diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_L.html | 68 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 225699 -> 224268 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 32 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
4 files changed, 48 insertions, 52 deletions
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 153be558..488d5dc8 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -80,12 +80,8 @@ img { <div id="laboratory-data-l1" class="section level2"> <h2>Laboratory Data L1</h2> <p>The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:</p> -<pre class="r"><code>library("mkin")</code></pre> -<pre><code>## Loading required package: minpack.lm -## Loading required package: rootSolve -## Loading required package: inline -## Loading required package: methods</code></pre> -<pre class="r"><code>FOCUS_2006_L1 = data.frame( +<pre class="r"><code>library("mkin") +FOCUS_2006_L1 = data.frame( t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2), parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 72.0, 71.9, 50.3, 59.4, 47.0, 45.1, @@ -97,15 +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 18:38:53 2015 -## Date of summary: Mon Jun 22 18:38:53 2015 +## Date of fit: Mon Jun 22 20:44:34 2015 +## Date of summary: Mon Jun 22 20:44:34 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.089 s +## Fitted with method Port using 37 model solutions performed in 0.093 s ## ## Weighting: none ## @@ -187,8 +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 18:38:54 2015 -## Date of summary: Mon Jun 22 18:38:54 2015 +## Date of fit: Mon Jun 22 20:44:35 2015 +## Date of summary: Mon Jun 22 20:44:35 2015 ## ## ## Warning: Optimisation by method Port did not converge. @@ -200,7 +196,7 @@ summary(m.L1.SFO)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.397 s +## Fitted with method Port using 188 model solutions performed in 0.48 s ## ## Weighting: none ## @@ -267,15 +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 18:38:54 2015 -## Date of summary: Mon Jun 22 18:38:54 2015 +## Date of fit: Mon Jun 22 20:44:35 2015 +## Date of summary: Mon Jun 22 20:44:35 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.086 s +## Fitted with method Port using 41 model solutions performed in 0.104 s ## ## Weighting: none ## @@ -355,15 +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 18:38:54 2015 -## Date of summary: Mon Jun 22 18:38:54 2015 +## Date of fit: Mon Jun 22 20:44:36 2015 +## Date of summary: Mon Jun 22 20:44:36 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 0.175 s +## Fitted with method Port using 81 model solutions performed in 0.203 s ## ## Weighting: none ## @@ -427,8 +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 18:38:56 2015 -## Date of summary: Mon Jun 22 18:38:56 2015 +## Date of fit: Mon Jun 22 20:44:38 2015 +## Date of summary: Mon Jun 22 20:44:38 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -437,7 +433,7 @@ plot(m.L2.DFOP)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.751 s +## Fitted with method Port using 336 model solutions performed in 0.926 s ## ## Weighting: none ## @@ -504,15 +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 18:38:56 2015 -## Date of summary: Mon Jun 22 18:38:56 2015 +## Date of fit: Mon Jun 22 20:44:38 2015 +## Date of summary: Mon Jun 22 20:44:38 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.088 s +## Fitted with method Port using 43 model solutions performed in 0.132 s ## ## Weighting: none ## @@ -580,15 +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 18:38:57 2015 -## Date of summary: Mon Jun 22 18:38:57 2015 +## Date of fit: Mon Jun 22 20:44:39 2015 +## Date of summary: Mon Jun 22 20:44:39 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 0.178 s +## Fitted with method Port using 83 model solutions performed in 0.221 s ## ## Weighting: none ## @@ -646,8 +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 18:38:57 2015 -## Date of summary: Mon Jun 22 18:38:57 2015 +## Date of fit: Mon Jun 22 20:44:39 2015 +## Date of summary: Mon Jun 22 20:44:39 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -656,7 +652,7 @@ plot(m.L3.DFOP)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.292 s +## Fitted with method Port using 137 model solutions performed in 0.372 s ## ## Weighting: none ## @@ -728,15 +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 18:38:57 2015 -## Date of summary: Mon Jun 22 18:38:57 2015 +## Date of fit: Mon Jun 22 20:44:40 2015 +## Date of summary: Mon Jun 22 20:44:40 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.102 s +## Fitted with method Port using 46 model solutions performed in 0.115 s ## ## Weighting: none ## @@ -793,15 +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 18:38:58 2015 -## Date of summary: Mon Jun 22 18:38:58 2015 +## Date of fit: Mon Jun 22 20:44:40 2015 +## Date of summary: Mon Jun 22 20:44:40 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 0.137 s +## Fitted with method Port using 66 model solutions performed in 0.169 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 95d5f949..d75b1288 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index fc71debe..ed61b47a 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -99,18 +99,18 @@ 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 5379.4269 5431.6605 5455.0396 5483.8940 5492.8460 -## Eigenvalue based 930.6245 951.6701 959.4653 972.7157 973.8857 -## deSolve, compiled 755.9828 771.1000 794.1810 786.2172 813.2800 +## 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 5501.7979 3 -## Eigenvalue based 975.0556 3 -## deSolve, compiled 840.3428 3</code></pre> -<p>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:</p> +## 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 class="r"><code>smb.1["median"]/smb.1["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 6.975037 -## Eigenvalue based 1.237210 +## deSolve, not compiled 8.720318 +## Eigenvalue based 1.287591 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -127,17 +127,17 @@ print(smb.1)</code></pre> 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 11.815894 11.84960 12.03290 11.883305 12.141404 -## deSolve, compiled 1.387086 1.43514 1.45956 1.483194 1.495796 +<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 ## max neval -## deSolve, not compiled 12.399502 3 -## deSolve, compiled 1.508399 3</code></pre> +## deSolve, not compiled 14.340272 3 +## deSolve, compiled 1.457372 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 8.011968 +## deSolve, not compiled 9.995841 ## deSolve, compiled 1.000000</code></pre> -<p>Here we get a performance benefit of a factor of 8 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 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 11da2863..d7381e6f 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |