From 05ca1ca375414b974b13da3bdb565e20d0cd46d6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Dec 2016 08:18:52 +0100 Subject: Static documentation articles rebuilt by pkgdown::build_articles() Split out an extra pd_articles target in the Makefile --- GNUmakefile | 11 +++++- docs/articles/FOCUS_L.html | 42 ++++++++++----------- docs/articles/compiled_models.html | 37 ++++++++++-------- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 9742 -> 9519 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 10742 -> 10832 bytes docs/articles/index.html | 2 +- 6 files changed, 52 insertions(+), 40 deletions(-) diff --git a/GNUmakefile b/GNUmakefile index ec8443e2..1d986246 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -87,9 +87,16 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/%.Rmd vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html pd: - "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" + "$(RBIN)/Rscript" -e "pkgdown::build_news()" + "$(RBIN)/Rscript" -e "pkgdown::build_reference(run_dont_run = TRUE)" + "$(RBIN)/Rscript" -e "pkgdown::build_home()" git add -A - git commit -m 'Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)' -e + git commit -m 'Static documentation except articles rebuilt by pkgdown' -e + +pd_articles: + "$(RBIN)/Rscript" -e "pkgdown::build_articles()" + git add -A + git commit -m 'Static documentation articles rebuilt by pkgdown::build_articles()' -e r-forge: rm -rf $(SDDIR)/* diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 6a25282b..feceab6f 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -76,15 +76,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO) 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:15 2016 
-## Date of summary: Thu Dec  8 07:59:15 2016 
+## Date of fit:     Thu Dec  8 08:18:47 2016 
+## Date of summary: Thu Dec  8 08:18:47 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.084 s
 ## 
 ## Weighting: none
 ## 
@@ -169,8 +169,8 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:15 2016 
-## Date of summary: Thu Dec  8 07:59:15 2016 
+## Date of fit:     Thu Dec  8 08:18:47 2016 
+## Date of summary: Thu Dec  8 08:18:47 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin <-  
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:16 2016 
-## Date of summary: Thu Dec  8 07:59:16 2016 
+## Date of fit:     Thu Dec  8 08:18:48 2016 
+## Date of summary: Thu Dec  8 08:18:48 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.201 s
 ## 
 ## Weighting: none
 ## 
@@ -336,8 +336,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:17 2016 
-## Date of summary: Thu Dec  8 07:59:17 2016 
+## Date of fit:     Thu Dec  8 08:18:49 2016 
+## Date of summary: Thu Dec  8 08:18:49 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:18 2016 
-## Date of summary: Thu Dec  8 07:59:18 2016 
+## Date of fit:     Thu Dec  8 08:18:50 2016 
+## Date of summary: Thu Dec  8 08:18:51 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:19 2016 
-## Date of summary: Thu Dec  8 07:59:19 2016 
+## Date of fit:     Thu Dec  8 08:18:51 2016 
+## Date of summary: Thu Dec  8 08:18:51 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.118 s
 ## 
 ## Weighting: none
 ## 
@@ -585,15 +585,15 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 07:59:19 2016 
-## Date of summary: Thu Dec  8 07:59:19 2016 
+## Date of fit:     Thu Dec  8 08:18:51 2016 
+## Date of summary: Thu Dec  8 08:18:51 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.152 s
+## Fitted with method Port using 66 model solutions performed in 0.151 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index d39caf12..2850a9ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -67,8 +67,13 @@
 
##            gcc 
 ## "/usr/bin/gcc"

 
First, we build a simple degradation model for a parent compound with one metabolite.

-
library("mkin")
-SFO_SFO <- mkinmod(
+
library("mkin")

+
## Loading required package: minpack.lm

+
## Loading required package: rootSolve

+
## Loading required package: inline

+
## Loading required package: methods

+
## Loading required package: parallel

+
SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))

 
## Successfully compiled differential equation model from auto-generated C code.

@@ -91,21 +96,21 @@ mb.1 <- micr
 print(mb.1)

 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394
-##       Eigenvalue based  865.5257  872.4146  892.2705  879.3036  905.6429
-##      deSolve, compiled  716.7534  717.9075  724.6869  719.0617  728.6537
+##  deSolve, not compiled 4973.8901 4975.2320 5000.4065 4976.5739 5013.6648
+##       Eigenvalue based  848.4335  859.7111  886.9766  870.9887  906.2481
+##      deSolve, compiled  702.8916  705.1930  706.2696  707.4944  707.9587
 ##        max neval cld
-##  6313.5506     3   c
-##   931.9821     3  b 
-##   738.2457     3 a

+##  5050.7556     3   c
+##   941.5075     3  b 
+##   708.4229     3 a

 
autoplot(mb.1)

 

-
We see that using the compiled model is by a factor of 8.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

+
We see that using the compiled model is by a factor of 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

 
rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

 
##                         median
-## deSolve, not compiled 8.738789
-## Eigenvalue based      1.222849
+## deSolve, not compiled 7.034082
+## Eigenvalue based      1.231089
 ## deSolve, compiled     1.000000

 
 

@@ -127,18 +132,18 @@ smb.1["median"]/smbprint(mb.2)

 
## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.487097 13.492149 13.528060 13.497201 13.548541
-##      deSolve, compiled  1.307845  1.318979  1.322967  1.330114  1.330528
+##  deSolve, not compiled 10.819486 10.846433 10.863732 10.873381 10.885855
+##      deSolve, compiled  1.300192  1.301168  1.304769  1.302144  1.307058
 ##        max neval cld
-##  13.599881     3   b
-##   1.330941     3  a

+##  10.898330     3   b
+##   1.311972     3  a

 
smb.2["median"]/smb.2["deSolve, compiled", "median"]

 
##   median
 ## 1     NA
 ## 2     NA

 
autoplot(mb.2)

 

-
Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!

+
Here we get a performance benefit of a factor of 8.4 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.44.9000 on

 
## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index d881a0a2..c30550c9 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index b3faa16f..5f95613a 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png differ
diff --git a/docs/articles/index.html b/docs/articles/index.html
index de5643c2..20792ba1 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -90,7 +90,7 @@
       
 
       

-  
Vignette reference version 0.9.44.9000

+  
Vignette reference version 0.9.45

 

 
 

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