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| -rw-r--r-- | Rplots.pdf | bin | 0 -> 4805 bytes | |||
| -rw-r--r-- | vignettes/FOCUS_D.html | 6 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 58 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 225020 -> 224997 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 30 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
6 files changed, 47 insertions, 47 deletions
diff --git a/Rplots.pdf b/Rplots.pdf Binary files differnew file mode 100644 index 00000000..9af1946c --- /dev/null +++ b/Rplots.pdf diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 099004ad..45104f6a 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: Tue Jun 23 11:42:55 2015 -## Date of summary: Tue Jun 23 11:42:55 2015 +## Date of fit: Tue Jun 23 12:22:01 2015 +## Date of summary: Tue Jun 23 12:22:01 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 0.719 s +## Fitted with method Port using 153 model solutions performed in 0.689 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index ec4203b7..715b6a20 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: Tue Jun 23 11:42:56 2015 -## Date of summary: Tue Jun 23 11:42:56 2015 +## Date of fit: Tue Jun 23 12:22:02 2015 +## Date of summary: Tue Jun 23 12:22:02 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.096 s +## Fitted with method Port using 37 model solutions performed in 0.098 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: Tue Jun 23 11:42:57 2015 -## Date of summary: Tue Jun 23 11:42:57 2015 +## Date of fit: Tue Jun 23 12:22:03 2015 +## Date of summary: Tue Jun 23 12:22:03 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 0.466 s +## Fitted with method Port using 188 model solutions performed in 0.53 s ## ## Weighting: none ## @@ -263,8 +263,8 @@ 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: Tue Jun 23 11:42:57 2015 -## Date of summary: Tue Jun 23 11:42:57 2015 +## Date of fit: Tue Jun 23 12:22:03 2015 +## Date of summary: Tue Jun 23 12:22:03 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent @@ -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: Tue Jun 23 11:42:57 2015 -## Date of summary: Tue Jun 23 11:42:57 2015 +## Date of fit: Tue Jun 23 12:22:04 2015 +## Date of summary: Tue Jun 23 12:22:04 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 0.214 s +## Fitted with method Port using 81 model solutions performed in 0.205 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: Tue Jun 23 11:43:00 2015 -## Date of summary: Tue Jun 23 11:43:00 2015 +## Date of fit: Tue Jun 23 12:22:06 2015 +## Date of summary: Tue Jun 23 12:22:06 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 0.917 s +## Fitted with method Port using 336 model solutions performed in 0.913 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: Tue Jun 23 11:43:00 2015 -## Date of summary: Tue Jun 23 11:43:00 2015 +## Date of fit: Tue Jun 23 12:22:06 2015 +## Date of summary: Tue Jun 23 12:22:06 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.108 s +## Fitted with method Port using 43 model solutions performed in 0.107 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: Tue Jun 23 11:43:00 2015 -## Date of summary: Tue Jun 23 11:43:00 2015 +## Date of fit: Tue Jun 23 12:22:07 2015 +## Date of summary: Tue Jun 23 12:22:07 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 0.207 s +## Fitted with method Port using 83 model solutions performed in 0.214 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: Tue Jun 23 11:43:01 2015 -## Date of summary: Tue Jun 23 11:43:01 2015 +## Date of fit: Tue Jun 23 12:22:07 2015 +## Date of summary: Tue Jun 23 12:22:07 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 0.349 s +## Fitted with method Port using 137 model solutions performed in 0.356 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: Tue Jun 23 11:43:01 2015 -## Date of summary: Tue Jun 23 11:43:01 2015 +## Date of fit: Tue Jun 23 12:22:08 2015 +## Date of summary: Tue Jun 23 12:22:08 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.114 s +## Fitted with method Port using 46 model solutions performed in 0.117 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: Tue Jun 23 11:43:02 2015 -## Date of summary: Tue Jun 23 11:43:02 2015 +## Date of fit: Tue Jun 23 12:22:08 2015 +## Date of summary: Tue Jun 23 12:22:08 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 0.166 s +## Fitted with method Port using 66 model solutions performed in 0.177 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 1ac6002b..5ed80680 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 814f3a52..2fbef8ae 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 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 +## deSolve, not compiled 6760.8015 6766.0464 6785.8509 6771.2913 6798.3756 +## Eigenvalue based 930.9980 944.5895 973.5743 958.1810 994.8625 +## deSolve, compiled 758.2721 811.0584 836.3348 863.8448 875.3661 ## max neval -## 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> +## deSolve, not compiled 6825.4600 3 +## Eigenvalue based 1031.5439 3 +## deSolve, compiled 886.8875 3</code></pre> +<p>We see that using the compiled model is by a factor of 7.8 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 8.911519 -## Eigenvalue based 1.233763 +## deSolve, not compiled 7.838551 +## Eigenvalue based 1.109205 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -127,15 +127,15 @@ 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 14.32061 14.336413 14.380847 14.352216 14.410966 -## deSolve, compiled 1.34366 1.344778 1.371116 1.345897 1.384844 +<pre><code>## min lq mean median uq +## deSolve, not compiled 14.231863 14.287058 14.336780 14.342252 14.389238 +## deSolve, compiled 1.344761 1.345452 1.361713 1.346142 1.370189 ## max neval -## deSolve, not compiled 14.469716 3 -## deSolve, compiled 1.423791 3</code></pre> +## deSolve, not compiled 14.436224 3 +## deSolve, compiled 1.394235 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 10.66368 +## deSolve, not compiled 10.65434 ## deSolve, compiled 1.00000</code></pre> <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> diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex 7534bc6d..79b6a5ab 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |