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

Using branch 'jranke' on jranke/pkgdown, fixing issues
hadley/pgkdown#178 and hadley/pkgdown#213

Remove plot=TRUE from mkinfit calls also in dontrun sections of examples
to avoid a flood png files documenting the progress of the fit.

1 files changed, 40 insertions, 22 deletions

diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index f328c34a..9477d648 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -164,28 +164,46 @@
 <span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span>
-<span class='co'># SFO_SFO &lt;- mkinmod(</span>
-<span class='co'>#   parent = list(type = "SFO", to = "m1"),</span>
-<span class='co'>#   m1 = list(type = "SFO"))</span>
-<span class='co'># </span>
-<span class='co'># # Show details of creating the C function</span>
-<span class='co'># SFO_SFO &lt;- mkinmod(</span>
-<span class='co'>#   parent = mkinsub("SFO", "m1"),</span>
-<span class='co'>#   m1 = mkinsub("SFO"), verbose = TRUE)</span>
-<span class='co'># </span>
-<span class='co'># # If we have several parallel metabolites </span>
-<span class='co'># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
-<span class='co'># m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span>
-<span class='co'>#                            M1 = mkinsub("SFO"),</span>
-<span class='co'>#                            M2 = mkinsub("SFO"),</span>
-<span class='co'>#                            use_of_ff = "max", quiet = TRUE)</span>
-<span class='co'># </span>
-<span class='co'># fit_DFOP_par_c &lt;- mkinfit(m_synth_DFOP_par, </span>
-<span class='co'>#                           synthetic_data_for_UBA_2014[[12]]$data,</span>
-<span class='co'>#                           quiet = TRUE)</span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+
+<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span>
+<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
+  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='co'># Show details of creating the C function</span>
+<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
+  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
+  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
+#&gt;  /usr/lib/R/bin/R CMD SHLIB file21efdcf882f.c 2&gt; file21efdcf882f.c.err.txt 
+#&gt; Program source:
+#&gt;   1: #include &lt;R.h&gt;
+#&gt;   2: 
+#&gt;   3: 
+#&gt;   4: static double parms [3];
+#&gt;   5: #define k_parent_sink parms[0]
+#&gt;   6: #define k_parent_m1 parms[1]
+#&gt;   7: #define k_m1_sink parms[2]
+#&gt;   8: 
+#&gt;   9: void initpar(void (* odeparms)(int *, double *)) {
+#&gt;  10:     int N = 3;
+#&gt;  11:     odeparms(&amp;N, parms);
+#&gt;  12: }
+#&gt;  13: 
+#&gt;  14: 
+#&gt;  15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
+#&gt;  16: 
+#&gt;  17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
+#&gt;  18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
+#&gt;  19: }</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+<span class='co'># If we have several parallel metabolites </span>
+<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
+<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
+                           <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
+                           <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
+                           <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
+<span class='no'>fit_DFOP_par_c</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>,
+                          <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>,
+                          <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre>
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