Static documentation articles rebuilt by pkgdown::build_articles()

5 files changed, 37 insertions, 37 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index de1e1072..50b3d00a 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -132,8 +132,8 @@
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
 <pre><code>## mkin version:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:12 2016 
-## Date of summary: Thu Dec  8 09:23:13 2016 
+## Date of fit:     Thu Dec  8 09:39:23 2016 
+## Date of summary: Thu Dec  8 09:39:24 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -141,7 +141,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.639 s
+## Fitted with method Port using 153 model solutions performed in 0.627 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index a6ec5532..366a0e46 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -79,15 +79,15 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:13 2016 
-## Date of summary: Thu Dec  8 09:23:13 2016 
+## Date of fit:     Thu Dec  8 09:39:24 2016 
+## Date of summary: Thu Dec  8 09:39:24 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 0.088 s
+## Fitted with method Port using 37 model solutions performed in 0.084 s
 ## 
 ## Weighting: none
 ## 
@@ -172,8 +172,8 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:14 2016 
-## Date of summary: Thu Dec  8 09:23:14 2016 
+## Date of fit:     Thu Dec  8 09:39:25 2016 
+## Date of summary: Thu Dec  8 09:39:25 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -269,15 +269,15 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:14 2016 
-## Date of summary: Thu Dec  8 09:23:14 2016 
+## Date of fit:     Thu Dec  8 09:39:26 2016 
+## Date of summary: Thu Dec  8 09:39:26 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 0.185 s
+## Fitted with method Port using 81 model solutions performed in 0.183 s
 ## 
 ## Weighting: none
 ## 
@@ -339,8 +339,8 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:15 2016 
-## Date of summary: Thu Dec  8 09:23:15 2016 
+## Date of fit:     Thu Dec  8 09:39:27 2016 
+## Date of summary: Thu Dec  8 09:39:27 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -349,7 +349,7 @@ 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 0.765 s
+## Fitted with method Port using 336 model solutions performed in 0.771 s
 ## 
 ## Weighting: none
 ## 
@@ -428,8 +428,8 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:17 2016 
-## Date of summary: Thu Dec  8 09:23:17 2016 
+## Date of fit:     Thu Dec  8 09:39:28 2016 
+## Date of summary: Thu Dec  8 09:39:28 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -438,7 +438,7 @@ 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 0.309 s
+## Fitted with method Port using 137 model solutions performed in 0.304 s
 ## 
 ## Weighting: none
 ## 
@@ -528,15 +528,15 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:17 2016 
-## Date of summary: Thu Dec  8 09:23:17 2016 
+## Date of fit:     Thu Dec  8 09:39:28 2016 
+## Date of summary: Thu Dec  8 09:39:29 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 0.106 s
+## Fitted with method Port using 46 model solutions performed in 0.107 s
 ## 
 ## Weighting: none
 ## 
@@ -588,15 +588,15 @@ 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:    0.9.45 
 ## R version:       3.3.2 
-## Date of fit:     Thu Dec  8 09:23:17 2016 
-## Date of summary: Thu Dec  8 09:23:17 2016 
+## Date of fit:     Thu Dec  8 09:39:28 2016 
+## Date of summary: Thu Dec  8 09:39:29 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 0.148 s
+## Fitted with method Port using 66 model solutions performed in 0.145 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 660af1d1..457f5a1d 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -99,21 +99,21 @@ 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 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
+##  deSolve, not compiled 5185.0893 5231.5690 5266.8769 5278.0487 5307.7706
+##       Eigenvalue based  843.3153  847.1503  876.5398  850.9853  893.1520
+##      deSolve, compiled  723.0636  740.5682  755.9995  758.0729  772.4674
 ##        max neval cld
-##  5309.2087     3   b
-##   927.4680     3  a 
-##   744.7077     3  a</code></pre>
+##  5337.4926     3   b
+##   935.3187     3  a 
+##   786.8620     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>) &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 6.989197
-## Eigenvalue based      1.264108
+## deSolve, not compiled 6.962456
+## Eigenvalue based      1.122564
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -134,19 +134,19 @@ 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 11.015990 11.17783 11.24827 11.339674 11.364403
-##      deSolve, compiled  1.285264  1.29794  1.32988  1.310616  1.352189
+##                   expr       min        lq      mean   median        uq
+##  deSolve, not compiled 10.963655 10.992677 11.033360 11.02170 11.068212
+##      deSolve, compiled  1.287898  1.309754  1.322972  1.33161  1.340509
 ##        max neval cld
-##  11.389132     3   b
-##   1.393762     3  a</code></pre>
+##  11.114726     3   b
+##   1.349408     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 8.7 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 8.3 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)
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 53ff97f7..dae2c9d4 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 d3a507bd..696236dc 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