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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-21 18:16:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-21 18:16:08 +0200
commit5bd8716b2e4c880b798d1e5e231d49816bbdebd1 (patch)
tree0e1b51583d185f191e91d8358d5660e2a17f513b
parent46b8c7507d2d5fbf0741aeade5b0e7b0614f753f (diff)
Rebuild vignettes with the released package installed
-rw-r--r--vignettes/FOCUS_D.html6
-rw-r--r--vignettes/FOCUS_L.html60
-rw-r--r--vignettes/FOCUS_Z.pdfbin224249 -> 224241 bytes
-rw-r--r--vignettes/compiled_models.Rmd14
-rw-r--r--vignettes/compiled_models.html42
-rw-r--r--vignettes/mkin.pdfbin160260 -> 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
index 649410cf..a42e6e01 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
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 &lt;- microbenchmark(
smb.1 &lt;- summary(mb.1)[-1]
rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
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[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</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 &lt;- summary(mb.2)[-1]
rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
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[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</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
index 825bb36a..7454e688 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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