Static documentation articles rebuilt by pkgdown::build_articles()

Split out an extra pd_articles target in the Makefile

6 files changed, 52 insertions, 40 deletions

diff --git a/GNUmakefile b/GNUmakefile
index ec8443e2..1d986246 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -87,9 +87,16 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/%.Rmd
 vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html
 
 pd:
-	"$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)"
+	"$(RBIN)/Rscript" -e "pkgdown::build_news()"
+	"$(RBIN)/Rscript" -e "pkgdown::build_reference(run_dont_run = TRUE)"
+	"$(RBIN)/Rscript" -e "pkgdown::build_home()"
 	git add -A
-	git commit -m 'Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)' -e
+	git commit -m 'Static documentation except articles rebuilt by pkgdown' -e
+
+pd_articles:
+	"$(RBIN)/Rscript" -e "pkgdown::build_articles()"
+	git add -A
+	git commit -m 'Static documentation articles rebuilt by pkgdown::build_articles()' -e
 
 r-forge: 
 	rm -rf $(SDDIR)/*
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 6a25282b..feceab6f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -76,15 +76,15 @@ FOCUS_2006_L1_mkin &lt;-<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:     Thu Dec  8 07:59:15 2016 
-## Date of summary: Thu Dec  8 07:59:15 2016 
+## Date of fit:     Thu Dec  8 08:18:47 2016 
+## Date of summary: Thu Dec  8 08:18:47 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 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.084 s
 ## 
 ## Weighting: none
 ## 
@@ -169,8 +169,8 @@ FOCUS_2006_L1_mkin &lt;-<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:     Thu Dec  8 07:59:15 2016 
-## Date of summary: Thu Dec  8 07:59:15 2016 
+## Date of fit:     Thu Dec  8 08:18:47 2016 
+## Date of summary: Thu Dec  8 08:18:47 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin &lt;-<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 0.436 s
+## Fitted with method Port using 188 model solutions performed in 0.462 s
 ## 
 ## Weighting: none
 ## 
@@ -266,15 +266,15 @@ FOCUS_2006_L2_mkin &lt;-<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:     Thu Dec  8 07:59:16 2016 
-## Date of summary: Thu Dec  8 07:59:16 2016 
+## Date of fit:     Thu Dec  8 08:18:48 2016 
+## Date of summary: Thu Dec  8 08:18:48 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 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.201 s
 ## 
 ## Weighting: none
 ## 
@@ -336,8 +336,8 @@ FOCUS_2006_L2_mkin &lt;-<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:     Thu Dec  8 07:59:17 2016 
-## Date of summary: Thu Dec  8 07:59:17 2016 
+## Date of fit:     Thu Dec  8 08:18:49 2016 
+## Date of summary: Thu Dec  8 08:18:49 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ FOCUS_2006_L2_mkin &lt;-<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 0.785 s
+## Fitted with method Port using 336 model solutions performed in 0.767 s
 ## 
 ## Weighting: none
 ## 
@@ -425,8 +425,8 @@ mm.L3 &lt;-<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:     Thu Dec  8 07:59:18 2016 
-## Date of summary: Thu Dec  8 07:59:18 2016 
+## Date of fit:     Thu Dec  8 08:18:50 2016 
+## Date of summary: Thu Dec  8 08:18:51 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ mm.L3 &lt;-<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 0.319 s
+## Fitted with method Port using 137 model solutions performed in 0.311 s
 ## 
 ## Weighting: none
 ## 
@@ -525,15 +525,15 @@ mm.L4 &lt;-<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:     Thu Dec  8 07:59:19 2016 
-## Date of summary: Thu Dec  8 07:59:19 2016 
+## Date of fit:     Thu Dec  8 08:18:51 2016 
+## Date of summary: Thu Dec  8 08:18:51 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 0.118 s
 ## 
 ## Weighting: none
 ## 
@@ -585,15 +585,15 @@ mm.L4 &lt;-<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:     Thu Dec  8 07:59:19 2016 
-## Date of summary: Thu Dec  8 07:59:19 2016 
+## Date of fit:     Thu Dec  8 08:18:51 2016 
+## Date of summary: Thu Dec  8 08:18:51 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 0.152 s
+## Fitted with method Port using 66 model solutions performed in 0.151 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index d39caf12..2850a9ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -67,8 +67,13 @@
 <pre><code>##            gcc 
 ## "/usr/bin/gcc"</code></pre>
 <p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>)
-SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>)</code></pre></div>
+<pre><code>## Loading required package: minpack.lm</code></pre>
+<pre><code>## Loading required package: rootSolve</code></pre>
+<pre><code>## Loading required package: inline</code></pre>
+<pre><code>## Loading required package: methods</code></pre>
+<pre><code>## Loading required package: parallel</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(
   <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),
   <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
@@ -91,21 +96,21 @@ mb<span class="fl">.1</span> &lt;-<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 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394
-##       Eigenvalue based  865.5257  872.4146  892.2705  879.3036  905.6429
-##      deSolve, compiled  716.7534  717.9075  724.6869  719.0617  728.6537
+##  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
 ##        max neval cld
-##  6313.5506     3   c
-##   931.9821     3  b 
-##   738.2457     3 a</code></pre>
+##  5050.7556     3   c
+##   941.5075     3  b 
+##   708.4229     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 8.7 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>
+<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>) &lt;-<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 8.738789
-## Eigenvalue based      1.222849
+## deSolve, not compiled 7.034082
+## Eigenvalue based      1.231089
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -127,18 +132,18 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
 <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 13.487097 13.492149 13.528060 13.497201 13.548541
-##      deSolve, compiled  1.307845  1.318979  1.322967  1.330114  1.330528
+##  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
 ##        max neval cld
-##  13.599881     3   b
-##   1.330941     3  a</code></pre>
+##  10.898330     3   b
+##   1.311972     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 10.1 using the version of the differential equation model compiled from C code!</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>
 <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 d881a0a2..c30550c9 100644
--- 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
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 b3faa16f..5f95613a 100644
--- 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
diff --git a/docs/articles/index.html b/docs/articles/index.html
index de5643c2..20792ba1 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -90,7 +90,7 @@
       </header>
 
       <div class="page-header">
-  <h1>Vignette reference <small>version&nbsp;0.9.44.9000</small></h1>
+  <h1>Vignette reference <small>version&nbsp;0.9.45</small></h1>
 </div>
 
 <div class="row">