
 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] pkgbuild_1.4.0    utf8_1.2.2        rlang_1.0.6       pkgdown_2.0.7    
-[17] jquerylib_0.1.4   pillar_1.8.1      glue_1.6.2        DBI_1.1.3        
-[21] lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0     gtable_0.3.1     
-[25] ragg_1.2.4        codetools_0.2-18  memoise_2.0.1     evaluate_0.19    
-[29] inline_0.3.19     callr_3.7.3       fastmap_1.1.0     ps_1.7.2         
-[33] lmtest_0.9-40     fansi_1.0.3       highr_0.9         scales_1.2.1     
-[37] cachem_1.0.6      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
-[41] fs_1.5.2          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.0    
-[45] digest_0.6.31     stringi_1.7.8     processx_3.8.0    dplyr_1.0.10     
-[49] grid_4.2.2        rprojroot_2.0.3   cli_3.5.0         tools_4.2.2      
-[53] magrittr_2.0.3    sass_0.4.4        tibble_3.1.8      crayon_1.5.2     
-[57] pkgconfig_2.0.3   prettyunits_1.1.1 assertthat_0.2.1  rmarkdown_2.19   
-[61] R6_2.5.1          mclust_6.0.0      nlme_3.1-161      compiler_4.2.2   

+ [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   

 

 

 
Hardware info
 

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

-
MemTotal:       64940452 kB

+
MemTotal:       64936316 kB
-- cgit v1.2.1