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-rw-r--r--Rplots.pdfbin4805 -> 4805 bytes
-rw-r--r--vignettes/FOCUS_D.html6
-rw-r--r--vignettes/FOCUS_L.html60
-rw-r--r--vignettes/FOCUS_Z.pdfbin224997 -> 225008 bytes
-rw-r--r--vignettes/compiled_models.html32
-rw-r--r--vignettes/mkin.pdfbin160260 -> 160260 bytes
6 files changed, 49 insertions, 49 deletions
diff --git a/Rplots.pdf b/Rplots.pdf
index 9af1946c..a0b55668 100644
--- a/Rplots.pdf
+++ b/Rplots.pdf
Binary files differ
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 45104f6a..0ec2542c 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 12:22:01 2015
-## Date of summary: Tue Jun 23 12:22:01 2015
+## Date of fit: Tue Jun 23 13:14:52 2015
+## Date of summary: Tue Jun 23 13:14:52 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 0.689 s
+## Fitted with method Port using 153 model solutions performed in 0.682 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 715b6a20..bb012d65 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: 0.9.37
## R version: 3.2.1
-## Date of fit: Tue Jun 23 12:22:02 2015
-## Date of summary: Tue Jun 23 12:22:02 2015
+## Date of fit: Tue Jun 23 13:14:53 2015
+## Date of summary: Tue Jun 23 13:14:53 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.098 s
+## Fitted with method Port using 37 model solutions performed in 0.1 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 12:22:03 2015
-## Date of summary: Tue Jun 23 12:22:03 2015
+## Date of fit: Tue Jun 23 13:14:54 2015
+## Date of summary: Tue Jun 23 13:14:54 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 0.53 s
+## Fitted with method Port using 188 model solutions performed in 0.539 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: 0.9.37
## R version: 3.2.1
-## Date of fit: Tue Jun 23 12:22:03 2015
-## Date of summary: Tue Jun 23 12:22:03 2015
+## Date of fit: Tue Jun 23 13:14:54 2015
+## Date of summary: Tue Jun 23 13:14:54 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 41 model solutions performed in 0.108 s
+## Fitted with method Port using 41 model solutions performed in 0.109 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: 0.9.37
## R version: 3.2.1
-## Date of fit: Tue Jun 23 12:22:04 2015
-## Date of summary: Tue Jun 23 12:22:04 2015
+## Date of fit: Tue Jun 23 13:14:54 2015
+## Date of summary: Tue Jun 23 13:14:54 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 0.205 s
+## Fitted with method Port using 81 model solutions performed in 0.228 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 12:22:06 2015
-## Date of summary: Tue Jun 23 12:22:06 2015
+## Date of fit: Tue Jun 23 13:14:57 2015
+## Date of summary: Tue Jun 23 13:14:57 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 0.913 s
+## Fitted with method Port using 336 model solutions performed in 0.907 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 12:22:06 2015
-## Date of summary: Tue Jun 23 12:22:06 2015
+## Date of fit: Tue Jun 23 13:14:57 2015
+## Date of summary: Tue Jun 23 13:14:57 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 43 model solutions performed in 0.107 s
+## Fitted with method Port using 43 model solutions performed in 0.112 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 12:22:07 2015
-## Date of summary: Tue Jun 23 12:22:07 2015
+## Date of fit: Tue Jun 23 13:14:58 2015
+## Date of summary: Tue Jun 23 13:14:58 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 0.214 s
+## Fitted with method Port using 83 model solutions performed in 0.204 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 12:22:07 2015
-## Date of summary: Tue Jun 23 12:22:07 2015
+## Date of fit: Tue Jun 23 13:14:58 2015
+## Date of summary: Tue Jun 23 13:14:58 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 0.356 s
+## Fitted with method Port using 137 model solutions performed in 0.359 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 12:22:08 2015
-## Date of summary: Tue Jun 23 12:22:08 2015
+## Date of fit: Tue Jun 23 13:14:59 2015
+## Date of summary: Tue Jun 23 13:14:59 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.117 s
+## Fitted with method Port using 46 model solutions performed in 0.12 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 12:22:08 2015
-## Date of summary: Tue Jun 23 12:22:08 2015
+## Date of fit: Tue Jun 23 13:14:59 2015
+## Date of summary: Tue Jun 23 13:14:59 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 0.177 s
+## Fitted with method Port using 66 model solutions performed in 0.163 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 5ed80680..43592d51 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 2fbef8ae..a415c735 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 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
+## deSolve, not compiled 6958.1752 7034.5639 7074.0173 7110.9526 7131.9383
+## Eigenvalue based 978.8821 988.5741 1012.6283 998.2660 1029.5014
+## deSolve, compiled 756.0280 767.9740 800.3639 779.9199 822.5318
## max neval
-## 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>
+## deSolve, not compiled 7152.9240 3
+## Eigenvalue based 1060.7367 3
+## deSolve, compiled 865.1437 3</code></pre>
+<p>We see that using the compiled model is by a factor of 9.1 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:</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 7.838551
-## Eigenvalue based 1.109205
+## deSolve, not compiled 9.117542
+## Eigenvalue based 1.279960
## 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 14.231863 14.287058 14.336780 14.342252 14.389238
-## deSolve, compiled 1.344761 1.345452 1.361713 1.346142 1.370189
+## deSolve, not compiled 14.586587 14.604167 14.614147 14.621747 14.627927
+## deSolve, compiled 1.428573 1.449463 1.459828 1.470352 1.475455
## max neval
-## deSolve, not compiled 14.436224 3
-## deSolve, compiled 1.394235 3</code></pre>
+## deSolve, not compiled 14.634107 3
+## deSolve, compiled 1.480558 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 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>
+## deSolve, not compiled 9.944383
+## deSolve, compiled 1.000000</code></pre>
+<p>Here we get a performance benefit of a factor of 9.9 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>
<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 79b6a5ab..fe600666 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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