diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-23 11:44:00 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-06-23 11:44:00 +0200 |
| commit | c6759635fbea7f541d421b3de78f0d8868856486 (patch) | |
| tree | 7a6d602aa505aedf6ef35a0afb2541e67b245ee1 | |
| parent | 6c62c42eb57631aa0f4ab7e008621ffb519bd7be (diff) | |
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge
| -rw-r--r-- | Rplots.pdf | bin | 0 -> 4805 bytes | |||
| -rw-r--r-- | vignettes/FOCUS_D.html | 14 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 60 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 224278 -> 225020 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 42 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
6 files changed, 58 insertions, 58 deletions
diff --git a/Rplots.pdf b/Rplots.pdf Binary files differnew file mode 100644 index 00000000..38604cf9 --- /dev/null +++ b/Rplots.pdf diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 45c5810a..099004ad 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-06-22" /> +<meta name="date" content="2015-06-23" /> <title>Example evaluation of FOCUS Example Dataset D</title> @@ -64,7 +64,7 @@ img { <div id="header"> <h1 class="title">Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-06-22</em></h4> +<h4 class="date"><em>2015-06-23</em></h4> </div> @@ -117,9 +117,9 @@ print(FOCUS_2006_D)</code></pre> ## 43 m1 120 25.15 ## 44 m1 120 33.31</code></pre> <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p> -<p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If the gcc compiler is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> +<p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> <pre class="r"><code>SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</code></pre> -<pre><code>## Compiling differential equation model from auto-generated C code...</code></pre> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre class="r"><code>print(SFO_SFO$diffs)</code></pre> <pre><code>## parent ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" @@ -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 23:02:24 2015 -## Date of summary: Mon Jun 22 23:02:25 2015 +## Date of fit: Tue Jun 23 11:42:55 2015 +## Date of summary: Tue Jun 23 11:42:55 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 0.772 s +## Fitted with method Port using 153 model solutions performed in 0.719 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 7ea5d342..ec4203b7 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-06-22" /> +<meta name="date" content="2015-06-23" /> <title>Example evaluation of FOCUS Laboratory Data L1 to L3</title> @@ -65,7 +65,7 @@ img { <div id="header"> <h1 class="title">Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-06-22</em></h4> +<h4 class="date"><em>2015-06-23</em></h4> </div> <div id="TOC"> @@ -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 23:02:25 2015 -## Date of summary: Mon Jun 22 23:02:25 2015 +## Date of fit: Tue Jun 23 11:42:56 2015 +## Date of summary: Tue Jun 23 11:42:56 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.097 s +## Fitted with method Port using 37 model solutions performed in 0.096 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 23:02:26 2015 -## Date of summary: Mon Jun 22 23:02:26 2015 +## Date of fit: Tue Jun 23 11:42:57 2015 +## Date of summary: Tue Jun 23 11:42:57 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 0.492 s +## Fitted with method Port using 188 model solutions performed in 0.466 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 23:02:26 2015 -## Date of summary: Mon Jun 22 23:02:26 2015 +## Date of fit: Tue Jun 23 11:42:57 2015 +## Date of summary: Tue Jun 23 11:42:57 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.111 s +## Fitted with method Port using 41 model solutions performed in 0.108 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 23:02:27 2015 -## Date of summary: Mon Jun 22 23:02:27 2015 +## Date of fit: Tue Jun 23 11:42:57 2015 +## Date of summary: Tue Jun 23 11:42:57 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 0.217 s +## Fitted with method Port using 81 model solutions performed in 0.214 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 23:02:29 2015 -## Date of summary: Mon Jun 22 23:02:29 2015 +## Date of fit: Tue Jun 23 11:43:00 2015 +## Date of summary: Tue Jun 23 11:43:00 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 0.967 s +## Fitted with method Port using 336 model solutions performed in 0.917 s ## ## Weighting: none ## @@ -500,8 +500,8 @@ 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 23:02:29 2015 -## Date of summary: Mon Jun 22 23:02:29 2015 +## Date of fit: Tue Jun 23 11:43:00 2015 +## Date of summary: Tue Jun 23 11:43:00 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent @@ -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 23:02:30 2015 -## Date of summary: Mon Jun 22 23:02:30 2015 +## Date of fit: Tue Jun 23 11:43:00 2015 +## Date of summary: Tue Jun 23 11:43:00 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 0.243 s +## Fitted with method Port using 83 model solutions performed in 0.207 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 23:02:30 2015 -## Date of summary: Mon Jun 22 23:02:30 2015 +## Date of fit: Tue Jun 23 11:43:01 2015 +## Date of summary: Tue Jun 23 11:43:01 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -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 23:02:31 2015 -## Date of summary: Mon Jun 22 23:02:31 2015 +## Date of fit: Tue Jun 23 11:43:01 2015 +## Date of summary: Tue Jun 23 11:43:01 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.151 s +## Fitted with method Port using 46 model solutions performed in 0.114 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 23:02:31 2015 -## Date of summary: Mon Jun 22 23:02:31 2015 +## Date of fit: Tue Jun 23 11:43:02 2015 +## Date of summary: Tue Jun 23 11:43:02 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 0.186 s +## Fitted with method Port using 66 model solutions performed in 0.166 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 98cf0c4d..1ac6002b 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 8fb08136..814f3a52 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -10,7 +10,7 @@ <meta name="author" content="Johannes Ranke" /> -<meta name="date" content="2015-06-22" /> +<meta name="date" content="2015-06-23" /> <title>Performance benefit by using compiled model definitions in mkin</title> @@ -65,7 +65,7 @@ img { <div id="header"> <h1 class="title">Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author"><em>Johannes Ranke</em></h4> -<h4 class="date"><em>2015-06-22</em></h4> +<h4 class="date"><em>2015-06-23</em></h4> </div> <div id="TOC"> @@ -77,7 +77,7 @@ img { <div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level2"> <h2>Benchmark for a model that can also be solved with Eigenvalues</h2> -<p>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 compiler (gcc) is installed, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The package tests for presence of the gcc compiler using</p> +<p>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 <code>mkinmod()</code> function checks for presence of the gcc compiler using</p> <pre class="r"><code>Sys.which("gcc")</code></pre> <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> @@ -86,7 +86,7 @@ img { SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</code></pre> -<pre><code>## Compiling differential equation model from auto-generated C code...</code></pre> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the microbenchmark package.</p> <pre class="r"><code>library("microbenchmark") mb.1 <- microbenchmark( @@ -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 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 +## deSolve, not compiled 6650.2684 6684.4530 6774.1607 6718.6377 6836.1068 +## Eigenvalue based 903.5520 916.8598 927.3873 930.1676 939.3049 +## deSolve, compiled 751.1205 752.5239 756.1227 753.9273 758.6238 ## 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> +## deSolve, not compiled 6953.5760 3 +## Eigenvalue based 948.4423 3 +## deSolve, compiled 763.3202 3</code></pre> +<p>We see that using the compiled model is by a factor of 8.9 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 8.387131 -## Eigenvalue based 1.134448 +## deSolve, not compiled 8.911519 +## Eigenvalue based 1.233763 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -119,7 +119,7 @@ print(smb.1)</code></pre> <pre class="r"><code>FOMC_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), m1 = mkinsub( "SFO"))</code></pre> -<pre><code>## Compiling differential equation model from auto-generated C code...</code></pre> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre class="r"><code>mb.2 <- microbenchmark( mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE), mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE), @@ -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 14.661881 14.668453 14.701870 14.675025 14.721864 -## deSolve, compiled 1.393051 1.394908 1.415653 1.396764 1.426953 +<pre><code>## min lq mean median uq +## deSolve, not compiled 14.32061 14.336413 14.380847 14.352216 14.410966 +## deSolve, compiled 1.34366 1.344778 1.371116 1.345897 1.384844 ## max neval -## deSolve, not compiled 14.768704 3 -## deSolve, compiled 1.457143 3</code></pre> +## deSolve, not compiled 14.469716 3 +## deSolve, compiled 1.423791 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 10.50644 +## deSolve, not compiled 10.66368 ## deSolve, compiled 1.00000</code></pre> -<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>Here we get a performance benefit of a factor of 10.7 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 f7795162..7534bc6d 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |