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| -rw-r--r-- | vignettes/FOCUS_D.html | 6 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 60 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 224249 -> 224241 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.Rmd | 14 | ||||
| -rw-r--r-- | vignettes/compiled_models.html | 42 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
6 files changed, 63 insertions, 59 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index edcfc53d..074847f0 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -316,8 +316,8 @@ objects.</p> <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:54 2015 -## Date of summary: Sun Jun 21 15:31:54 2015 +## Date of fit: Sun Jun 21 18:14:52 2015 +## Date of summary: Sun Jun 21 18:14:52 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -325,7 +325,7 @@ objects.</p> ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.611 s +## Fitted with method Port using 153 model solutions performed in 0.733 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 84a91652..3782847e 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -238,15 +238,15 @@ summary(m.L1.SFO) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:55 2015 -## Date of summary: Sun Jun 21 15:31:55 2015 +## Date of fit: Sun Jun 21 18:14:52 2015 +## Date of summary: Sun Jun 21 18:14:52 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.084 s +## Fitted with method Port using 37 model solutions performed in 0.096 s ## ## Weighting: none ## @@ -346,8 +346,8 @@ is checked.</p> <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:55 2015 -## Date of summary: Sun Jun 21 15:31:55 2015 +## Date of fit: Sun Jun 21 18:14:53 2015 +## Date of summary: Sun Jun 21 18:14:53 2015 ## ## ## Warning: Optimisation by method Port did not converge. @@ -359,7 +359,7 @@ is checked.</p> ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.406 s +## Fitted with method Port using 188 model solutions performed in 0.486 s ## ## Weighting: none ## @@ -448,15 +448,15 @@ summary(m.L2.SFO) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:55 2015 -## Date of summary: Sun Jun 21 15:31:55 2015 +## Date of fit: Sun Jun 21 18:14:53 2015 +## Date of summary: Sun Jun 21 18:14:53 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.09 s +## Fitted with method Port using 41 model solutions performed in 0.101 s ## ## Weighting: none ## @@ -558,15 +558,15 @@ mkinresplot(m.L2.FOMC) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:56 2015 -## Date of summary: Sun Jun 21 15:31:56 2015 +## Date of fit: Sun Jun 21 18:14:54 2015 +## Date of summary: Sun Jun 21 18:14:54 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 0.173 s +## Fitted with method Port using 81 model solutions performed in 0.213 s ## ## Weighting: none ## @@ -647,8 +647,8 @@ plot(m.L2.DFOP) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:58 2015 -## Date of summary: Sun Jun 21 15:31:58 2015 +## Date of fit: Sun Jun 21 18:14:56 2015 +## Date of summary: Sun Jun 21 18:14:56 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -657,7 +657,7 @@ plot(m.L2.DFOP) ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.746 s +## Fitted with method Port using 336 model solutions performed in 0.851 s ## ## Weighting: none ## @@ -739,15 +739,15 @@ plot(m.L3.SFO) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:58 2015 -## Date of summary: Sun Jun 21 15:31:58 2015 +## Date of fit: Sun Jun 21 18:14:56 2015 +## Date of summary: Sun Jun 21 18:14:56 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.089 s +## Fitted with method Port using 43 model solutions performed in 0.103 s ## ## Weighting: none ## @@ -825,15 +825,15 @@ plot(m.L3.FOMC) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:58 2015 -## Date of summary: Sun Jun 21 15:31:58 2015 +## Date of fit: Sun Jun 21 18:14:56 2015 +## Date of summary: Sun Jun 21 18:14:56 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 0.181 s +## Fitted with method Port using 83 model solutions performed in 0.197 s ## ## Weighting: none ## @@ -901,8 +901,8 @@ plot(m.L3.DFOP) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:59 2015 -## Date of summary: Sun Jun 21 15:31:59 2015 +## Date of fit: Sun Jun 21 18:14:57 2015 +## Date of summary: Sun Jun 21 18:14:57 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -911,7 +911,7 @@ plot(m.L3.DFOP) ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.309 s +## Fitted with method Port using 137 model solutions performed in 0.341 s ## ## Weighting: none ## @@ -1002,15 +1002,15 @@ plot(m.L4.SFO) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:59 2015 -## Date of summary: Sun Jun 21 15:31:59 2015 +## Date of fit: Sun Jun 21 18:14:57 2015 +## Date of summary: Sun Jun 21 18:14:57 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.1 s +## Fitted with method Port using 46 model solutions performed in 0.111 s ## ## Weighting: none ## @@ -1077,15 +1077,15 @@ plot(m.L4.FOMC) <pre><code>## mkin version: 0.9.36 ## R version: 3.2.1 -## Date of fit: Sun Jun 21 15:31:59 2015 -## Date of summary: Sun Jun 21 15:31:59 2015 +## Date of fit: Sun Jun 21 18:14:57 2015 +## Date of summary: Sun Jun 21 18:14:57 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 0.139 s +## Fitted with method Port using 66 model solutions performed in 0.162 s ## ## Weighting: none ## diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 649410cf..a42e6e01 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd index 5d83cf3a..3b24acbb 100644 --- a/vignettes/compiled_models.Rmd +++ b/vignettes/compiled_models.Rmd @@ -53,9 +53,11 @@ rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, comp print(smb.1)
```
-We see that using the compiled model is almost a factor of 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:
+We see that using the compiled model is by a factor of
+`r round(smb.1["deSolve, not compiled", "median"]/smb.1["deSolve, compiled", "median"], 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:
```{r}
smb.1["median"]/smb.1["deSolve, compiled", "median"]
@@ -81,5 +83,7 @@ smb.2["median"]/smb.2["deSolve, compiled", "median"] ```
-Here we get a performance benefit of more than a factor of 10 using the version
-of the differential equation model compiled from C code using the inline package!
+Here we get a performance benefit of a factor of
+`r round(smb.2["deSolve, not compiled", "median"]/smb.2["deSolve, compiled", "median"], 1)`
+using the version of the differential equation model compiled from C code using
+the inline package!
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index e6f21b09..5fcd88fb 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -94,20 +94,20 @@ mb.1 <- microbenchmark( 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 4969.585 5033.7311 5092.7389 5097.8773 5154.3160 -## Eigenvalue based 868.731 891.7239 909.6449 914.7169 930.1018 -## deSolve, compiled 4935.049 4935.4796 4968.2150 4935.9097 4984.7978 +<pre><code>## min lq mean median uq +## deSolve, not compiled 6980.8002 6996.4739 7024.5611 7012.1476 7046.4415 +## Eigenvalue based 925.3350 928.9405 951.8405 932.5460 965.0932 +## deSolve, compiled 747.2635 761.9405 771.4339 776.6174 783.5191 ## max neval -## deSolve, not compiled 5210.7547 3 -## Eigenvalue based 945.4867 3 -## deSolve, compiled 5033.6858 3</code></pre> -<p>We see that using the compiled model is almost a factor of 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> +## deSolve, not compiled 7080.7354 3 +## Eigenvalue based 997.6404 3 +## deSolve, compiled 790.4207 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 1.0328141 -## Eigenvalue based 0.1853188 -## deSolve, compiled 1.0000000</code></pre> +<pre><code>## median +## deSolve, not compiled 9.029089 +## Eigenvalue based 1.200779 +## deSolve, compiled 1.000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level1"> <h1>Benchmark for a model that can not be solved with Eigenvalues</h1> @@ -124,16 +124,16 @@ 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 11.745276 11.754288 11.820726 11.763300 11.858451 -## deSolve, compiled 1.385829 1.386407 1.400841 1.386985 1.408347 -## max neval -## deSolve, not compiled 11.95360 3 -## deSolve, compiled 1.42971 3</code></pre> +## deSolve, not compiled 14.127630 14.245064 14.298201 14.362497 14.383486 +## deSolve, compiled 1.354744 1.362167 1.366362 1.369589 1.372171 +## max neval +## deSolve, not compiled 14.404474 3 +## deSolve, compiled 1.374752 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> -<pre><code>## median -## deSolve, not compiled 8.4812 -## deSolve, compiled 1.0000</code></pre> -<p>Here we get a performance benefit of more than a factor of 10 using the version of the differential equation model compiled from C code using the inline package!</p> +<pre><code>## median +## deSolve, not compiled 10.48672 +## 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> </div> diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex 825bb36a..7454e688 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |