diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_D.html | 15 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 69 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 226105 -> 225094 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 39 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
5 files changed, 54 insertions, 69 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index e8ab70de..6b4d8b95 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -69,13 +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 -## Loading required package: methods -## Loading required package: parallel</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 @@ -142,8 +137,8 @@ img { <pre class="r"><code>summary(fit)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:39 2015 -## Date of summary: Fri Jun 26 14:41:40 2015 +## Date of fit: Fri Jun 26 16:06:46 2015 +## Date of summary: Fri Jun 26 16:06:47 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -151,7 +146,7 @@ img { ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.629 s +## Fitted with method Port using 153 model solutions performed in 0.741 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 7e0ef4dd..7fb65960 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -80,13 +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 -## Loading required package: parallel</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, @@ -98,15 +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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:41 2015 -## Date of summary: Fri Jun 26 14:41:41 2015 +## Date of fit: Fri Jun 26 16:06:47 2015 +## Date of summary: Fri Jun 26 16:06:47 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.08 s +## Fitted with method Port using 37 model solutions performed in 0.096 s ## ## Weighting: none ## @@ -188,8 +183,8 @@ summary(m.L1.SFO)</code></pre> <pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:41 2015 -## Date of summary: Fri Jun 26 14:41:41 2015 +## Date of fit: Fri Jun 26 16:06:48 2015 +## Date of summary: Fri Jun 26 16:06:48 2015 ## ## ## Warning: Optimisation by method Port did not converge. @@ -201,7 +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 0.555 s ## ## Weighting: none ## @@ -268,15 +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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:42 2015 -## Date of summary: Fri Jun 26 14:41:42 2015 +## Date of fit: Fri Jun 26 16:06:48 2015 +## Date of summary: Fri Jun 26 16:06:48 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.087 s +## Fitted with method Port using 41 model solutions performed in 0.112 s ## ## Weighting: none ## @@ -356,15 +351,15 @@ mkinresplot(m.L2.FOMC)</code></pre> <pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:42 2015 -## Date of summary: Fri Jun 26 14:41:42 2015 +## Date of fit: Fri Jun 26 16:06:49 2015 +## Date of summary: Fri Jun 26 16:06:49 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 0.21 s ## ## Weighting: none ## @@ -428,8 +423,8 @@ plot(m.L2.DFOP)</code></pre> <pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:44 2015 -## Date of summary: Fri Jun 26 14:41:44 2015 +## Date of fit: Fri Jun 26 16:06:52 2015 +## Date of summary: Fri Jun 26 16:06:52 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -438,7 +433,7 @@ plot(m.L2.DFOP)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.744 s +## Fitted with method Port using 336 model solutions performed in 0.945 s ## ## Weighting: none ## @@ -505,15 +500,15 @@ plot(m.L3.SFO)</code></pre> <pre class="r"><code>summary(m.L3.SFO)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:44 2015 -## Date of summary: Fri Jun 26 14:41:44 2015 +## Date of fit: Fri Jun 26 16:06:52 2015 +## Date of summary: Fri Jun 26 16:06:52 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.087 s +## Fitted with method Port using 43 model solutions performed in 0.122 s ## ## Weighting: none ## @@ -581,15 +576,15 @@ plot(m.L3.FOMC)</code></pre> <pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:44 2015 -## Date of summary: Fri Jun 26 14:41:44 2015 +## Date of fit: Fri Jun 26 16:06:52 2015 +## Date of summary: Fri Jun 26 16:06:52 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 0.235 s ## ## Weighting: none ## @@ -647,8 +642,8 @@ plot(m.L3.DFOP)</code></pre> <pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:45 2015 -## Date of summary: Fri Jun 26 14:41:45 2015 +## Date of fit: Fri Jun 26 16:06:53 2015 +## Date of summary: Fri Jun 26 16:06:53 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -657,7 +652,7 @@ plot(m.L3.DFOP)</code></pre> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.287 s +## Fitted with method Port using 137 model solutions performed in 0.385 s ## ## Weighting: none ## @@ -729,15 +724,15 @@ plot(m.L4.SFO)</code></pre> <pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:45 2015 -## Date of summary: Fri Jun 26 14:41:45 2015 +## Date of fit: Fri Jun 26 16:06:53 2015 +## Date of summary: Fri Jun 26 16:06:53 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.097 s +## Fitted with method Port using 46 model solutions performed in 0.116 s ## ## Weighting: none ## @@ -794,15 +789,15 @@ plot(m.L4.FOMC)</code></pre> <pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre> <pre><code>## mkin version: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 14:41:45 2015 -## Date of summary: Fri Jun 26 14:41:45 2015 +## Date of fit: Fri Jun 26 16:06:54 2015 +## Date of summary: Fri Jun 26 16:06:54 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 0.143 s +## Fitted with method Port using 66 model solutions performed in 0.175 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex d03b7e01..3245544c 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 12454559..a62f3826 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -82,13 +82,8 @@ img { <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</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 -## Loading required package: parallel</code></pre> -<pre class="r"><code>SFO_SFO <- mkinmod( +<pre class="r"><code>library("mkin") +SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</code></pre> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> @@ -104,18 +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 5292.0165 5313.7620 5364.5733 5335.5075 5400.8517 -## Eigenvalue based 893.9459 921.1984 936.1750 948.4509 957.2895 -## deSolve, compiled 742.7723 745.4243 750.1963 748.0763 753.9083 +## deSolve, not compiled 7047.6039 7083.3201 7123.5962 7119.0364 7161.5924 +## Eigenvalue based 901.5593 924.3357 968.8689 947.1121 1002.5238 +## deSolve, compiled 765.7604 770.7657 786.8638 775.7709 797.4156 ## max neval -## deSolve, not compiled 5466.1959 3 -## Eigenvalue based 966.1282 3 -## deSolve, compiled 759.7404 3</code></pre> -<p>We see that using the compiled model is by a factor of 7.1 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 7204.1483 3 +## Eigenvalue based 1057.9355 3 +## deSolve, compiled 819.0602 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 7.132304 -## Eigenvalue based 1.267853 +## deSolve, not compiled 9.176725 +## Eigenvalue based 1.220866 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -133,16 +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 11.277340 11.336373 11.392883 11.395407 11.450654 -## deSolve, compiled 1.339204 1.342662 1.350783 1.346121 1.356573 +## deSolve, not compiled 14.080456 14.209689 14.287313 14.338922 14.390742 +## deSolve, compiled 1.467266 1.521451 1.555168 1.575636 1.599119 ## max neval -## deSolve, not compiled 11.505901 3 -## deSolve, compiled 1.367025 3</code></pre> +## deSolve, not compiled 14.442561 3 +## deSolve, compiled 1.622601 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 8.465368 +## deSolve, not compiled 9.100402 ## deSolve, compiled 1.000000</code></pre> -<p>Here we get a performance benefit of a factor of 8.5 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 9.1 using the version of the differential equation model compiled from C code using the inline package!</p> <p>This vignette was built with mkin 0.9.39 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 be82f41f..76426c30 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |