9 files changed, 41 insertions, 36 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 2244a359..4c3e5c9b 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -63,15 +63,15 @@ 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:     Fri Nov  4 16:56:21 2016 
-## Date of summary: Fri Nov  4 16:56:21 2016 
+## Date of fit:     Fri Nov  4 17:13:56 2016 
+## Date of summary: Fri Nov  4 17:13:56 2016 
 ## 
 ## Equations:
 ## d_parent = - 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 0.089 s
 ## 
 ## Weighting: none
 ## 
@@ -156,8 +156,8 @@ 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:     Fri Nov  4 16:56:21 2016 
-## Date of summary: Fri Nov  4 16:56:21 2016 
+## Date of fit:     Fri Nov  4 17:13:57 2016 
+## Date of summary: Fri Nov  4 17:13:57 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -169,7 +169,7 @@ 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 0.46 s
+## Fitted with method Port using 188 model solutions performed in 0.444 s
 ## 
 ## Weighting: none
 ## 
@@ -253,15 +253,15 @@ 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:     Fri Nov  4 16:56:22 2016 
-## Date of summary: Fri Nov  4 16:56:22 2016 
+## Date of fit:     Fri Nov  4 17:13:58 2016 
+## Date of summary: Fri Nov  4 17:13:58 2016 
 ## 
 ## 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 0.199 s
+## Fitted with method Port using 81 model solutions performed in 0.194 s
 ## 
 ## Weighting: none
 ## 
@@ -323,8 +323,8 @@ 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:     Fri Nov  4 16:56:23 2016 
-## Date of summary: Fri Nov  4 16:56:23 2016 
+## Date of fit:     Fri Nov  4 17:13:59 2016 
+## Date of summary: Fri Nov  4 17:13:59 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -333,7 +333,7 @@ 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 0.81 s
+## Fitted with method Port using 336 model solutions performed in 0.82 s
 ## 
 ## Weighting: none
 ## 
@@ -412,8 +412,8 @@ 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:     Fri Nov  4 16:56:24 2016 
-## Date of summary: Fri Nov  4 16:56:25 2016 
+## Date of fit:     Fri Nov  4 17:14:00 2016 
+## Date of summary: Fri Nov  4 17:14:00 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -422,7 +422,7 @@ 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 0.335 s
+## Fitted with method Port using 137 model solutions performed in 0.336 s
 ## 
 ## Weighting: none
 ## 
@@ -512,15 +512,15 @@ 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:     Fri Nov  4 16:56:25 2016 
-## Date of summary: Fri Nov  4 16:56:25 2016 
+## Date of fit:     Fri Nov  4 17:14:01 2016 
+## Date of summary: Fri Nov  4 17:14:01 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.114 s
 ## 
 ## Weighting: none
 ## 
@@ -572,15 +572,15 @@ 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:     Fri Nov  4 16:56:25 2016 
-## Date of summary: Fri Nov  4 16:56:25 2016 
+## Date of fit:     Fri Nov  4 17:14:01 2016 
+## Date of summary: Fri Nov  4 17:14:01 2016 
 ## 
 ## 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 0.16 s
+## Fitted with method Port using 66 model solutions performed in 0.162 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index e1572b17..153841ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -78,21 +78,21 @@ 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 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
-##       Eigenvalue based  925.7797  935.9924  939.8725  946.2051  946.9189
-##      deSolve, compiled  740.2821  750.0017  767.8440  759.7212  781.6249
+##  deSolve, not compiled 6282.2220 6293.7637 6323.0479 6305.3053 6343.4608
+##       Eigenvalue based  873.2553  886.5949  903.6178  899.9345  918.7990
+##      deSolve, compiled  737.7899  738.8794  752.3343  739.9689  759.6065
 ##        max neval cld
-##  6671.1797     3   b
-##   947.6327     3  a 
-##   803.5287     3  a</code></pre>
+##  6381.6162     3   c
+##   937.6634     3  b 
+##   779.2441     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 8.5 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 8.464993
-## Eigenvalue based      1.245464
+## deSolve, not compiled 8.521041
+## Eigenvalue based      1.216179
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -114,18 +114,18 @@ 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 13.619556 13.761382 13.825679 13.903207 13.928741
-##      deSolve, compiled  1.316871  1.322577  1.358847  1.328283  1.379834
+##  deSolve, not compiled 13.644880 13.648332 13.835874 13.651784 13.931372
+##      deSolve, compiled  1.422381  1.448574  1.495091  1.474767  1.531446
 ##        max neval cld
-##  13.954275     3   b
-##   1.431386     3  a</code></pre>
+##  14.210959     3   b
+##   1.588125     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 10.5 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 9.3 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 57730131..c52ccd5d 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 50adff32..c89ef9a5 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/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index c8b1e877..03ece635 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,8 +1,13 @@
 base
+datasets
+utils
+grDevices
+graphics
+stats
 knitr
 minpack.lm
 rootSolve
+methods
 inline
+parallel
 mkin
-microbenchmark
-ggplot2
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
new file mode 100644
index 00000000..d11ccf31
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb
new file mode 100644
index 00000000..5ac4f484
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
new file mode 100644
index 00000000..8983f69e
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index d34e3805..2e7e2244 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png