From d852e9e000f57f280deb84611ae1af58daa883cc Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 18 Nov 2016 23:08:45 +0100
Subject: Fix links in README, configure navbar, rebuild docs
---
docs/articles/FOCUS_D.R | 20 ++++++++++
docs/articles/FOCUS_D.html | 2 +-
docs/articles/FOCUS_L.html | 44 ++++++++++-----------
docs/articles/FOCUS_Z.pdf | Bin 239558 -> 239561 bytes
docs/articles/compiled_models.html | 32 +++++++--------
.../figure-html/benchmark_FOMC_SFO-1.png | Bin 9843 -> 9618 bytes
.../figure-html/benchmark_SFO_SFO-1.png | Bin 11615 -> 10679 bytes
docs/articles/index.html | 2 +-
docs/articles/mkin.html | 2 +-
9 files changed, 61 insertions(+), 41 deletions(-)
(limited to 'docs/articles')
diff --git a/docs/articles/FOCUS_D.R b/docs/articles/FOCUS_D.R
index 9eaf41f7..51723496 100644
--- a/docs/articles/FOCUS_D.R
+++ b/docs/articles/FOCUS_D.R
@@ -2,3 +2,23 @@
library(knitr)
opts_chunk$set(tidy = FALSE, cache = TRUE)
+## ----data----------------------------------------------------------------
+library("mkin")
+print(FOCUS_2006_D)
+
+## ----model---------------------------------------------------------------
+SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+print(SFO_SFO$diffs)
+
+## ----fit-----------------------------------------------------------------
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+
+## ----plot, fig.height = 6, fig.width = 8---------------------------------
+plot_sep(fit, lpos = c("topright", "bottomright"))
+
+## ----plot_2, fig.height = 4, fig.width = 8-------------------------------
+mkinparplot(fit)
+
+## ------------------------------------------------------------------------
+summary(fit)
+
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index ad53126e..782a789d 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -16,7 +16,7 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Function reference</a>
+ <a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 8f3dbe7c..68054ec1 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -16,7 +16,7 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Function reference</a>
+ <a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
@@ -76,15 +76,15 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:11 2016
-## Date of summary: Fri Nov 18 16:48:11 2016
+## Date of fit: Fri Nov 18 22:54:43 2016
+## Date of summary: Fri Nov 18 22:54:43 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.085 s
+## Fitted with method Port using 37 model solutions performed in 0.09 s
##
## Weighting: none
##
@@ -169,8 +169,8 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:12 2016
-## Date of summary: Fri Nov 18 16:48:12 2016
+## Date of fit: Fri Nov 18 22:54:44 2016
+## Date of summary: Fri Nov 18 22:54:44 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.448 s
+## Fitted with method Port using 188 model solutions performed in 0.43 s
##
## Weighting: none
##
@@ -266,15 +266,15 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:13 2016
-## Date of summary: Fri Nov 18 16:48:13 2016
+## Date of fit: Fri Nov 18 22:54:44 2016
+## Date of summary: Fri Nov 18 22:54:44 2016
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.196 s
+## Fitted with method Port using 81 model solutions performed in 0.184 s
##
## Weighting: none
##
@@ -336,8 +336,8 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:14 2016
-## Date of summary: Fri Nov 18 16:48:14 2016
+## Date of fit: Fri Nov 18 22:54:45 2016
+## Date of summary: Fri Nov 18 22:54:46 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.793 s
+## Fitted with method Port using 336 model solutions performed in 0.784 s
##
## Weighting: none
##
@@ -425,8 +425,8 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:15 2016
-## Date of summary: Fri Nov 18 16:48:15 2016
+## Date of fit: Fri Nov 18 22:54:47 2016
+## Date of summary: Fri Nov 18 22:54:47 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.325 s
+## Fitted with method Port using 137 model solutions performed in 0.328 s
##
## Weighting: none
##
@@ -525,15 +525,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:15 2016
-## Date of summary: Fri Nov 18 16:48:16 2016
+## Date of fit: Fri Nov 18 22:54:47 2016
+## Date of summary: Fri Nov 18 22:54:48 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.108 s
##
## Weighting: none
##
@@ -585,15 +585,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Fri Nov 18 16:48:16 2016
-## Date of summary: Fri Nov 18 16:48:16 2016
+## Date of fit: Fri Nov 18 22:54:47 2016
+## Date of summary: Fri Nov 18 22:54:48 2016
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.15 s
+## Fitted with method Port using 66 model solutions performed in 0.145 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf
index 6f8929ea..d8bfd68c 100644
Binary files a/docs/articles/FOCUS_Z.pdf and b/docs/articles/FOCUS_Z.pdf differ
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 31340867..87913685 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -16,7 +16,7 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Function reference</a>
+ <a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
@@ -91,21 +91,21 @@ mb<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">micr
<span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div>
<pre><code>## Unit: milliseconds
## expr min lq mean median uq
-## deSolve, not compiled 6559.0772 6574.0500 6642.0659 6589.0229 6683.5603
-## Eigenvalue based 921.0723 931.1284 940.3973 941.1845 950.0598
-## deSolve, compiled 736.6534 741.6706 756.3600 746.6878 766.2132
+## deSolve, not compiled 6126.4954 6152.1764 6170.8152 6177.8573 6192.9751
+## Eigenvalue based 864.8441 891.7069 902.0212 918.5697 920.6098
+## deSolve, compiled 706.9115 711.1015 714.9195 715.2915 718.9235
## max neval cld
-## 6778.0978 3 c
-## 958.9351 3 b
-## 785.7386 3 a</code></pre>
+## 6208.0929 3 c
+## 922.6498 3 b
+## 722.5556 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p>
-<p>We see that using the compiled model is by a factor of 8.8 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>
+<p>We see that using the compiled model is by a factor of 8.6 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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) <-<span class="st"> </span>smb<span class="fl">.1</span>$expr
smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
-## deSolve, not compiled 8.824334
-## Eigenvalue based 1.260479
+## deSolve, not compiled 8.636839
+## Eigenvalue based 1.284189
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -126,19 +126,19 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>)
<span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div>
<pre><code>## Unit: seconds
-## expr min lq mean median uq
-## deSolve, not compiled 13.587184 13.616178 13.673277 13.64517 13.716324
-## deSolve, compiled 1.307508 1.317114 1.337594 1.32672 1.352637
+## expr min lq mean median uq
+## deSolve, not compiled 13.163796 13.205491 13.478255 13.247187 13.635484
+## deSolve, compiled 1.267154 1.268198 1.272722 1.269242 1.275506
## max neval cld
-## 13.787476 3 b
-## 1.378553 3 a</code></pre>
+## 14.023782 3 b
+## 1.281771 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
## 1 NA
## 2 NA</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p>
-<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!</p>
+<p>Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.44.9000 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index b7fda1ed..55aca8fa 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index bacdb814..90ac9cbc 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png differ
diff --git a/docs/articles/index.html b/docs/articles/index.html
index de2a8a61..de5643c2 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -49,7 +49,7 @@
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
- <a href="../reference/index.html">Function reference</a>
+ <a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 49c0389b..1292480b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -16,7 +16,7 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Function reference</a>
+ <a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
--
cgit v1.2.1