Static documentation rebuilt by pkgdown

7 files changed, 29 insertions, 27 deletions

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index e554432f..2a3b1c78 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -263,7 +263,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.234   0.000   0.234 
+#>   0.242   0.000   0.244 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -452,8 +452,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x5555578e66e0>
-#> <environment: 0x555559cd9780>
+#> <bytecode: 0x5555578ff9d0>
+#> <environment: 0x555559a0da40>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -475,8 +475,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555acf3f50>
-#> <environment: 0x555559cd9780>
+#> <bytecode: 0x555559b90d60>
+#> <environment: 0x555559a0da40>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -543,13 +543,13 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Sun Mar 11 22:10:21 2018"
+#> [1] "Wed Mar 21 18:14:20 2018"
 #> 
 #> $version
 #> [1] "0.9.47.1"
 #> 
 #> $Rversion
-#> [1] "3.4.3"
+#> [1] "3.4.4"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 80cac442..cb70e68c 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -150,9 +150,9 @@
                  <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</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>)
   <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.47.1 
-#&gt; R version used for fitting:       3.4.3 
-#&gt; Date of fit:     Sun Mar 11 22:10:30 2018 
-#&gt; Date of summary: Sun Mar 11 22:10:30 2018 
+#&gt; R version used for fitting:       3.4.4 
+#&gt; Date of fit:     Wed Mar 21 18:14:30 2018 
+#&gt; Date of summary: Wed Mar 21 18:14:30 2018 
 #&gt; 
 #&gt; Equations:
 #&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -162,7 +162,7 @@
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted with method Port using 246 model solutions performed in 1.318 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.403 s
 #&gt; 
 #&gt; Weighting: none
 #&gt; 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 991df1cc..8ac8295f 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -413,16 +413,16 @@
     <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
 <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.47.1 
-#&gt; R version used for fitting:       3.4.3 
-#&gt; Date of fit:     Sun Mar 11 22:10:32 2018 
-#&gt; Date of summary: Sun Mar 11 22:10:32 2018 
+#&gt; R version used for fitting:       3.4.4 
+#&gt; Date of fit:     Wed Mar 21 18:14:33 2018 
+#&gt; Date of summary: Wed Mar 21 18:14:33 2018 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted with method Port using 64 model solutions performed in 0.135 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.14 s
 #&gt; 
 #&gt; Weighting: none
 #&gt; 
@@ -491,7 +491,7 @@
   <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'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
                            <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   0.829   0.000   0.829 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt;          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#&gt;   0.834   0.000   0.835 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt;          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #&gt;          99.59848          -3.03822          -2.98030          -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 044b2d92..4768215b 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -306,7 +306,7 @@
                 <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   0.002   0.000   0.003 </div><div class='input'>  <span class='fu'>system.time</span>(
+#&gt;   0.003   0.000   0.003 </div><div class='input'>  <span class='fu'>system.time</span>(
     <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
                 <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
@@ -316,7 +316,7 @@
                 <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   0.029   0.000   0.029 </div></pre>
+#&gt;   0.033   0.000   0.032 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 65c37898..6c99f07b 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -134,7 +134,9 @@
     <tr>
       <th>cores</th>
       <td><p>The number of cores to be used for multicore processing. This is only
-    used when the <code>cluster</code> argument is <code>NULL</code>.</p></td>
+    used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines,
+    cores &gt; 1 is not supported, you need to use the <code>cluster</code> argument
+    to use multiple logical processors.</p></td>
     </tr>
     <tr>
       <th>cluster</th>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index e462fd17..37b8fff8 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -190,16 +190,16 @@
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>  <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></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='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.47.1 
-#&gt; R version used for fitting:       3.4.3 
-#&gt; Date of fit:     Sun Mar 11 22:10:41 2018 
-#&gt; Date of summary: Sun Mar 11 22:10:41 2018 
+#&gt; R version used for fitting:       3.4.4 
+#&gt; Date of fit:     Wed Mar 21 18:14:42 2018 
+#&gt; Date of summary: Wed Mar 21 18:14:42 2018 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent_sink * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted with method Port using 35 model solutions performed in 0.07 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.072 s
 #&gt; 
 #&gt; Weighting: none
 #&gt; 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 5c89f8e2..fb03cdac 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -184,9 +184,9 @@ The transformation of sets of formation fractions is fragile, as it supposes
   <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'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting:    0.9.47.1 
-#&gt; R version used for fitting:       3.4.3 
-#&gt; Date of fit:     Sun Mar 11 22:10:42 2018 
-#&gt; Date of summary: Sun Mar 11 22:10:42 2018 
+#&gt; R version used for fitting:       3.4.4 
+#&gt; Date of fit:     Wed Mar 21 18:14:43 2018 
+#&gt; Date of summary: Wed Mar 21 18:14:43 2018 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -194,7 +194,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted with method Port using 153 model solutions performed in 0.564 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.585 s
 #&gt; 
 #&gt; Weighting: none
 #&gt;