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/web_only/FOCUS_Z.html | 4 +- docs/dev/articles/web_only/NAFTA_examples.html | 4 +- docs/dev/articles/web_only/benchmarks.html | 82 ++++++++++++++++--- docs/dev/articles/web_only/compiled_models.html | 20 ++--- docs/dev/articles/web_only/dimethenamid_2018.html | 43 +++++----- docs/dev/articles/web_only/multistart.html | 4 +- docs/dev/articles/web_only/saem_benchmarks.html | 96 ++++++++++++++++++++--- 7 files changed, 192 insertions(+), 61 deletions(-) (limited to 'docs/dev/articles/web_only') diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html index 979cf2c6..917a6865 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.5 @@ -135,7 +135,7 @@ Ranke

Last change 16 January 2018 -(rebuilt 2023-04-16)

+(rebuilt 2023-05-19) Source: vignettes/web_only/FOCUS_Z.rmd diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index 9feecfce..e4e457fc 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.5 @@ -136,7 +136,7 @@ to the US EPA SOP for the NAFTA guidance Ranke

26 February 2019 (rebuilt -2023-04-16)

+2023-05-19) Source: vignettes/web_only/NAFTA_examples.rmd diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index 87bdd55f..b3c12f66 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.5 @@ -135,7 +135,7 @@ Ranke

Last change 17 February 2023 -(rebuilt 2023-04-16)

+(rebuilt 2023-05-19) Source: vignettes/web_only/benchmarks.rmd @@ -423,8 +423,24 @@ models fitted to two datasets, i.e. eight fits for each test.

Ryzen 9 7950X 4.2.3 1.2.3 -1.404 -1.933 +1.406 +1.948 + + +Linux +Ryzen 9 7950X +4.3.0 +1.2.4 +1.386 +1.960 + + +Linux +Ryzen 9 7950X +4.3.0 +1.2.5 +1.400 +1.936 @@ -649,9 +665,27 @@ for each test.

Ryzen 9 7950X 4.2.3 1.2.3 -0.797 -2.124 -1.182 +0.793 +2.109 +1.178 + + +Linux +Ryzen 9 7950X +4.3.0 +1.2.4 +0.779 +2.080 +1.106 + + +Linux +Ryzen 9 7950X +4.3.0 +1.2.5 +0.800 +2.118 +1.172 @@ -958,11 +992,35 @@ dataset, i.e. one fit for each test.

4.2.3 1.2.3 0.432 -0.551 -0.616 -1.039 -0.734 -0.981 +0.549 +0.609 +1.052 +0.743 +0.989 + + +Linux +Ryzen 9 7950X +4.3.0 +1.2.4 +0.410 +0.526 +0.553 +1.249 +0.712 +0.948 + + +Linux +Ryzen 9 7950X +4.3.0 +1.2.5 +0.433 +0.558 +0.618 +1.053 +0.745 +0.986 diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index e7905860..a0b34dda 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.5 @@ -135,7 +135,7 @@ definitions in mkin

Johannes Ranke

-

2023-04-16

+

2023-05-19

Source: vignettes/web_only/compiled_models.rmd @@ -214,10 +214,10 @@ solution is also implemented, which is included in the tests below.

print("R package rbenchmark is not available") } 
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.105
-## 3     deSolve, compiled            1    1.276   0.134
-## 2      Eigenvalue based            1    1.762   0.185
-## 1 deSolve, not compiled            1   21.914   2.301
+## 4 analytical 1 1.000 0.108 +## 3 deSolve, compiled 1 1.259 0.136 +## 2 Eigenvalue based 1 1.704 0.184 +## 1 deSolve, not compiled 1 21.574 2.330

We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

@@ -248,12 +248,12 @@ compiled code is available.

} 
## Temporary DLL for differentials generated and loaded
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.176
-## 1 deSolve, not compiled            1   23.938   4.213
+## 2 deSolve, compiled 1 1.000 0.178 +## 1 deSolve, not compiled 1 23.708 4.220

Here we get a performance benefit of a factor of 24 using the version of the differential equation model compiled from C code!

-

This vignette was built with mkin 1.2.3 on

-
## R version 4.2.3 (2023-03-15)
+
This vignette was built with mkin 1.2.5 on

+
## R version 4.3.0 (2023-04-21)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 12 (bookworm)

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

diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html
index eb4a11a5..60e65367 100644
--- a/docs/dev/articles/web_only/dimethenamid_2018.html
+++ b/docs/dev/articles/web_only/dimethenamid_2018.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.3
+        1.2.5
       
     
 
@@ -136,7 +136,7 @@ from 2018
 Ranke
             
             
Last change 1 July 2022,
-built on 16 Apr 2023

+built on 19 May 2023
       
       Source: vignettes/web_only/dimethenamid_2018.rmd
       
@@ -615,13 +615,13 @@ satisfactory precision.

 
 
-
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              
@@ -631,27 +631,30 @@ 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] saemix_3.2   npde_3.3     nlme_3.1-162 mkin_1.2.5   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    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       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 highr_0.10       
+[49] xfun_0.39         tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0 
+[53] htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.0   

 
 

 
References
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index 2de5059c..7855f177 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.4
+        1.2.5
       
     

 
@@ -135,7 +135,7 @@
 Ranke
             
             
Last change 20 April 2023
-(rebuilt 2023-04-20)

+(rebuilt 2023-05-19)
       
       Source: vignettes/web_only/multistart.rmd
       
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index 66740a11..22acf655 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.3
+        1.2.5
       
     
 
@@ -135,7 +135,7 @@
 Ranke
             
             
Last change 17 February 2023
-(rebuilt 2023-04-16)

+(rebuilt 2023-05-19)
       
       Source: vignettes/web_only/saem_benchmarks.rmd
       
@@ -398,10 +398,30 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.3
 3.2
-1.389
-2.300
-1.880
-2.355
+1.419
+2.374
+1.926
+2.398
+
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+0.972
+2.550
+1.987
+2.055
+
+
+Ryzen 9 7950X
+Linux
+1.2.5
+3.2
+0.994
+2.546
+1.999
+2.070
 
 
 
@@ -473,10 +493,30 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.3
 3.2
-2.300
-3.075
-3.206
-3.471
+2.348
+3.134
+3.253
+3.530
+
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+2.127
+3.587
+3.433
+3.595
+
+
+Ryzen 9 7950X
+Linux
+1.2.5
+3.2
+2.152
+3.316
+3.309
+3.337
 
 
 
@@ -540,8 +580,24 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.3
 3.2
-12.951
-294.082
+12.841
+292.688
+
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+12.160
+265.934
+
+
+Ryzen 9 7950X
+Linux
+1.2.5
+3.2
+11.249
+290.918
 
 
 
@@ -599,7 +655,21 @@ systems. All trademarks belong to their respective owners.

 Linux
 1.2.3
 3.2
-477.297
+483.027
+
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+456.252
+
+
+Ryzen 9 7950X
+Linux
+1.2.5
+3.2
+479.637
 
 
 
-- 
cgit v1.2.1