diff options
| -rw-r--r-- | vignettes/FOCUS_D.Rmd | 6 | ||||
| -rw-r--r-- | vignettes/FOCUS_D.html | 6 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.Rmd | 4 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 60 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 224263 -> 224278 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.Rmd | 4 | ||||
| -rw-r--r-- | vignettes/compiled_models.html | 34 | ||||
| -rw-r--r-- | 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)</code></pre> <pre class="r"><code>summary(fit)</code></pre> <pre><code>## 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)</code></pre> ## ## 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)</code></pre> summary(m.L1.SFO)</code></pre> <pre><code>## 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)</code></pre> <pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre> <pre><code>## 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)</code></pre> ## ## 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)</code></pre> summary(m.L2.SFO)</code></pre> <pre><code>## 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)</code></pre> <pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre> <pre><code>## 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)</code></pre> <pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre> <pre><code>## 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)</code></pre> ## ## 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)</code></pre> <pre class="r"><code>summary(m.L3.SFO)</code></pre> <pre><code>## 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)</code></pre> <pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre> <pre><code>## 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)</code></pre> <pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre> <pre><code>## 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)</code></pre> ## ## 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)</code></pre> <pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre> <pre><code>## 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)</code></pre> <pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre> <pre><code>## 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 Binary files differindex 94084bca..98cf0c4d 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf 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)</code></pre> -<pre><code>## 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</code></pre> -<p>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:</p> +<pre><code>## 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</code></pre> +<p>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:</p> <pre class="r"><code>smb.1["median"]/smb.1["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 9.163798 -## Eigenvalue based 1.318062 +## deSolve, not compiled 8.387131 +## Eigenvalue based 1.134448 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -128,16 +128,16 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2)</code></pre> <pre><code>## 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</code></pre> +## deSolve, not compiled 14.768704 3 +## deSolve, compiled 1.457143 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 10.03443 +## deSolve, not compiled 10.50644 ## deSolve, compiled 1.00000</code></pre> -<p>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!</p> +<p>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!</p> <p>This vignette was built with mkin 0.9.37 on</p> <pre><code>## 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 Binary files differindex f2178a99..f7795162 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |