From 4f62f39b8979cb3a5c52d65d425e530dc0770665 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 16 Feb 2025 17:27:18 +0100 Subject: Fix solution type "deSolve" for a special case The special case occurs if not observed data for time zero are available. Fixes #16. Write NEWS and update docs. A lot of html was regenerated, because I had checked out the main branch in between, which made pkgdown believe that I have changed the help files. --- docs/dev/articles/web_only/FOCUS_Z.html | 2 +- docs/dev/articles/web_only/NAFTA_examples.html | 2 +- docs/dev/articles/web_only/benchmarks.html | 24 +++++++++++------------ docs/dev/articles/web_only/compiled_models.html | 14 ++++++------- docs/dev/articles/web_only/dimethenamid_2018.html | 12 ++++++------ docs/dev/articles/web_only/multistart.html | 2 +- docs/dev/articles/web_only/saem_benchmarks.html | 22 ++++++++++----------- 7 files changed, 39 insertions(+), 39 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 40ce9e01..9db2cf7e 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.html @@ -85,7 +85,7 @@ Ranke

Last change 16 January 2018 -(rebuilt 2025-02-14)

+(rebuilt 2025-02-16) Source: vignettes/web_only/FOCUS_Z.rmd
FOCUS_Z.rmd
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index 6bf39b2c..54c45b3e 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -85,7 +85,7 @@ Ranke

26 February 2019 (rebuilt -2025-02-14)

+2025-02-16) Source: vignettes/web_only/NAFTA_examples.rmd
NAFTA_examples.rmd
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index bd6a443a..bb5647d3 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -85,7 +85,7 @@ Ranke

Last change 17 February 2023 -(rebuilt 2025-02-14)

+(rebuilt 2025-02-16) Source: vignettes/web_only/benchmarks.rmd
benchmarks.rmd
@@ -428,8 +428,8 @@ models fitted to two datasets, i.e. eight fits for each test.

Ryzen 9 7950X 4.4.2 1.2.10 -1.371 -1.980 +1.407 +1.990 @@ -717,9 +717,9 @@ for each test.

Ryzen 9 7950X 4.4.2 1.2.10 -0.762 -2.179 -1.131 +0.775 +2.199 +1.161 @@ -1097,12 +1097,12 @@ dataset, i.e. one fit for each test.

Ryzen 9 7950X 4.4.2 1.2.10 -0.426 -0.533 -0.565 -1.296 -0.728 -0.978 +0.433 +0.541 +0.576 +1.307 +0.744 +0.988 diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index 113f7b67..a88a19ee 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -84,7 +84,7 @@

Johannes Ranke

-

2025-02-14

+

2025-02-16

Source: vignettes/web_only/compiled_models.rmd
compiled_models.rmd
@@ -162,10 +162,10 @@ 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   0.102
-## 3     deSolve, compiled            1    1.324   0.135
-## 2      Eigenvalue based            1    1.706   0.174
-## 1 deSolve, not compiled            1   22.627   2.308
+## 4 analytical 1 1.000 0.115 +## 3 deSolve, compiled 1 1.217 0.140 +## 2 Eigenvalue based 1 1.652 0.190 +## 1 deSolve, not compiled 1 20.522 2.360

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

@@ -196,8 +196,8 @@ compiled code is available.

} 
## Temporary DLL for differentials generated and loaded
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.170
-## 1 deSolve, not compiled            1   23.865   4.057
+## 2 deSolve, compiled 1 1.000 0.180 +## 1 deSolve, not compiled 1 23.656 4.258

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 1.2.10 on

diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html index 572f253d..0bbf0b73 100644 --- a/docs/dev/articles/web_only/dimethenamid_2018.html +++ b/docs/dev/articles/web_only/dimethenamid_2018.html @@ -85,7 +85,7 @@ Ranke

Last change 1 July 2022, -built on 14 Feb 2025

+built on 16 Feb 2025 Source: vignettes/web_only/dimethenamid_2018.rmd
dimethenamid_2018.rmd
@@ -586,7 +586,7 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.3 npde_3.5 nlme_3.1-166 mkin_1.2.10 knitr_1.49 +[1] nlme_3.1-166 mkin_1.2.10 knitr_1.49 loaded via a namespace (and not attached): [1] gtable_0.3.6 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2 @@ -598,10 +598,10 @@ loaded via a namespace (and not attached): [25] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 [29] xfun_0.49 fs_1.6.5 sass_0.4.9 cli_3.6.3 [33] pkgdown_2.1.1 magrittr_2.0.3 digest_0.6.37 grid_4.4.2 -[37] mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.1 -[41] glue_1.8.0 codetools_0.2-20 ragg_1.3.3 zoo_1.8-12 -[45] fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 pkgconfig_2.0.3 -[49] tools_4.4.2 htmltools_0.5.8.1 +[37] npde_3.5 mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 +[41] evaluate_1.0.1 glue_1.8.0 ragg_1.3.3 zoo_1.8-12 +[45] saemix_3.3 fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 +[49] pkgconfig_2.0.3 tools_4.4.2 htmltools_0.5.8.1

References diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 83073979..39bb2947 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -85,7 +85,7 @@ Ranke

Last change 20 April 2023 -(rebuilt 2025-02-14)

+(rebuilt 2025-02-16) Source: vignettes/web_only/multistart.rmd
multistart.rmd
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index d4cd0d6f..b76384da 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.html @@ -85,7 +85,7 @@ Ranke

Last change 17 February 2023 -(rebuilt 2025-02-14)

+(rebuilt 2025-02-16) Source: vignettes/web_only/saem_benchmarks.rmd
saem_benchmarks.rmd
@@ -408,9 +408,9 @@ systems. All trademarks belong to their respective owners.

1.2.10 3.3 1.115 -2.277 -1.945 -2.134 +2.263 +1.991 +2.193 @@ -542,10 +542,10 @@ systems. All trademarks belong to their respective owners.

Linux 1.2.10 3.3 -2.372 -3.137 -3.100 -3.281 +2.380 +3.147 +3.131 +3.331 @@ -657,8 +657,8 @@ systems. All trademarks belong to their respective owners.

Linux 1.2.10 3.3 -11.590 -279.782 +11.581 +296.184 @@ -758,7 +758,7 @@ systems. All trademarks belong to their respective owners.

Linux 1.2.10 3.3 -469.036 +486.856 -- cgit v1.2.1