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| -rw-r--r-- | README.Rmd | 3 | ||||
| -rw-r--r-- | README.md | 3 | ||||
| -rw-r--r-- | vignettes/FOCUS_D.html | 6 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 60 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 225094 -> 225060 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 32 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
7 files changed, 53 insertions, 51 deletions
@@ -154,7 +154,8 @@ for installation instructions and a manual. ## News -Yes, there is a . +Yes, there is a ChangeLog, for the latest [CRAN release](http://cran.r-project.org/web/packages/mkin/NEWS.html) +and one for the [github master branch](https://github.com/jranke/mkin/blob/master/NEWS.md). ## Credits and historical remarks @@ -168,7 +168,8 @@ for installation instructions and a manual. ## News -Yes, there is a . +Yes, there is a ChangeLog, for the latest [CRAN release](http://cran.r-project.org/web/packages/mkin/NEWS.html) +and one for the [github master branch](https://github.com/jranke/mkin/blob/master/NEWS.md). ## Credits and historical remarks diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 6b4d8b95..b8264c22 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:46 2015 -## Date of summary: Fri Jun 26 16:06:47 2015 +## Date of fit: Fri Jun 26 16:35:59 2015 +## Date of summary: Fri Jun 26 16:35:59 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 0.741 s +## Fitted with method Port using 153 model solutions performed in 0.71 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 7fb65960..d1a10e6a 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:47 2015 -## Date of summary: Fri Jun 26 16:06:47 2015 +## Date of fit: Fri Jun 26 16:36:00 2015 +## Date of summary: Fri Jun 26 16:36:00 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 0.095 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:48 2015 -## Date of summary: Fri Jun 26 16:06:48 2015 +## Date of fit: Fri Jun 26 16:36:00 2015 +## Date of summary: Fri Jun 26 16:36:00 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 0.555 s +## Fitted with method Port using 188 model solutions performed in 0.48 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:48 2015 -## Date of summary: Fri Jun 26 16:06:48 2015 +## Date of fit: Fri Jun 26 16:36:01 2015 +## Date of summary: Fri Jun 26 16:36:01 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.112 s +## Fitted with method Port using 41 model solutions performed in 0.103 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:49 2015 -## Date of summary: Fri Jun 26 16:06:49 2015 +## Date of fit: Fri Jun 26 16:36:01 2015 +## Date of summary: Fri Jun 26 16:36:01 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 0.21 s +## Fitted with method Port using 81 model solutions performed in 0.212 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:52 2015 -## Date of summary: Fri Jun 26 16:06:52 2015 +## Date of fit: Fri Jun 26 16:36:03 2015 +## Date of summary: Fri Jun 26 16:36:03 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 0.945 s +## Fitted with method Port using 336 model solutions performed in 0.862 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:52 2015 -## Date of summary: Fri Jun 26 16:06:52 2015 +## Date of fit: Fri Jun 26 16:36:04 2015 +## Date of summary: Fri Jun 26 16:36:04 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.122 s +## Fitted with method Port using 43 model solutions performed in 0.103 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:52 2015 -## Date of summary: Fri Jun 26 16:06:52 2015 +## Date of fit: Fri Jun 26 16:36:04 2015 +## Date of summary: Fri Jun 26 16:36:04 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 0.235 s +## Fitted with method Port using 83 model solutions performed in 0.205 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:53 2015 -## Date of summary: Fri Jun 26 16:06:53 2015 +## Date of fit: Fri Jun 26 16:36:05 2015 +## Date of summary: Fri Jun 26 16:36:05 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 0.385 s +## Fitted with method Port using 137 model solutions performed in 0.361 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:53 2015 -## Date of summary: Fri Jun 26 16:06:53 2015 +## Date of fit: Fri Jun 26 16:36:05 2015 +## Date of summary: Fri Jun 26 16:36:05 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.116 s +## Fitted with method Port using 46 model solutions performed in 0.11 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: 0.9.39 ## R version: 3.2.1 -## Date of fit: Fri Jun 26 16:06:54 2015 -## Date of summary: Fri Jun 26 16:06:54 2015 +## Date of fit: Fri Jun 26 16:36:05 2015 +## Date of summary: Fri Jun 26 16:36:05 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 0.175 s +## Fitted with method Port using 66 model solutions performed in 0.174 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 3245544c..8b8f7416 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index a62f3826..a8f6e3ef 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 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 +## deSolve, not compiled 6767.3728 6834.5128 6879.5969 6901.6528 6935.7090 +## Eigenvalue based 977.5545 1161.8591 1225.1262 1346.1637 1348.9120 +## deSolve, compiled 761.0689 761.8958 772.3379 762.7228 777.9724 ## max neval -## 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> +## deSolve, not compiled 6969.7653 3 +## Eigenvalue based 1351.6603 3 +## deSolve, compiled 793.2221 3</code></pre> +<p>We see that using the compiled model is by a factor of 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 9.176725 -## Eigenvalue based 1.220866 +## deSolve, not compiled 9.048704 +## Eigenvalue based 1.764945 ## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -128,16 +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 14.080456 14.209689 14.287313 14.338922 14.390742 -## deSolve, compiled 1.467266 1.521451 1.555168 1.575636 1.599119 +## deSolve, not compiled 14.161917 14.189080 14.201763 14.216243 14.221687 +## deSolve, compiled 1.358691 1.366613 1.393306 1.374535 1.410614 ## max neval -## deSolve, not compiled 14.442561 3 -## deSolve, compiled 1.622601 3</code></pre> +## deSolve, not compiled 14.227131 3 +## deSolve, compiled 1.446693 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> <pre><code>## median -## deSolve, not compiled 9.100402 -## deSolve, compiled 1.000000</code></pre> -<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> +## deSolve, not compiled 10.34258 +## deSolve, compiled 1.00000</code></pre> +<p>Here we get a performance benefit of a factor of 10.3 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 76426c30..4eb5dada 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |