Update online docs for release version

1 files changed, 33 insertions, 22 deletions

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index b2402e04..b8adde34 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -74,7 +74,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
       </span>
     </div>
 
@@ -111,6 +111,9 @@
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
   </ul>
 </li>
 <li>
@@ -119,7 +122,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -148,12 +151,12 @@
  extracts.</p>
     </div>
 
-    <pre class="usage"><span class='no'>mccall81_245T</span></pre>
+    <pre class="usage"><span class='va'>mccall81_245T</span></pre>
 
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A dataframe containing the following variables.</p><dl'>
+    <p>A dataframe containing the following variables.</p><dl>
     <dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as
                        an acronym for 2,4,5-T. T245 is a legitimate object name
                        in R, which is necessary for specifying models using
@@ -171,27 +174,31 @@
   <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></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'>"phenol"</span>),
-                         <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></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'>"anisole"</span>),
-                         <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></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'># \dontrun{</span>
-    <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                         Estimate  se_notrans   t value       Pr(&gt;t)
-#&gt; T245_0              1.038550e+02 2.184707509 47.537272 4.472189e-18
+    <pre class="examples"><div class='input'>  <span class='va'>SFO_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>,
+                         phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span><span class='op'>)</span>,
+                         anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</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'># \dontrun{</span>
+    <span class='va'>fit.1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
+</div><div class='output co'>#&gt;                         Estimate  se_notrans   t value       Pr(&gt;t)
+#&gt; T245_0              1.038550e+02 2.184707514 47.537272 4.472189e-18
 #&gt; k_T245              4.337042e-02 0.001898397 22.845818 2.276912e-13
-#&gt; k_phenol            4.050581e-01 0.298699410  1.356073 9.756993e-02
+#&gt; k_phenol            4.050581e-01 0.298699428  1.356073 9.756994e-02
 #&gt; k_anisole           6.678742e-03 0.000802144  8.326114 2.623179e-07
-#&gt; f_T245_to_phenol    6.227599e-01 0.398534147  1.562626 6.949418e-02
-#&gt; f_phenol_to_anisole 1.000000e+00 0.671844135  1.488440 7.867793e-02
-#&gt; sigma               2.514628e+00 0.490755933  5.123989 6.233163e-05
+#&gt; f_T245_to_phenol    6.227599e-01 0.398534167  1.562626 6.949418e-02
+#&gt; f_phenol_to_anisole 1.000000e+00 0.671844168  1.488440 7.867794e-02
+#&gt; sigma               2.514628e+00 0.490755943  5.123989 6.233164e-05
 #&gt;                            Lower        Upper
-#&gt; T245_0              99.246061427 1.084640e+02
+#&gt; T245_0              99.246061371 1.084640e+02
 #&gt; k_T245               0.039631621 4.746194e-02
 #&gt; k_phenol             0.218013878 7.525762e-01
 #&gt; k_anisole            0.005370739 8.305299e-03
 #&gt; f_T245_to_phenol     0.547559082 6.924813e-01
 #&gt; f_phenol_to_anisole  0.000000000 1.000000e+00
-#&gt; sigma                1.706607296 3.322649e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; sigma                1.706607296 3.322649e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
 #&gt;    T245_phenol      T245_sink phenol_anisole    phenol_sink 
-#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   1.005127e-10 
+#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   1.748047e-10 
 #&gt; 
 #&gt; $distimes
 #&gt;               DT50      DT90
@@ -199,18 +206,22 @@
 #&gt; phenol    1.711229   5.68458
 #&gt; anisole 103.784092 344.76329
 #&gt; </div><div class='input'>    <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
-    <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
-                   <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
-                   <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#&gt; <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+    <span class='va'>fit.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>,
+                   parms.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_phenol_sink <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
+                   fixed_parms <span class='op'>=</span> <span class='st'>"k_phenol_sink"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#&gt; <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; $ff
 #&gt;    T245_phenol      T245_sink phenol_anisole    phenol_sink 
-#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   1.005127e-10 
+#&gt;   6.227599e-01   3.772401e-01   1.000000e+00   1.748047e-10 
 #&gt; 
 #&gt; $distimes
 #&gt;               DT50      DT90
 #&gt; T245     15.982025  53.09114
 #&gt; phenol    1.711229   5.68458
 #&gt; anisole 103.784092 344.76329
-#&gt; </div><div class='input'>    <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): object 'fit.2' not found</span></div><div class='input'>  # }
+#&gt; </div><div class='input'>    <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): object 'fit.2' not found</span></div><div class='input'>  <span class='co'># }</span>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -227,7 +238,7 @@
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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