Fix links in README, configure navbar, rebuild docs

9 files changed, 61 insertions, 41 deletions

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 &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 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 &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 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 &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 0.448 s
+## Fitted with method Port using 188 model solutions performed in 0.43 s
 ## 
 ## Weighting: none
 ## 
@@ -266,15 +266,15 @@ FOCUS_2006_L2_mkin &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 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 &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 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 &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 0.793 s
+## Fitted with method Port using 336 model solutions performed in 0.784 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:     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 &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 0.325 s
+## Fitted with method Port using 137 model solutions performed in 0.328 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:     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 &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 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
--- a/docs/articles/FOCUS_Z.pdf
+++ b/docs/articles/FOCUS_Z.pdf
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> &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 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>) &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 8.824334
-## 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> &lt;-<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
--- 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 bacdb814..90ac9cbc 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 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">