Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)

11 files changed, 52 insertions, 132 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 782a789d..9640c62f 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -54,7 +54,7 @@
       <h1>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2016-11-18</h4>
+            <h4 class="date">2016-12-08</h4>
           </div>
 
     
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 68054ec1..6a25282b 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -54,7 +54,7 @@
       <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2016-11-18</h4>
+            <h4 class="date">2016-12-08</h4>
           </div>
 
     
@@ -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 22:54:43 2016 
-## Date of summary: Fri Nov 18 22:54:43 2016 
+## Date of fit:     Thu Dec  8 07:59:15 2016 
+## Date of summary: Thu Dec  8 07:59:15 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 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.087 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 22:54:44 2016 
-## Date of summary: Fri Nov 18 22:54:44 2016 
+## Date of fit:     Thu Dec  8 07:59:15 2016 
+## Date of summary: Thu Dec  8 07:59:15 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 0.43 s
+## Fitted with method Port using 188 model solutions performed in 0.436 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 22:54:44 2016 
-## Date of summary: Fri Nov 18 22:54:44 2016 
+## Date of fit:     Thu Dec  8 07:59:16 2016 
+## Date of summary: Thu Dec  8 07:59:16 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 0.184 s
+## Fitted with method Port using 81 model solutions performed in 0.19 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 22:54:45 2016 
-## Date of summary: Fri Nov 18 22:54:46 2016 
+## Date of fit:     Thu Dec  8 07:59:17 2016 
+## Date of summary: Thu Dec  8 07:59:17 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 0.784 s
+## Fitted with method Port using 336 model solutions performed in 0.785 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 22:54:47 2016 
-## Date of summary: Fri Nov 18 22:54:47 2016 
+## Date of fit:     Thu Dec  8 07:59:18 2016 
+## Date of summary: Thu Dec  8 07:59:18 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 0.328 s
+## Fitted with method Port using 137 model solutions performed in 0.319 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 22:54:47 2016 
-## Date of summary: Fri Nov 18 22:54:48 2016 
+## Date of fit:     Thu Dec  8 07:59:19 2016 
+## Date of summary: Thu Dec  8 07:59:19 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 0.108 s
+## Fitted with method Port using 46 model solutions performed in 0.107 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 22:54:47 2016 
-## Date of summary: Fri Nov 18 22:54:48 2016 
+## Date of fit:     Thu Dec  8 07:59:19 2016 
+## Date of summary: Thu Dec  8 07:59:19 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 0.145 s
+## Fitted with method Port using 66 model solutions performed in 0.152 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index 5c70b57e..eacefa90 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -20,96 +20,3 @@ FOCUS_2006_Z = data.frame(
 
 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/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData
new file mode 100644
index 00000000..282678c3
--- /dev/null
+++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.RData
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb
new file mode 100644
index 00000000..9c88c526
--- /dev/null
+++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdb
diff --git a/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx
new file mode 100644
index 00000000..5f5be10e
--- /dev/null
+++ b/docs/articles/cache/FOCUS_2006_Z_data_79c4b384b7a683bb55d11555628a14dc.rdx
diff --git a/docs/articles/cache/__packages b/docs/articles/cache/__packages
new file mode 100644
index 00000000..03ece635
--- /dev/null
+++ b/docs/articles/cache/__packages
@@ -0,0 +1,13 @@
+base
+datasets
+utils
+grDevices
+graphics
+stats
+knitr
+minpack.lm
+rootSolve
+methods
+inline
+parallel
+mkin
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 87913685..d39caf12 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -54,7 +54,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2016-11-18</h4>
+            <h4 class="date">2016-12-08</h4>
           </div>
 
     
@@ -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 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
+##  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
 ##        max neval cld
-##  6208.0929     3   c
-##   922.6498     3  b 
-##   722.5556     3 a</code></pre>
+##  6313.5506     3   c
+##   931.9821     3  b 
+##   738.2457     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 8.6 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>
+<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>
 <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 8.636839
-## Eigenvalue based      1.284189
+## deSolve, not compiled 8.738789
+## Eigenvalue based      1.222849
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -127,18 +127,18 @@ 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 13.163796 13.205491 13.478255 13.247187 13.635484
-##      deSolve, compiled  1.267154  1.268198  1.272722  1.269242  1.275506
+##  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
 ##        max neval cld
-##  14.023782     3   b
-##   1.281771     3  a</code></pre>
+##  13.599881     3   b
+##   1.330941     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 10.4 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 10.1 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 55aca8fa..d881a0a2 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 90ac9cbc..b3faa16f 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.html b/docs/articles/mkin.html
index 1292480b..c70f8ddf 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -54,7 +54,7 @@
       <h1>Introduction to mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2016-11-18</h4>
+            <h4 class="date">2016-12-08</h4>
           </div>