Static documentation rebuilt by pkgdown 1.1.0

1 files changed, 32 insertions, 15 deletions

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
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@@ -21,12 +21,15 @@
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+
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-  
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 <meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" />
 
 <meta property="og:description" content="This function uses the Flexible Modelling Environment package
@@ -39,8 +42,11 @@
   In each step of the optimsation, the kinetic model is solved using the
   function mkinpredict. The variance of the residuals for each
   observed variable can optionally be iteratively reweighted until convergence
-  using the argument reweight.method = "obs"." />
+  using the argument reweight.method = &quot;obs&quot;." />
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@@ -63,8 +69,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">mkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -105,6 +115,7 @@
       <ul class="nav navbar-nav navbar-right">
         
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@@ -112,12 +123,15 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Fit a kinetic model to data with one or more state variables</h1>
+    
+    <div class="hidden name"><code>mkinfit.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>This function uses the Flexible Modelling Environment package
   <code>FME</code> to create a function calculating the model cost, i.e. the
@@ -131,6 +145,7 @@
   observed variable can optionally be iteratively reweighted until convergence
   using the argument <code>reweight.method = "obs"</code>.</p>
     
+    </div>
 
     <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>,
   <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
@@ -154,7 +169,7 @@
   <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>,
   <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
     
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
@@ -384,10 +399,10 @@
     
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
+    <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
   <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
 <p>Fitting of several models to several datasets in a single call to
-  <code><a href='mmkin.html'>mmkin</a></code>.</p>
+  <code><a href='mmkin.html'>mmkin</a></code>.</p></div>
     
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
 
@@ -413,16 +428,16 @@
     <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:       3.4.4 
-#&gt; Date of fit:     Wed Mar 21 18:14:33 2018 
-#&gt; Date of summary: Wed Mar 21 18:14:33 2018 
+#&gt; R version used for fitting:       3.5.0 
+#&gt; Date of fit:     Wed Jun  6 01:21:36 2018 
+#&gt; Date of summary: Wed Jun  6 01:21:36 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 0.14 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.143 s
 #&gt; 
 #&gt; Weighting: none
 #&gt; 
@@ -490,8 +505,8 @@
   <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'># 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;   0.834   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 
+                           <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 verstrichen 
+#&gt;       0.927       0.000       0.929 </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 
@@ -597,6 +612,8 @@
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