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/web_only/dimethenamid_2018.html | 55 ++++++++++++++------------- 1 file changed, 29 insertions(+), 26 deletions(-) (limited to 'docs/articles/web_only/dimethenamid_2018.html') diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 4575067b..a89631a2 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -135,7 +135,7 @@ from 2018 Ranke

Last change 1 July 2022, -built on 20 Apr 2023

+built on 19 May 2023 Source: vignettes/web_only/dimethenamid_2018.rmd @@ -222,12 +222,12 @@ 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 @@ -239,7 +239,7 @@ 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 @@ -251,7 +251,7 @@ 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 @@ -341,7 +341,7 @@ 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)

@@ -549,7 +549,7 @@ 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) @@ -614,13 +614,13 @@ satisfactory precision.

 sessionInfo()
-
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              
@@ -630,27 +630,30 @@ 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] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.2   npde_3.3     nlme_3.1-162 mkin_1.2.3   knitr_1.42  
+[1] nlme_3.1-162 mkin_1.2.4   knitr_1.42  
 
 loaded via a namespace (and not attached):
- [1] highr_0.10        pillar_1.9.0      bslib_0.4.2       compiler_4.2.3   
- [5] jquerylib_0.1.4   tools_4.2.3       mclust_6.0.0      digest_0.6.31    
- [9] tibble_3.2.1      jsonlite_1.8.4    evaluate_0.20     memoise_2.0.1    
-[13] lifecycle_1.0.3   gtable_0.3.3      lattice_0.21-8    pkgconfig_2.0.3  
-[17] rlang_1.1.0       DBI_1.1.3         cli_3.6.1         yaml_2.3.7       
-[21] parallel_4.2.3    pkgdown_2.0.7     xfun_0.38         fastmap_1.1.1    
-[25] gridExtra_2.3     dplyr_1.1.1       stringr_1.5.0     generics_0.1.3   
-[29] desc_1.4.2        fs_1.6.1          vctrs_0.6.1       sass_0.4.5       
-[33] systemfonts_1.0.4 tidyselect_1.2.0  rprojroot_2.0.3   lmtest_0.9-40    
-[37] grid_4.2.3        glue_1.6.2        R6_2.5.1          textshaping_0.3.6
-[41] fansi_1.0.4       rmarkdown_2.21    purrr_1.0.1       ggplot2_3.4.2    
-[45] magrittr_2.0.3    codetools_0.2-19  scales_1.2.1      htmltools_0.5.5  
-[49] colorspace_2.1-0  ragg_1.2.5        utf8_1.2.3        stringi_1.7.12   
-[53] munsell_0.5.0     cachem_1.0.7      zoo_1.8-12       

+ [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    saemix_3.2       
+ [5] stringi_1.7.12    lattice_0.21-8    digest_0.6.31     magrittr_2.0.3   
+ [9] evaluate_0.21     grid_4.3.0        fastmap_1.1.1     rprojroot_2.0.3  
+[13] jsonlite_1.8.4    DBI_1.1.3         mclust_6.0.0      gridExtra_2.3    
+[17] purrr_1.0.1       fansi_1.0.4       scales_1.2.1      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       parallel_4.3.0   
+[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          ragg_1.2.5        pkgconfig_2.0.3  
+[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0     
+[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 xfun_0.39        
+[49] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  npde_3.3         
+[53] htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.0

References -- cgit v1.2.1

Degradation model