From cf54ccca37d27480dbf8d59eb027300518f7ad75 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 17:08:43 +0200 Subject: Prepare release of v1.2.4 - Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release --- docs/articles/prebuilt/2022_dmta_pathway.html | 168 ++++++++++++++------------ 1 file changed, 88 insertions(+), 80 deletions(-) (limited to 'docs/articles/prebuilt/2022_dmta_pathway.html') diff --git a/docs/articles/prebuilt/2022_dmta_pathway.html b/docs/articles/prebuilt/2022_dmta_pathway.html index c8323add..ea4bd087 100644 --- a/docs/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/articles/prebuilt/2022_dmta_pathway.html @@ -33,7 +33,7 @@ mkin - 1.2.3.1 + 1.2.4 @@ -135,7 +135,7 @@ 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 @@ -155,7 +155,7 @@ 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 @@ -1496,7 +1496,7 @@ of parent models tested here.

dfop_path_1 OK OK -C +OK OK OK OK @@ -1514,7 +1514,7 @@ of parent models tested here.

hs_path_1 C C -C +OK C C C @@ -1552,24 +1552,24 @@ not converge with default settings.

fomc_path_1 OK OK -C OK OK -C +OK +OK dfop_path_1 OK C OK -OK +C OK OK sforb_path_1 OK -C +OK OK OK OK @@ -1582,7 +1582,7 @@ not converge with default settings.

C C C -OK +C @@ -1643,8 +1643,6 @@ than twenty minutes.

successfully.

 anova(saem_1) |> kable(digits = 1)
-
Warning in FUN(X[[i]], ...): Could not obtain log likelihood with 'is' method
-for sforb_path_1 const
@@ -1664,58 +1662,65 @@ for sforb_path_1 const - - - + + + - - - + + + - - - + + + - - - + + + - + - - - + + + + + + + + + + - - - + + + - + - - - + + + - + - - - + + +
sfo_path_1 tc 182276.32272.5-1120.12276.42272.7-1120.2
fomc_path_1 const 192099.02095.0-1030.52095.92091.9-1028.9
fomc_path_1 tc 201939.61935.5-949.81939.01934.8-949.5
dfop_path_1 const 212038.82034.4-998.42039.72035.3-998.8
hs_path_1 constsforb_path_1 const 212024.22019.8-991.12017.72013.4-987.9
hs_path_1 const212023.72019.3-990.9
dfop_path_1 tc 221879.81875.2-917.91881.71877.1-918.9
sforb_path_1 tc 221832.91828.3-894.41832.71828.1-894.3
hs_path_1 tc 221831.41826.8-893.71831.61827.0-893.8
@@ -1740,7 +1745,7 @@ Matrix
+
 illparms(saem_1) |> kable()

 
@@ -1766,7 +1771,7 @@ found.

-
+
@@ -1786,13 +1791,13 @@ two-component error, the random effect for the rate constant from
 reversibly bound DMTA to the free DMTA (k_DMTA_bound_free)
 is not well-defined. Therefore, the fit is updated without assuming a
 random effect for this parameter.

-
+
 saem_sforb_path_1_tc_reduced <- update(saem_1[["sforb_path_1", "tc"]],
   no_random_effect = "log_k_DMTA_bound_free")
 illparms(saem_sforb_path_1_tc_reduced)

 
As expected, no ill-defined parameters remain. The model comparison
 below shows that the reduced model is preferable.

-
+
 anova(saem_1[["sforb_path_1", "tc"]], saem_sforb_path_1_tc_reduced) |> kable(digits = 1)

 

 

 

 

 sforb_path_1sd(log_k_DMTA_bound_free)
 sd(log_k_DMTA_bound_free)
 

 

@@ -1806,21 +1811,21 @@ below shows that the reduced model is preferable.

-
-
+
+
-
-
-
+
+
+

 

 

 saem_sforb_path_1_tc_reduced
 211830.31825.91830.41826.0
 -894.2
 

 

 saem_1[[“sforb_path_1”, “tc”]]
 221832.91828.3-894.41832.71828.1-894.3
 

 
 

 
The convergence plot of the refined fit is shown below.

-
+
 plot(saem_sforb_path_1_tc_reduced$so, plot.type = "convergence")

 

 
For some parameters, for example for f_DMTA_ilr_1 and
@@ -1839,14 +1844,14 @@ saemix.

 
 
As an alternative check of parameter identifiability (Duchesne et al. 2021), multistart runs were
 performed on the basis of the refined fit shown above.

-
+
 saem_sforb_path_1_tc_reduced_multi <- multistart(saem_sforb_path_1_tc_reduced,
   n = 32, cores = 10)

-
+
 print(saem_sforb_path_1_tc_reduced_multi)

 
<multistart> object with 32 fits:
  E OK 
-15 17 
+ 7 25 
 OK: Fit terminated successfully
 E: Error

 
Out of the 32 fits that were initiated, only 17 terminated without an
@@ -1856,7 +1861,7 @@ the SAEM algorithm leads to parameter combinations for the degradation
 model that the numerical integration routine cannot cope with. Because
 of this variation of initial parameters, some of the model fits take up
 to two times more time than the original fit.

-
+
 par(mar = c(12.1, 4.1, 2.1, 2.1))
 parplot(saem_sforb_path_1_tc_reduced_multi, ylim = c(0.5, 2), las = 2)

 

@@ -1875,14 +1880,14 @@ ill-defined parameters.

 
 
The SFORB pathway fits with full and reduced parameter distribution
 model are shown below.

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

 

 SFORB pathway fit with two-component error

 SFORB pathway fit with two-component error
 

 

-
+
 plot(saem_sforb_path_1_tc_reduced)

 

 SFORB pathway fit with two-component error, reduced parameter model

@@ -1891,7 +1896,7 @@ 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.

-
 

@@ -1931,21 +1936,21 @@ 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
 

 

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

 

 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

@@ -1971,13 +1976,13 @@ error
 
Session info
 

-
R version 4.2.3 (2023-03-15)
+
R version 4.3.0 Patched (2023-05-18 r84448)
 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:   /home/jranke/svn/R/r-patched/build/lib/libRblas.so 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3;  LAPACK version 3.11.0
 
 locale:
  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
@@ -1987,36 +1992,39 @@ 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_1.2.3
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.4
 
 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

 

 

   

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