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| -rw-r--r-- | vignettes/FOCUS_D.html | 13 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 60 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 224268 -> 224263 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 34 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
5 files changed, 52 insertions, 55 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 53711e88..58399198 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -69,11 +69,8 @@ img { <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look a the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p> -<pre class="r"><code>library("mkin")</code></pre> -<pre><code>## Loading required package: minpack.lm -## Loading required package: rootSolve -## Loading required package: inline</code></pre> -<pre class="r"><code>print(FOCUS_2006_D)</code></pre> +<pre class="r"><code>library("mkin") +print(FOCUS_2006_D)</code></pre> <pre><code>## name time value ## 1 parent 0 99.46 ## 2 parent 0 102.04 @@ -140,8 +137,8 @@ img { <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 18:45:34 2015 -## Date of summary: Mon Jun 22 18:45:34 2015 +## Date of fit: Mon Jun 22 22:17:05 2015 +## Date of summary: Mon Jun 22 22:17:05 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -149,7 +146,7 @@ img { ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.609 s +## Fitted with method Port using 153 model solutions performed in 0.744 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 488d5dc8..276c7c35 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 20:44:34 2015 -## Date of summary: Mon Jun 22 20:44:34 2015 +## Date of fit: Mon Jun 22 22:17:06 2015 +## Date of summary: Mon Jun 22 22:17:06 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.093 s +## Fitted with method Port using 37 model solutions performed in 0.09 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 20:44:35 2015 -## Date of summary: Mon Jun 22 20:44:35 2015 +## Date of fit: Mon Jun 22 22:17:07 2015 +## Date of summary: Mon Jun 22 22:17:07 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 0.48 s +## Fitted with method Port using 188 model solutions performed in 0.476 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 20:44:35 2015 -## Date of summary: Mon Jun 22 20:44:35 2015 +## Date of fit: Mon Jun 22 22:17:07 2015 +## Date of summary: Mon Jun 22 22:17:07 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.104 s +## Fitted with method Port using 41 model solutions performed in 0.099 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 20:44:36 2015 -## Date of summary: Mon Jun 22 20:44:36 2015 +## Date of fit: Mon Jun 22 22:17:07 2015 +## Date of summary: Mon Jun 22 22:17:07 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 0.203 s +## Fitted with method Port using 81 model solutions performed in 0.237 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 20:44:38 2015 -## Date of summary: Mon Jun 22 20:44:38 2015 +## Date of fit: Mon Jun 22 22:17:10 2015 +## Date of summary: Mon Jun 22 22:17:10 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 0.926 s +## Fitted with method Port using 336 model solutions performed in 0.841 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 20:44:38 2015 -## Date of summary: Mon Jun 22 20:44:38 2015 +## Date of fit: Mon Jun 22 22:17:10 2015 +## Date of summary: Mon Jun 22 22:17:10 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.132 s +## Fitted with method Port using 43 model solutions performed in 0.11 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 20:44:39 2015 -## Date of summary: Mon Jun 22 20:44:39 2015 +## Date of fit: Mon Jun 22 22:17:10 2015 +## Date of summary: Mon Jun 22 22:17:10 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 0.221 s +## Fitted with method Port using 83 model solutions performed in 0.2 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 20:44:39 2015 -## Date of summary: Mon Jun 22 20:44:39 2015 +## Date of fit: Mon Jun 22 22:17:11 2015 +## Date of summary: Mon Jun 22 22:17:11 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 0.372 s +## Fitted with method Port using 137 model solutions performed in 0.423 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 20:44:40 2015 -## Date of summary: Mon Jun 22 20:44:40 2015 +## Date of fit: Mon Jun 22 22:17:11 2015 +## Date of summary: Mon Jun 22 22:17:11 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.115 s +## Fitted with method Port using 46 model solutions performed in 0.113 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 20:44:40 2015 -## Date of summary: Mon Jun 22 20:44:40 2015 +## Date of fit: Mon Jun 22 22:17:12 2015 +## Date of summary: Mon Jun 22 22:17:12 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 0.169 s +## Fitted with method Port using 66 model solutions performed in 0.179 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex d75b1288..94084bca 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index ed61b47a..0b77f1c2 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 6585.7039 6651.4937 6685.6248 6717.2836 6735.5853 -## Eigenvalue based 971.2893 981.5618 998.2746 991.8344 1011.7673 -## deSolve, compiled 760.5522 765.4274 780.3243 770.3026 790.2103 -## max neval -## deSolve, not compiled 6753.8871 3 -## Eigenvalue based 1031.7003 3 -## deSolve, compiled 810.1179 3</code></pre> -<p>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:</p> +<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 class="r"><code>smb.1["median"]/smb.1["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 8.720318 -## Eigenvalue based 1.287591 +## deSolve, not compiled 9.163798 +## Eigenvalue based 1.318062 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -128,15 +128,15 @@ 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 14.271472 14.285039 14.303450 14.298607 14.319440 -## deSolve, compiled 1.350642 1.390549 1.412823 1.430456 1.443914 +## 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 ## max neval -## deSolve, not compiled 14.340272 3 -## deSolve, compiled 1.457372 3</code></pre> +## deSolve, not compiled 14.202672 3 +## deSolve, compiled 1.401743 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 9.995841 -## deSolve, compiled 1.000000</code></pre> +## deSolve, not compiled 10.03443 +## 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>This vignette was built with mkin 0.9.37 on</p> <pre><code>## R version 3.2.1 (2015-06-18) diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex d7381e6f..f2178a99 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |