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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-26 16:38:15 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-26 16:38:15 +0200
commite3fa9f6d27369abcbbc6045a9a7b40c2b17c122e (patch)
tree0092f4a4a55e715592cf209a95bc17b2d3a5a7c7 /vignettes
parent8b272c47c858a4bad5aff94aa005a4efe75ca1d6 (diff)
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forgev0.9-39
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_D.html6
-rw-r--r--vignettes/FOCUS_L.html60
-rw-r--r--vignettes/FOCUS_Z.pdfbin225094 -> 225060 bytes
-rw-r--r--vignettes/compiled_models.html32
-rw-r--r--vignettes/mkin.pdfbin160260 -> 160260 bytes
5 files changed, 49 insertions, 49 deletions
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 &lt;- 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 &lt;- 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
index 3245544c..8b8f7416 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
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 &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 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[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</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 &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 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[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</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
index 76426c30..4eb5dada 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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