Merge branch 'master' into mxkin

Merge DESCRIPTION manually to combine dependencies and rerun check to
update check.log

1 files changed, 51 insertions, 27 deletions

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 0eca973c..fe5bc975 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -71,7 +71,7 @@ kinetic parameters and initial values for the state variables." />
       </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">0.9.49.6</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span>
       </span>
     </div>
 
@@ -140,24 +140,49 @@ kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, u
 kinetic parameters and initial values for the state variables.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
-  <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
-  <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>mkinpredict</span>(
+  <span class='no'>x</span>,
+  <span class='no'>odeparms</span>,
+  <span class='no'>odeini</span>,
+  <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
+  <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+  <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+  <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+  <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='no'>...</span>
+)
 
 <span class='co'># S3 method for mkinmod</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
-  <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
-  <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
-  <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+<span class='fu'>mkinpredict</span>(
+  <span class='no'>x</span>,
+  <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+  <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+  <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
+  <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+  <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+  <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+  <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='no'>...</span>
+)
 
 <span class='co'># S3 method for mkinfit</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>,
-  <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
-  <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
-  <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>mkinpredict</span>(
+  <span class='no'>x</span>,
+  <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>,
+  <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>,
+  <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='st'>"auto"</span>,
+  <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+  <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+  <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+  <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='no'>...</span>
+)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -350,7 +375,7 @@ solver is used.</p></td>
                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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 verstrichen 
-#&gt;       0.004       0.000       0.003 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
+#&gt;       0.003       0.000       0.003 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(
     <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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
@@ -360,7 +385,7 @@ solver is used.</p></td>
                 <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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 verstrichen 
-#&gt;       0.021       0.000       0.022 </div><div class='input'>
+#&gt;       0.021       0.000       0.021 </div><div class='input'>
   <span class='co'># \dontrun{</span>
     <span class='co'># Predict from a fitted model</span>
     <span class='no'>f</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_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
@@ -372,10 +397,10 @@ solver is used.</p></td>
 #&gt; Sum of squared residuals at call 9: 279.9294
 #&gt; Sum of squared residuals at call 12: 200.3629
 #&gt; Sum of squared residuals at call 13: 200.3629
-#&gt; Sum of squared residuals at call 18: 197.9039
-#&gt; Sum of squared residuals at call 23: 197.9039
-#&gt; Sum of squared residuals at call 25: 196.6754
-#&gt; Sum of squared residuals at call 27: 196.6754
+#&gt; Sum of squared residuals at call 18: 197.904
+#&gt; Sum of squared residuals at call 22: 197.904
+#&gt; Sum of squared residuals at call 25: 196.6753
+#&gt; Sum of squared residuals at call 27: 196.6753
 #&gt; Sum of squared residuals at call 32: 196.5742
 #&gt; Sum of squared residuals at call 33: 196.5742
 #&gt; Sum of squared residuals at call 34: 196.5742
@@ -390,14 +415,13 @@ solver is used.</p></td>
 #&gt; Sum of squared residuals at call 58: 196.5334
 #&gt; Sum of squared residuals at call 59: 196.5334
 #&gt; Sum of squared residuals at call 65: 196.5334
-#&gt; Sum of squared residuals at call 73: 196.5334
 #&gt; Negative log-likelihood at call 75: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt;   time   parent       m1
 #&gt; 1  0.0 82.49216 0.000000
-#&gt; 2  0.1 80.00563 1.179955
-#&gt; 3  0.2 77.59404 2.312580
-#&gt; 4  0.3 75.25515 3.399419
-#&gt; 5  0.4 72.98675 4.441969
-#&gt; 6  0.5 70.78673 5.441679</div><div class='input'>  # }
+#&gt; 2  0.1 80.00563 1.179963
+#&gt; 3  0.2 77.59404 2.312596
+#&gt; 4  0.3 75.25515 3.399443
+#&gt; 5  0.4 72.98675 4.442000
+#&gt; 6  0.5 70.78673 5.441717</div><div class='input'>  # }
 
 </div></pre>
   </div>