From 00d164d6d40172c6f8b83578fd30ca28f8c378c7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 22 Jun 2015 23:03:28 +0200 Subject: Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge --- vignettes/FOCUS_D.Rmd | 6 ++--- vignettes/FOCUS_D.html | 6 ++--- vignettes/FOCUS_L.Rmd | 4 +-- vignettes/FOCUS_L.html | 60 ++++++++++++++++++++--------------------- vignettes/FOCUS_Z.pdf | Bin 224263 -> 224278 bytes vignettes/compiled_models.Rmd | 4 +-- vignettes/compiled_models.html | 34 +++++++++++------------ vignettes/mkin.pdf | Bin 160260 -> 160260 bytes 8 files changed, 57 insertions(+), 57 deletions(-) diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd index ec0c9040..38613082 100644 --- a/vignettes/FOCUS_D.Rmd +++ b/vignettes/FOCUS_D.Rmd @@ -1,13 +1,13 @@ --- -title: "`r (vignette_title <- 'Example evaluation of FOCUS Example Dataset D')`" -author: "Johannes Ranke" +title: Example evaluation of FOCUS Example Dataset D +author: Johannes Ranke date: "`r Sys.Date()`" output: html_document: mathjax: null theme: united vignette: > - %\VignetteIndexEntry{`r vignette_title`} + %\VignetteIndexEntry{Example evaluation of FOCUS Example Dataset D} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} --- diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 58399198..45c5810a 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -137,8 +137,8 @@ print(FOCUS_2006_D) 
summary(fit)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:05 2015 
-## Date of summary: Mon Jun 22 22:17:05 2015 
+## Date of fit:     Mon Jun 22 23:02:24 2015 
+## Date of summary: Mon Jun 22 23:02:25 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)
## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.744 s +## Fitted with method Port using 153 model solutions performed in 0.772 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.Rmd b/vignettes/FOCUS_L.Rmd index 584c43eb..f2981c10 100644 --- a/vignettes/FOCUS_L.Rmd +++ b/vignettes/FOCUS_L.Rmd @@ -1,5 +1,5 @@ --- -title: "`r (vignette_title <- 'Example evaluation of FOCUS Laboratory Data L1 to L3')`" +title: "Example evaluation of FOCUS Laboratory Data L1 to L3" author: "Johannes Ranke" date: "`r Sys.Date()`" output: @@ -9,7 +9,7 @@ output: mathjax: null theme: united vignette: > - %\VignetteIndexEntry{`r vignette_title`} + %\VignetteIndexEntry{Example evaluation of FOCUS Laboratory Data L1 to L3} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} --- diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 276c7c35..7ea5d342 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -93,15 +93,15 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) summary(m.L1.SFO) 
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:06 2015 
-## Date of summary: Mon Jun 22 22:17:06 2015 
+## Date of fit:     Mon Jun 22 23:02:25 2015 
+## Date of summary: Mon Jun 22 23:02:25 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -183,8 +183,8 @@ summary(m.L1.SFO)
summary(m.L1.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:07 2015 
-## Date of summary: Mon Jun 22 22:17:07 2015 
+## Date of fit:     Mon Jun 22 23:02:26 2015 
+## Date of summary: Mon Jun 22 23:02:26 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.476 s +## Fitted with method Port using 188 model solutions performed in 0.492 s ## ## Weighting: none ## @@ -263,15 +263,15 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2) summary(m.L2.SFO) 
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:07 2015 
-## Date of summary: Mon Jun 22 22:17:07 2015 
+## Date of fit:     Mon Jun 22 23:02:26 2015 
+## Date of summary: Mon Jun 22 23:02:26 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.099 s
+## Fitted with method Port using 41 model solutions performed in 0.111 s
 ## 
 ## Weighting: none
 ## 
@@ -351,15 +351,15 @@ mkinresplot(m.L2.FOMC)
summary(m.L2.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:07 2015 
-## Date of summary: Mon Jun 22 22:17:07 2015 
+## Date of fit:     Mon Jun 22 23:02:27 2015 
+## Date of summary: Mon Jun 22 23:02:27 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.237 s
+## Fitted with method Port using 81 model solutions performed in 0.217 s
 ## 
 ## Weighting: none
 ## 
@@ -423,8 +423,8 @@ plot(m.L2.DFOP)
summary(m.L2.DFOP, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:10 2015 
-## Date of summary: Mon Jun 22 22:17:10 2015 
+## Date of fit:     Mon Jun 22 23:02:29 2015 
+## Date of summary: Mon Jun 22 23:02:29 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.841 s +## Fitted with method Port using 336 model solutions performed in 0.967 s ## ## Weighting: none ## @@ -500,15 +500,15 @@ plot(m.L3.SFO) 
summary(m.L3.SFO)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:10 2015 
-## Date of summary: Mon Jun 22 22:17:10 2015 
+## Date of fit:     Mon Jun 22 23:02:29 2015 
+## Date of summary: Mon Jun 22 23:02:29 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.11 s
+## Fitted with method Port using 43 model solutions performed in 0.108 s
 ## 
 ## Weighting: none
 ## 
@@ -576,15 +576,15 @@ plot(m.L3.FOMC)
summary(m.L3.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:10 2015 
-## Date of summary: Mon Jun 22 22:17:10 2015 
+## Date of fit:     Mon Jun 22 23:02:30 2015 
+## Date of summary: Mon Jun 22 23:02:30 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.2 s
+## Fitted with method Port using 83 model solutions performed in 0.243 s
 ## 
 ## Weighting: none
 ## 
@@ -642,8 +642,8 @@ plot(m.L3.DFOP)
summary(m.L3.DFOP, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:11 2015 
-## Date of summary: Mon Jun 22 22:17:11 2015 
+## Date of fit:     Mon Jun 22 23:02:30 2015 
+## Date of summary: Mon Jun 22 23:02:30 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)
## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.423 s +## Fitted with method Port using 137 model solutions performed in 0.349 s ## ## Weighting: none ## @@ -724,15 +724,15 @@ plot(m.L4.SFO) 
summary(m.L4.SFO, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:11 2015 
-## Date of summary: Mon Jun 22 22:17:11 2015 
+## Date of fit:     Mon Jun 22 23:02:31 2015 
+## Date of summary: Mon Jun 22 23:02:31 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.113 s
+## Fitted with method Port using 46 model solutions performed in 0.151 s
 ## 
 ## Weighting: none
 ## 
@@ -789,15 +789,15 @@ plot(m.L4.FOMC)
summary(m.L4.FOMC, data = FALSE)
## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Mon Jun 22 22:17:12 2015 
-## Date of summary: Mon Jun 22 22:17:12 2015 
+## Date of fit:     Mon Jun 22 23:02:31 2015 
+## Date of summary: Mon Jun 22 23:02:31 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.179 s
+## Fitted with method Port using 66 model solutions performed in 0.186 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 94084bca..98cf0c4d 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd
index 9aa8b133..5ee3f7bc 100644
--- a/vignettes/compiled_models.Rmd
+++ b/vignettes/compiled_models.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "`r (vignette_title <- 'Performance benefit by using compiled model definitions in mkin')`"
+title: "Performance benefit by using compiled model definitions in mkin"
 author: "Johannes Ranke"
 date: "`r Sys.Date()`"
 output:
@@ -9,7 +9,7 @@ output:
     mathjax: null
     theme: united
 vignette: >
-  %\VignetteIndexEntry{`r vignette_title`}
+  %\VignetteIndexEntry{Performance benefit by using compiled model definitions in mkin}
   %\VignetteEngine{knitr::rmarkdown}
   \usepackage[utf8]{inputenc}
 ---
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 0b77f1c2..8fb08136 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -98,19 +98,19 @@ mb.1 <- microbenchmark(
 smb.1 <- summary(mb.1)[-1]
 rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
 print(smb.1)
-
##                            min        lq      mean    median        uq
-## deSolve, not compiled 6737.589 6818.2149 6911.3916 6898.8407 6998.2929
-## Eigenvalue based       945.433  968.8592  979.7477  992.2854  996.9051
-## deSolve, compiled      744.785  748.8107  770.7521  752.8364  783.7357
-##                            max neval
-## deSolve, not compiled 7097.745     3
-## Eigenvalue based      1001.525     3
-## deSolve, compiled      814.635     3
-

We see that using the compiled model is by a factor of 9.2 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:

+
##                             min        lq      mean    median        uq
+## deSolve, not compiled 6896.8680 6933.3330 6963.5277 6969.7979 6996.8575
+## Eigenvalue based       933.0581  937.8984  963.5002  942.7388  978.7213
+## deSolve, compiled      784.9729  807.9919  822.4500  831.0110  841.1886
+##                             max neval
+## deSolve, not compiled 7023.9171     3
+## Eigenvalue based      1014.7039     3
+## deSolve, compiled      851.3663     3
+

We see that using the compiled model is by a factor of 8.4 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:

smb.1["median"]/smb.1["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 9.163798
-## Eigenvalue based      1.318062
+## deSolve, not compiled 8.387131
+## Eigenvalue based      1.134448
 ## deSolve, compiled     1.000000
@@ -128,16 +128,16 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2) 
##                             min        lq      mean    median        uq
-## deSolve, not compiled 13.955273 13.961009 14.041563 13.966745 14.084708
-## deSolve, compiled      1.350567  1.371225  1.381397  1.391882  1.396812
+## deSolve, not compiled 14.661881 14.668453 14.701870 14.675025 14.721864
+## deSolve, compiled      1.393051  1.394908  1.415653  1.396764  1.426953
 ##                             max neval
-## deSolve, not compiled 14.202672     3
-## deSolve, compiled      1.401743     3
+## deSolve, not compiled 14.768704 3 +## deSolve, compiled 1.457143 3 
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##                         median
-## deSolve, not compiled 10.03443
+## deSolve, not compiled 10.50644
 ## deSolve, compiled      1.00000
-

Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code using the inline package!

+

Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.37 on

## R version 3.2.1 (2015-06-18)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f2178a99..f7795162 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
-- 
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