From 9733b1ae5596228c50b3acdfdd78fe96ab1e0533 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 8 Dec 2016 09:23:22 +0100
Subject: Static documentation articles rebuilt by pkgdown::build_articles()
---
.gitignore | 2 +-
GNUmakefile | 3 +-
docs/articles/FOCUS_D.html | 11 ++-
docs/articles/FOCUS_D_cache/html/__packages | 6 +-
.../data_df09328a15a9c09625fe6f7d481671d8.RData | Bin 3178 -> 3173 bytes
.../fit_449df36a8c1e5c902ad4f45fc76df647.RData | Bin 2735 -> 2735 bytes
.../html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb | Bin 100468 -> 15583 bytes
.../html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx | Bin 169 -> 161 bytes
.../model_911bdb95adf8c19a8e50c4150b20f2fc.RData | Bin 2934 -> 2931 bytes
.../model_911bdb95adf8c19a8e50c4150b20f2fc.rdb | Bin 1777 -> 1775 bytes
.../model_911bdb95adf8c19a8e50c4150b20f2fc.rdx | Bin 147 -> 147 bytes
.../plot_2_2d898a5ad88ebcba8bdab623bfd497de.RData | Bin 2769 -> 2769 bytes
.../plot_a02b9c8bb9ae9921707cd87235ec2008.RData | Bin 2799 -> 2799 bytes
...-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData | Bin 4627 -> 4626 bytes
docs/articles/FOCUS_L.html | 59 +++++------
docs/articles/FOCUS_Z.R | 108 ++++++++++++++++++---
docs/articles/FOCUS_Z.pdf | Bin 239561 -> 239559 bytes
docs/articles/compiled_models.html | 33 ++++---
.../figure-html/benchmark_FOMC_SFO-1.png | Bin 9519 -> 10199 bytes
.../figure-html/benchmark_SFO_SFO-1.png | Bin 10832 -> 12764 bytes
docs/articles/figure/FOCUS_2006_Z_fits_1-1.pdf | Bin 7496 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_10-1.pdf | Bin 11048 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_11-1.pdf | Bin 11072 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_11a-1.pdf | Bin 10940 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_11b-1.pdf | Bin 5023 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_2-1.pdf | Bin 7481 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_3-1.pdf | Bin 7482 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_5-1.pdf | Bin 9099 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_6-1.pdf | Bin 10771 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_7-1.pdf | Bin 10754 -> 0 bytes
docs/articles/figure/FOCUS_2006_Z_fits_9-1.pdf | Bin 9392 -> 0 bytes
docs/articles/index.html | 3 +
docs/articles/mkin.R | 4 -
docs/articles/mkin.html | 3 +
docs/articles/mkin_cache/html/__packages | 11 ++-
...ed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdb | Bin 105229 -> 20262 bytes
...ed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdx | Bin 236 -> 227 bytes
37 files changed, 165 insertions(+), 78 deletions(-)
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_1-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_10-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_11-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_11a-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_11b-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_2-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_3-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_5-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_6-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_7-1.pdf
delete mode 100644 docs/articles/figure/FOCUS_2006_Z_fits_9-1.pdf
delete mode 100644 docs/articles/mkin.R
diff --git a/.gitignore b/.gitignore
index cff9abc0..c7cb7073 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,4 @@
-docs/articles/cache/
+docs/articles/*_cache/
install.log
mkin*.tar.gz
mkin.Rcheck
diff --git a/GNUmakefile b/GNUmakefile
index f41c2d3f..0ce9e64c 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -96,8 +96,9 @@ pd_articles:
git commit -m 'Static documentation articles rebuilt by pkgdown::build_articles()' -e
r-forge:
- rm -rf $(SDDIR)/*
+ rm -r $(SDDIR)/*
cp -a docs/* $(SDDIR)
+ rm -r $(SDDIR)/articles/cache
cd $(SDDIR) && svn add --force .
git archive master > $(HOME)/mkin.tar;\
cd $(RFDIR) && rm -r `ls` && tar -xf $(HOME)/mkin.tar;\
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 9640c62f..de1e1072 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -37,6 +37,9 @@
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
</ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -127,10 +130,10 @@
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
-<pre><code>## mkin version: 0.9.44.9000
+<pre><code>## mkin version: 0.9.45
## 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: Thu Dec 8 09:23:12 2016
+## Date of summary: Thu Dec 8 09:23:13 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -138,7 +141,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.638 s
+## Fitted with method Port using 153 model solutions performed in 0.639 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages
index f8bbf624..c8b1e877 100644
--- a/docs/articles/FOCUS_D_cache/html/__packages
+++ b/docs/articles/FOCUS_D_cache/html/__packages
@@ -1,12 +1,8 @@
base
-colorout
-setwidth
-nvimcom
+knitr
minpack.lm
rootSolve
inline
mkin
-rmarkdown
-knitr
microbenchmark
ggplot2
diff --git a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData
index f670208c..f5ad0de0 100644
Binary files a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData and b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData differ
diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData
index 9a067af3..5dab0855 100644
Binary files a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData and b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData differ
diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb
index a8bd13a3..b4e670d7 100644
Binary files a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb and b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb differ
diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx
index ddb76cc5..2e77c111 100644
Binary files a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx and b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx differ
diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData
index f9619505..2b27d5ad 100644
Binary files a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData and b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData differ
diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb
index 7c0b68b9..2782d71f 100644
Binary files a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb and b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb differ
diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx
index 9a551f67..9ecc2d70 100644
Binary files a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx and b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx differ
diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_2d898a5ad88ebcba8bdab623bfd497de.RData b/docs/articles/FOCUS_D_cache/html/plot_2_2d898a5ad88ebcba8bdab623bfd497de.RData
index b1195f70..bd1939c0 100644
Binary files a/docs/articles/FOCUS_D_cache/html/plot_2_2d898a5ad88ebcba8bdab623bfd497de.RData and b/docs/articles/FOCUS_D_cache/html/plot_2_2d898a5ad88ebcba8bdab623bfd497de.RData differ
diff --git a/docs/articles/FOCUS_D_cache/html/plot_a02b9c8bb9ae9921707cd87235ec2008.RData b/docs/articles/FOCUS_D_cache/html/plot_a02b9c8bb9ae9921707cd87235ec2008.RData
index e559f15f..abf23dfa 100644
Binary files a/docs/articles/FOCUS_D_cache/html/plot_a02b9c8bb9ae9921707cd87235ec2008.RData and b/docs/articles/FOCUS_D_cache/html/plot_a02b9c8bb9ae9921707cd87235ec2008.RData differ
diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData
index ca6eff0e..a90e3de4 100644
Binary files a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData and b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData differ
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index feceab6f..a6ec5532 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -37,6 +37,9 @@
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
</ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -74,17 +77,17 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_2006_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
-<pre><code>## mkin version: 0.9.44.9000
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:47 2016
-## Date of summary: Thu Dec 8 08:18:47 2016
+## Date of fit: Thu Dec 8 09:23:13 2016
+## Date of summary: Thu Dec 8 09:23:13 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 0.084 s
+## Fitted with method Port using 37 model solutions performed in 0.088 s
##
## Weighting: none
##
@@ -167,10 +170,10 @@ 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">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</code></pre></div>
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p>
<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
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:47 2016
-## Date of summary: Thu Dec 8 08:18:47 2016
+## Date of fit: Thu Dec 8 09:23:14 2016
+## Date of summary: Thu Dec 8 09:23:14 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -182,7 +185,7 @@ 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 0.462 s
+## Fitted with method Port using 188 model solutions performed in 0.427 s
##
## Weighting: none
##
@@ -264,17 +267,17 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</code></pre></div>
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
<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
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:48 2016
-## Date of summary: Thu Dec 8 08:18:48 2016
+## Date of fit: Thu Dec 8 09:23:14 2016
+## Date of summary: Thu Dec 8 09:23:14 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 0.201 s
+## Fitted with method Port using 81 model solutions performed in 0.185 s
##
## Weighting: none
##
@@ -334,10 +337,10 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re
<span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</code></pre></div>
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
<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
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:49 2016
-## Date of summary: Thu Dec 8 08:18:49 2016
+## Date of fit: Thu Dec 8 09:23:15 2016
+## Date of summary: Thu Dec 8 09:23:15 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +349,7 @@ 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 0.767 s
+## Fitted with method Port using 336 model solutions performed in 0.765 s
##
## Weighting: none
##
@@ -423,10 +426,10 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p>
<p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p>
<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
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:50 2016
-## Date of summary: Thu Dec 8 08:18:51 2016
+## Date of fit: Thu Dec 8 09:23:17 2016
+## Date of summary: Thu Dec 8 09:23:17 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +438,7 @@ 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 0.311 s
+## Fitted with method Port using 137 model solutions performed in 0.309 s
##
## Weighting: none
##
@@ -523,17 +526,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="672"></p>
<p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p>
<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
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:51 2016
-## Date of summary: Thu Dec 8 08:18:51 2016
+## Date of fit: Thu Dec 8 09:23:17 2016
+## Date of summary: Thu Dec 8 09:23:17 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 0.118 s
+## Fitted with method Port using 46 model solutions performed in 0.106 s
##
## Weighting: none
##
@@ -583,17 +586,17 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
## DT50 DT90
## parent 106 352</code></pre>
<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
+<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 08:18:51 2016
-## Date of summary: Thu Dec 8 08:18:51 2016
+## Date of fit: Thu Dec 8 09:23:17 2016
+## Date of summary: Thu Dec 8 09:23:17 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 0.151 s
+## Fitted with method Port using 66 model solutions performed in 0.148 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index eacefa90..0d5f0940 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -3,20 +3,96 @@ require(knitr)
opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE)
options(width=70)
-## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------
-require(mkin)
-LOD = 0.5
-FOCUS_2006_Z = data.frame(
- t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
- 42, 61, 96, 124),
- Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
- 2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
- Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
- 1.6, 0.6, 0.5 * LOD, NA, NA, NA),
- Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
- 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
- Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
- 25.2, 17.2, 4.8, 4.5, 2.8, 4.4))
-
-FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
+## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6-------------------
+Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
+ Z1 = mkinsub("SFO"))
+m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.2a)
+summary(m.Z.2a, data = FALSE)$bpar
+
+## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6-------------------
+Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
+ Z1 = mkinsub("SFO"),
+ use_of_ff = "max")
+
+m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.2a.ff)
+summary(m.Z.2a.ff, data = FALSE)$bpar
+
+## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6-------------------
+Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO"), use_of_ff = "max")
+m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.3)
+summary(m.Z.3, data = FALSE)$bpar
+
+## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7-------------------
+Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+ Z2 = mkinsub("SFO"), use_of_ff = "max")
+m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.5)
+
+## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8-------------------
+Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+ Z2 = mkinsub("SFO", "Z3"),
+ Z3 = mkinsub("SFO"),
+ use_of_ff = "max")
+m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
+ parms.ini = m.Z.5$bparms.ode,
+ quiet = TRUE)
+plot_sep(m.Z.FOCUS)
+summary(m.Z.FOCUS, data = FALSE)$bpar
+endpoints(m.Z.FOCUS)
+
+## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8-------------------
+Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+ Z2 = mkinsub("SFO", "Z3"),
+ Z3 = mkinsub("SFORB"))
+m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.mkin.1)
+summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
+
+## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8-------------------
+Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+ Z2 = mkinsub("SFO"))
+m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.mkin.3)
+
+## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------
+Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+ Z2 = mkinsub("SFO", "Z3"),
+ Z3 = mkinsub("SFO"))
+m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
+ parms.ini = m.Z.mkin.3$bparms.ode,
+ quiet = TRUE)
+plot_sep(m.Z.mkin.4)
+
+## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------
+Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+ Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+ Z2 = mkinsub("SFO", "Z3"),
+ Z3 = mkinsub("SFORB"))
+m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
+ parms.ini = m.Z.mkin.4$bparms.ode[1:4],
+ quiet = TRUE)
+plot_sep(m.Z.mkin.5)
+
+## ----FOCUS_2006_Z_fits_11a, echo=TRUE-------------------------------
+m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
+ parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
+ k_Z3_bound_free = 0),
+ fixed_parms = "k_Z3_bound_free",
+ quiet = TRUE)
+plot_sep(m.Z.mkin.5a)
+
+## ----FOCUS_2006_Z_fits_11b, echo=TRUE-------------------------------
+mkinparplot(m.Z.mkin.5a)
+
+## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE---------------------
+endpoints(m.Z.mkin.5a)
diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf
index d8bfd68c..fd313555 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 2850a9ae..660af1d1 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -37,6 +37,9 @@
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
</ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
@@ -96,21 +99,21 @@ 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 4973.8901 4975.2320 5000.4065 4976.5739 5013.6648
-## Eigenvalue based 848.4335 859.7111 886.9766 870.9887 906.2481
-## deSolve, compiled 702.8916 705.1930 706.2696 707.4944 707.9587
+## deSolve, not compiled 5006.3815 5014.4629 5112.7115 5022.5443 5165.8765
+## Eigenvalue based 840.3027 874.3549 892.0593 908.4071 917.9376
+## deSolve, compiled 706.9909 712.8031 723.4380 718.6154 731.6615
## max neval cld
-## 5050.7556 3 c
-## 941.5075 3 b
-## 708.4229 3 a</code></pre>
+## 5309.2087 3 b
+## 927.4680 3 a
+## 744.7077 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 7 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 7.034082
-## Eigenvalue based 1.231089
+## deSolve, not compiled 6.989197
+## Eigenvalue based 1.264108
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -131,20 +134,20 @@ 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 10.819486 10.846433 10.863732 10.873381 10.885855
-## deSolve, compiled 1.300192 1.301168 1.304769 1.302144 1.307058
+## expr min lq mean median uq
+## deSolve, not compiled 11.015990 11.17783 11.24827 11.339674 11.364403
+## deSolve, compiled 1.285264 1.29794 1.32988 1.310616 1.352189
## max neval cld
-## 10.898330 3 b
-## 1.311972 3 a</code></pre>
+## 11.389132 3 b
+## 1.393762 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 8.4 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>
+<p>Here we get a performance benefit of a factor of 8.7 using the version of the differential equation model compiled from C code!</p>
+<p>This vignette was built with mkin 0.9.45 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)</code></pre>
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 c30550c9..53ff97f7 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 5f95613a..d3a507bd 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/figure/FOCUS_2006_Z_fits_1-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_1-1.pdf
deleted file mode 100644
index 6f5cbd2a..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_1-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_10-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_10-1.pdf
deleted file mode 100644
index a2d3e91e..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_10-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_11-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_11-1.pdf
deleted file mode 100644
index 9a88c84b..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_11-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_11a-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_11a-1.pdf
deleted file mode 100644
index eda22e28..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_11a-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_11b-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_11b-1.pdf
deleted file mode 100644
index be61a972..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_11b-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_2-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_2-1.pdf
deleted file mode 100644
index 25616330..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_2-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_3-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_3-1.pdf
deleted file mode 100644
index ccb8e23a..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_3-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_5-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_5-1.pdf
deleted file mode 100644
index 9d0949cd..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_5-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_6-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_6-1.pdf
deleted file mode 100644
index 020a1ccd..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_6-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_7-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_7-1.pdf
deleted file mode 100644
index a34809c8..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_7-1.pdf and /dev/null differ
diff --git a/docs/articles/figure/FOCUS_2006_Z_fits_9-1.pdf b/docs/articles/figure/FOCUS_2006_Z_fits_9-1.pdf
deleted file mode 100644
index 26c4ff9d..00000000
Binary files a/docs/articles/figure/FOCUS_2006_Z_fits_9-1.pdf and /dev/null differ
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 20792ba1..7344840b 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,6 +71,9 @@
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
</ul>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul>
diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R
deleted file mode 100644
index fc39bfda..00000000
--- a/docs/articles/mkin.R
+++ /dev/null
@@ -1,4 +0,0 @@
-## ---- include = FALSE----------------------------------------------------
-require(knitr)
-opts_chunk$set(engine='R', tidy=FALSE)
-
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index c70f8ddf..4159c427 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -37,6 +37,9 @@
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
</ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index ff62e6df..45ea9824 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,12 +1,15 @@
base
+datasets
+utils
+grDevices
+graphics
+stats
knitr
minpack.lm
rootSolve
+methods
inline
+parallel
mkin
-colorout
-setwidth
-nvimcom
-rmarkdown
microbenchmark
ggplot2
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdb
index 02ed5e42..fca46a8c 100644
Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdb and b/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdb differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdx
index 85286890..9448b7d1 100644
Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdx and b/docs/articles/mkin_cache/html/unnamed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdx differ
--
cgit v1.2.1