## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:48 2016 -## Date of summary: Thu Nov 3 17:47:48 2016 +## Date of fit: Fri Nov 4 15:38:03 2016 +## Date of summary: Fri Nov 4 15:38:03 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.093 s +## Fitted with method Port using 37 model solutions performed in 0.089 s ## ## Weighting: none ## @@ -156,8 +150,8 @@ 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 Nov 3 17:47:49 2016 -## Date of summary: Thu Nov 3 17:47:49 2016 +## Date of fit: Fri Nov 4 15:38:04 2016 +## Date of summary: Fri Nov 4 15:38:04 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -169,7 +163,7 @@ 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 Nov 3 17:47:49 2016 -## Date of summary: Thu Nov 3 17:47:49 2016 +## Date of fit: Fri Nov 4 15:38:05 2016 +## Date of summary: Fri Nov 4 15:38:05 2016 ## ## 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 0.189 s +## Fitted with method Port using 81 model solutions performed in 0.19 s ## ## Weighting: none ## @@ -323,8 +317,8 @@ 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 Nov 3 17:47:50 2016 -## Date of summary: Thu Nov 3 17:47:50 2016 +## Date of fit: Fri Nov 4 15:38:06 2016 +## Date of summary: Fri Nov 4 15:38:06 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -333,7 +327,7 @@ FOCUS_2006_L2_mkin <- summary(mm.L3[["DFOP", 1]]) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:51 2016 -## Date of summary: Thu Nov 3 17:47:52 2016 +## Date of fit: Fri Nov 4 15:38:07 2016 +## Date of summary: Fri Nov 4 15:38:07 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -422,7 +416,7 @@ mm.L3 <- summary(mm.L4[["SFO", 1]], data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:52 2016 -## Date of summary: Thu Nov 3 17:47:52 2016 +## Date of fit: Fri Nov 4 15:38:07 2016 +## Date of summary: Fri Nov 4 15:38:08 2016 ## ## Equations: ## d_parent = - 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 0.112 s ## ## Weighting: none ## @@ -572,8 +566,8 @@ mm.L4 <- summary(mm.L4[["FOMC", 1]], data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Nov 3 17:47:52 2016 -## Date of summary: Thu Nov 3 17:47:52 2016 +## Date of fit: Fri Nov 4 15:38:08 2016 +## Date of summary: Fri Nov 4 15:38:08 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent diff --git a/docs/articles/compiled_models.R b/docs/articles/compiled_models.R index 4f544b0d..5ce343cb 100644 --- a/docs/articles/compiled_models.R +++ b/docs/articles/compiled_models.R @@ -1,3 +1,16 @@ +## ---- include = FALSE---------------------------------------------------- +library(knitr) +opts_chunk$set(tidy = FALSE, cache = FALSE) + +## ----check_gcc----------------------------------------------------------- +Sys.which("gcc") + +## ----create_SFO_SFO------------------------------------------------------ +library("mkin") +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) + ## ----benchmark_SFO_SFO, fig.height = 3----------------------------------- library("microbenchmark") library("ggplot2") diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 5a04168e..09039f62 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -24,13 +24,7 @@ News - - - - - - - + @@ -41,14 +35,14 @@ Performance benefit by using compiled model definitions in mkin Johannes Ranke - 2016-11-03 + 2016-11-04 - - Benchmark for a model that can also be solved with Eigenvalues + + Model that can also be solved with Eigenvalues This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using Sys.which("gcc") ## gcc @@ -78,25 +72,25 @@ mb.1 <- micr print(mb.1) ## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6306.4527 6340.7895 6403.5937 6375.1264 6452.1643 -## Eigenvalue based 918.0808 929.7217 948.9742 941.3626 964.4210 -## deSolve, compiled 736.1337 753.6016 773.5605 771.0696 792.2739 +## deSolve, not compiled 6581.1731 6598.7831 6630.0395 6616.3931 6654.4726 +## Eigenvalue based 880.1617 890.3517 911.2758 900.5416 926.8328 +## deSolve, compiled 739.4343 749.6078 753.6543 759.7813 760.7643 ## max neval cld -## 6529.2022 3 b -## 987.4793 3 a -## 813.4783 3 a +## 6692.5522 3 c +## 953.1240 3 b +## 761.7474 3 a autoplot(mb.1) -We see that using the compiled model is by a factor of 8.3 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 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: rownames(smb.1) <- smb.1$expr smb.1["median"]/smb.1["deSolve, compiled", "median"] ## median -## deSolve, not compiled 8.267900 -## Eigenvalue based 1.220853 +## deSolve, not compiled 8.708286 +## Eigenvalue based 1.185264 ## deSolve, compiled 1.000000 - - Benchmark for a model that can not be solved with Eigenvalues + + Model that can not be solved with Eigenvalues This evaluation is also taken from the example section of mkinfit. FOMC_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), @@ -114,18 +108,18 @@ smb.1["median"]/smbprint(mb.2) ## Unit: seconds ## expr min lq mean median uq -## deSolve, not compiled 13.604720 13.667244 13.689764 13.729768 13.732286 -## deSolve, compiled 1.305077 1.311124 1.328943 1.317172 1.340876 +## deSolve, not compiled 13.756286 13.813205 13.874083 13.870125 13.932982 +## deSolve, compiled 1.323196 1.372916 1.391915 1.422635 1.426274 ## max neval cld -## 13.734804 3 b -## 1.364579 3 a +## 13.995838 3 b +## 1.429913 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 10.4 using the version of the differential equation model compiled from C code! +Here we get a performance benefit of a factor of 9.7 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) @@ -138,8 +132,8 @@ smb.1["median"]/smb Contents - Benchmark for a model that can also be solved with Eigenvalues - Benchmark for a model that can not be solved with Eigenvalues + Model that can also be solved with Eigenvalues + Model that can not be solved with Eigenvalues 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 eec55773..51846e6c 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 b043c13b..f6e4cb08 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 cd6a7bea..9f7cdd74 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,12 +60,7 @@ - - - - - - + diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index dafaa0e4..5f6ae46c 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -24,13 +24,7 @@ News - - - - - - - + @@ -41,7 +35,7 @@ mkin - Kinetic evaluation of chemical degradation data Johannes Ranke - 2016-11-03 + 2016-11-04 @@ -70,7 +64,7 @@ d_SFO_SFO_SFO_err <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE) -plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright")) +plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright")) -- cgit v1.2.1

Model that can not be solved with Eigenvalues

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2016-11-03

2016-11-04

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

2016-11-03

2016-11-04

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

2016-11-03

2016-11-04

Benchmark for a model that can also be solved with Eigenvalues

Model that can also be solved with Eigenvalues

Benchmark for a model that can not be solved with Eigenvalues

Contents

mkin - Kinetic evaluation of chemical degradation data

Johannes Ranke

2016-11-03

2016-11-04