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-rw-r--r--docs/reference/Extract.mmkin.html24
-rw-r--r--docs/reference/SFO.solution-2.pngbin0 -> 6424 bytes
-rw-r--r--docs/reference/SFO.solution.html2
-rw-r--r--docs/reference/SFORB.solution-2.pngbin0 -> 6788 bytes
-rw-r--r--docs/reference/SFORB.solution.html2
-rw-r--r--docs/reference/index.html91
-rw-r--r--docs/reference/mccall81_245T.html250
-rw-r--r--docs/reference/mkinfit.html2169
-rw-r--r--docs/reference/mkinmod.html62
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mmkin-14.pngbin0 -> 30013 bytes
-rw-r--r--docs/reference/mmkin-16.pngbin0 -> 27062 bytes
-rw-r--r--docs/reference/mmkin-18.pngbin0 -> 25359 bytes
-rw-r--r--docs/reference/mmkin-20.pngbin0 -> 18905 bytes
-rw-r--r--docs/reference/mmkin-22.pngbin0 -> 17036 bytes
-rw-r--r--docs/reference/mmkin.html1129
-rw-r--r--docs/reference/schaefer07_complex_case.html1054
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/synthetic_data_for_UBA.html872
-rw-r--r--docs/reference/transform_odeparms.html527
20 files changed, 5957 insertions, 237 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index b437fc7d..09d7513c 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -193,7 +193,7 @@
#>
#> $time
#> user system elapsed
-#> 0.268 0.000 0.267
+#> 0.256 0.000 0.255
#>
#> $mkinmod
#> <mkinmod> model generated with
@@ -379,7 +379,7 @@
#> }
#> return(mC)
#> }
-#> <environment: 0x3a2f9e8>
+#> <environment: 0x3fc5fa0>
#>
#> $cost_notrans
#> function (P)
@@ -401,7 +401,7 @@
#> scaleVar = scaleVar)
#> return(mC)
#> }
-#> <environment: 0x3a2f9e8>
+#> <environment: 0x3fc5fa0>
#>
#> $hessian_notrans
#> parent_0 alpha beta
@@ -467,7 +467,7 @@
#> 99.66619
#>
#> $date
-#> [1] "Thu Nov 17 22:56:49 2016"
+#> [1] "Fri Nov 18 15:19:25 2016"
#>
#> attr(,"class")
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
@@ -546,7 +546,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.116 0.000 0.115
+#&gt; 0.064 0.000 0.066
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -733,7 +733,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x42fb560&gt;
+#&gt; &lt;environment: 0x3b66828&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -755,7 +755,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x42fb560&gt;
+#&gt; &lt;environment: 0x3b66828&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -818,7 +818,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Thu Nov 17 22:56:48 2016&quot;
+#&gt; [1] &quot;Fri Nov 18 15:19:25 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#&gt; [[1]]
@@ -894,7 +894,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.116 0.000 0.115
+#&gt; 0.064 0.000 0.066
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -1081,7 +1081,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x42fb560&gt;
+#&gt; &lt;environment: 0x3b66828&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -1103,7 +1103,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x42fb560&gt;
+#&gt; &lt;environment: 0x3b66828&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -1166,7 +1166,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Thu Nov 17 22:56:48 2016&quot;
+#&gt; [1] &quot;Fri Nov 18 15:19:25 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;
diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png
new file mode 100644
index 00000000..78c083c3
--- /dev/null
+++ b/docs/reference/SFO.solution-2.png
Binary files differ
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 2ead8f24..30d7acdf 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -110,7 +110,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre>
+ <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><img src='SFO.solution-2.png' alt='' width='540' height='400' /></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png
new file mode 100644
index 00000000..9625debf
--- /dev/null
+++ b/docs/reference/SFORB.solution-2.png
Binary files differ
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index be425d83..e8ee3e04 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -119,7 +119,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre>
+ <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><img src='SFORB.solution-2.png' alt='' width='540' height='400' /></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 32455baa..2d052a80 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,14 +86,14 @@
<p class="section-desc"><p>Essential functionality</p></p>
- <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p>
+ <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p>
<ul>
- <li><code><a href="mkinfit.html">mkinfit</a></code></li>
+ <li><code><a href="mkinmod.html">mkinmod</a></code></li>
</ul>
- <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p>
+ <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p>
<ul>
- <li><code><a href="mkinmod.html">mkinmod</a></code></li>
+ <li><code><a href="mkinfit.html">mkinfit</a></code></li>
</ul>
<p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p>
@@ -104,35 +104,35 @@
<p class="section-desc"><p>Functions working with mkinfit objects</p></p>
- <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p>
+ <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
<ul>
- <li><code><a href="endpoints.html">endpoints</a></code></li>
+ <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
</ul>
- <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p>
+ <p><a href="summary.mkinfit.html">Summary method for class &quot;mkinfit&quot;</a></p>
<ul>
- <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
+ <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
</ul>
- <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
- list(list(&quot;mkinfit&quot;))</a></p>
+ <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p>
<ul>
- <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
+ <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
</ul>
- <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p>
+ <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
+ list(list(&quot;mkinfit&quot;))</a></p>
<ul>
- <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
+ <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
</ul>
- <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
+ <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p>
<ul>
- <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
+ <li><code><a href="endpoints.html">endpoints</a></code></li>
</ul>
- <p><a href="summary.mkinfit.html">Summary method for class &quot;mkinfit&quot;</a></p>
+ <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p>
<ul>
- <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
+ <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
</ul>
<h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2>
<p class="section-desc"><p>Functions working with aggregated results</p></p>
@@ -151,9 +151,14 @@
<p class="section-desc"></p>
- <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p>
+ <p><a href="FOCUS_2006_datasets.html">Datasets A to F from the FOCUS Kinetics report from 2006</a></p>
<ul>
- <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
+ <li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code></li>
+ </ul>
+
+ <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p>
+ <ul>
+ <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
</ul>
<p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p>
@@ -166,9 +171,9 @@
<li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li>
</ul>
- <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p>
+ <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p>
<ul>
- <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
+ <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
</ul>
<p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p>
@@ -176,47 +181,47 @@
<li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
</ul>
- <p><a href="mkinds.html">A dataset class for mkin</a></p>
+ <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p>
<ul>
- <li><code><a href="mkinds.html">mkinds</a></code></li>
+ <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
</ul>
- <p><a href="print.mkinds.html">Print mkinds objects</a></p>
+ <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p>
<ul>
- <li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
+ <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
</ul>
- <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p>
+ <p><a href="mkinds.html">A dataset class for mkin</a></p>
<ul>
- <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
+ <li><code><a href="mkinds.html">mkinds</a></code></li>
</ul>
- <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p>
+ <p><a href="print.mkinds.html">Print mkinds objects</a></p>
<ul>
- <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
+ <li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
</ul>
<h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
<p class="section-desc"></p>
- <p><a href="geometric_mean.html">Calculate the geometric mean</a></p>
+ <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
<ul>
- <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
+ <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
</ul>
- <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p>
+ <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p>
<ul>
- <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
+ <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
</ul>
- <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p>
+ <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p>
<ul>
- <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
+ <li><code><a href="mkinsub.html">mkinsub</a></code></li>
</ul>
- <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
+ <p><a href="print.mkinmod.html">Print mkinmod objects</a></p>
<ul>
- <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
+ <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
</ul>
<p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p>
@@ -224,19 +229,19 @@
<li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
</ul>
- <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p>
+ <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p>
<ul>
- <li><code><a href="mkinsub.html">mkinsub</a></code></li>
+ <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
</ul>
- <p><a href="print.mkinmod.html">Print mkinmod objects</a></p>
+ <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p>
<ul>
- <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
+ <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
</ul>
- <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p>
+ <p><a href="geometric_mean.html">Calculate the geometric mean</a></p>
<ul>
- <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
+ <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
</ul>
<h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2>
<p class="section-desc"><p>Parent only model solutions</p></p>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 4314c84e..7b294129 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -111,19 +111,253 @@
<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'>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'>"phenol"</span>),
<span class='kw'>phenol</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'>"anisole"</span>),
- <span class='kw'>anisole</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'>## Not run: ------------------------------------</span>
-<span class='co'># fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
-<span class='co'># summary(fit.1, data = FALSE)</span>
-<span class='co'># </span>
-<span class='co'>## ---------------------------------------------</span>
+ <span class='kw'>anisole</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='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'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>))</div><div class='output co'>#&gt; Model cost at call 1 : 13655.2
+#&gt; Model cost at call 2 : 13655.2
+#&gt; Model cost at call 8 : 9191.59
+#&gt; Model cost at call 16 : 5663.584
+#&gt; Model cost at call 17 : 5663.582
+#&gt; Model cost at call 18 : 5663.566
+#&gt; Model cost at call 19 : 5663.55
+#&gt; Model cost at call 23 : 3035.567
+#&gt; Model cost at call 24 : 3035.566
+#&gt; Model cost at call 26 : 3035.561
+#&gt; Model cost at call 27 : 3035.559
+#&gt; Model cost at call 28 : 3035.558
+#&gt; Model cost at call 30 : 2252.97
+#&gt; Model cost at call 31 : 2252.965
+#&gt; Model cost at call 32 : 2252.965
+#&gt; Model cost at call 36 : 2252.958
+#&gt; Model cost at call 37 : 1220.201
+#&gt; Model cost at call 38 : 1220.2
+#&gt; Model cost at call 39 : 1220.199
+#&gt; Model cost at call 41 : 1220.183
+#&gt; Model cost at call 45 : 507.1358
+#&gt; Model cost at call 48 : 507.1353
+#&gt; Model cost at call 52 : 198.5695
+#&gt; Model cost at call 55 : 198.5694
+#&gt; Model cost at call 60 : 175.8239
+#&gt; Model cost at call 63 : 175.8239
+#&gt; Model cost at call 67 : 170.6316
+#&gt; Model cost at call 69 : 170.6316
+#&gt; Model cost at call 74 : 165.881
+#&gt; Model cost at call 77 : 165.881
+#&gt; Model cost at call 81 : 161.6423
+#&gt; Model cost at call 84 : 161.6423
+#&gt; Model cost at call 88 : 158.2953
+#&gt; Model cost at call 91 : 158.2953
+#&gt; Model cost at call 95 : 156.7311
+#&gt; Model cost at call 97 : 156.731
+#&gt; Model cost at call 103 : 155.998
+#&gt; Model cost at call 106 : 155.998
+#&gt; Model cost at call 110 : 155.6263
+#&gt; Model cost at call 113 : 155.6262
+#&gt; Model cost at call 116 : 155.6262
+#&gt; Model cost at call 117 : 155.1202
+#&gt; Model cost at call 120 : 155.1202
+#&gt; Model cost at call 124 : 154.4133
+#&gt; Model cost at call 125 : 153.8489
+#&gt; Model cost at call 126 : 152.7413
+#&gt; Model cost at call 129 : 152.7413
+#&gt; Model cost at call 132 : 152.7413
+#&gt; Model cost at call 133 : 150.3995
+#&gt; Model cost at call 134 : 148.7256
+#&gt; Model cost at call 135 : 147.2618
+#&gt; Model cost at call 137 : 147.2618
+#&gt; Model cost at call 139 : 147.2618
+#&gt; Model cost at call 142 : 145.115
+#&gt; Model cost at call 144 : 145.115
+#&gt; Model cost at call 145 : 145.115
+#&gt; Model cost at call 146 : 145.115
+#&gt; Model cost at call 147 : 145.115
+#&gt; Model cost at call 150 : 143.7878
+#&gt; Model cost at call 157 : 142.8531
+#&gt; Model cost at call 160 : 142.8531
+#&gt; Model cost at call 164 : 142.7325
+#&gt; Model cost at call 167 : 142.7325
+#&gt; Model cost at call 169 : 142.7325
+#&gt; Model cost at call 172 : 141.8393
+#&gt; Model cost at call 173 : 141.8393
+#&gt; Model cost at call 174 : 141.8393
+#&gt; Model cost at call 179 : 141.3446
+#&gt; Model cost at call 180 : 141.3446
+#&gt; Model cost at call 181 : 141.3446
+#&gt; Model cost at call 186 : 141.1111
+#&gt; Model cost at call 193 : 140.7786
+#&gt; Model cost at call 200 : 140.451
+#&gt; Model cost at call 207 : 140.1395
+#&gt; Model cost at call 214 : 139.7903
+#&gt; Model cost at call 221 : 139.5476
+#&gt; Model cost at call 228 : 139.4441
+#&gt; Model cost at call 235 : 139.3204
+#&gt; Model cost at call 242 : 139.2508
+#&gt; Model cost at call 249 : 139.1891
+#&gt; Model cost at call 256 : 139.1561
+#&gt; Model cost at call 263 : 139.137
+#&gt; Model cost at call 270 : 139.1278
+#&gt; Model cost at call 271 : 139.1278
+#&gt; Model cost at call 279 : 139.1211
+#&gt; Model cost at call 280 : 139.1211
+#&gt; Model cost at call 281 : 139.1211
+#&gt; Model cost at call 282 : 139.1211
+#&gt; Model cost at call 286 : 139.1179
+#&gt; Model cost at call 287 : 139.1179
+#&gt; Model cost at call 291 : 139.1179
+#&gt; Model cost at call 294 : 139.1179
+#&gt; Model cost at call 298 : 139.1158
+#&gt; Model cost at call 299 : 139.1158
+#&gt; Model cost at call 302 : 139.1158
+#&gt; Model cost at call 310 : 139.1148
+#&gt; Model cost at call 311 : 139.1148
+#&gt; Model cost at call 315 : 139.1148
+#&gt; Model cost at call 322 : 139.1143
+#&gt; Model cost at call 323 : 139.1143
+#&gt; Model cost at call 326 : 139.1143
+#&gt; Model cost at call 334 : 139.114
+#&gt; Model cost at call 335 : 139.114
+#&gt; Model cost at call 338 : 139.114
+#&gt; Model cost at call 339 : 139.114
+#&gt; Model cost at call 346 : 139.1139
+#&gt; Model cost at call 347 : 139.1139
+#&gt; Model cost at call 350 : 139.1139
+#&gt; Model cost at call 351 : 139.1139
+#&gt; Model cost at call 358 : 139.1139
+#&gt; Model cost at call 359 : 139.1139
+#&gt; Model cost at call 362 : 139.1139
+#&gt; Model cost at call 363 : 139.1139
+#&gt; Model cost at call 370 : 139.1138
+#&gt; Model cost at call 382 : 139.1138
+#&gt; Model cost at call 390 : 139.1138
+#&gt; Model cost at call 395 : 139.1138
+#&gt; Model cost at call 403 : 139.1138
+#&gt; Model cost at call 408 : 139.1138
+#&gt; Model cost at call 416 : 139.1138
+#&gt; Model cost at call 421 : 139.1138
+#&gt; Model cost at call 429 : 139.1138
+#&gt; Model cost at call 434 : 139.1138
+#&gt; Model cost at call 442 : 139.1138
+#&gt; Model cost at call 447 : 139.1138
+#&gt; Model cost at call 455 : 139.1138
+#&gt; Model cost at call 460 : 139.1138
+#&gt; Model cost at call 468 : 139.1138
+#&gt; Model cost at call 473 : 139.1138
+#&gt; Model cost at call 481 : 139.1138
+#&gt; Model cost at call 486 : 139.1138
+#&gt; Model cost at call 494 : 139.1138
+#&gt; Model cost at call 499 : 139.1138
+#&gt; Model cost at call 507 : 139.1138
+#&gt; Model cost at call 512 : 139.1138
+#&gt; Model cost at call 519 : 139.1138
+#&gt; Model cost at call 520 : 139.1138
+#&gt; Model cost at call 525 : 139.1138
+#&gt; Model cost at call 538 : 139.1138
+#&gt; Model cost at call 545 : 139.1138
+#&gt; Model cost at call 546 : 139.1138
+#&gt; Model cost at call 551 : 139.1138
+#&gt; Model cost at call 558 : 139.1138
+#&gt; Model cost at call 559 : 139.1138
+#&gt; Model cost at call 564 : 139.1138
+#&gt; Model cost at call 571 : 139.1138
+#&gt; Model cost at call 580 : 139.1138
+#&gt; Model cost at call 588 : 139.1138 </div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
+#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:33 2016
+#&gt; Date of summary: Fri Nov 18 15:19:33 2016
+#&gt;
+#&gt;
+#&gt; Warning: Optimisation by method Port did not converge.
+#&gt; Convergence code is 1
+#&gt;
+#&gt;
+#&gt; Equations:
+#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
+#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#&gt; k_phenol_anisole * phenol
+#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 590 model solutions performed in 3.45 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; T245_0 100.9000 state
+#&gt; k_T245_sink 0.1000 deparm
+#&gt; k_T245_phenol 0.1001 deparm
+#&gt; k_phenol_sink 0.1002 deparm
+#&gt; k_phenol_anisole 0.1003 deparm
+#&gt; k_anisole_sink 0.1004 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; T245_0 100.900000 -Inf Inf
+#&gt; log_k_T245_sink -2.302585 -Inf Inf
+#&gt; log_k_T245_phenol -2.301586 -Inf Inf
+#&gt; log_k_phenol_sink -2.300587 -Inf Inf
+#&gt; log_k_phenol_anisole -2.299590 -Inf Inf
+#&gt; log_k_anisole_sink -2.298593 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; phenol_0 0 state
+#&gt; anisole_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; T245_0 103.9000 NA NA NA
+#&gt; log_k_T245_sink -4.1130 NA NA NA
+#&gt; log_k_T245_phenol -3.6120 NA NA NA
+#&gt; log_k_phenol_sink -26.3900 NA NA NA
+#&gt; log_k_phenol_anisole -0.9037 NA NA NA
+#&gt; log_k_anisole_sink -5.0090 NA NA NA
+#&gt;
+#&gt; Parameter correlation:</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#&gt; Could not estimate covariance matrix; singular system:
+#&gt;
+#&gt; Residual standard error: 2.78 on 18 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA
+#&gt; k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA
+#&gt; k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA
+#&gt; k_phenol_sink 3.457e-12 1.230e-11 5.000e-01 NA NA
+#&gt; k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA
+#&gt; k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 10.070 6 16
+#&gt; T245 7.908 3 5
+#&gt; phenol 106.445 2 5
+#&gt; anisole 5.379 1 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; T245_sink 3.772e-01
+#&gt; T245_phenol 6.228e-01
+#&gt; phenol_sink 8.534e-12
+#&gt; phenol_anisole 1.000e+00
+#&gt; anisole_sink 1.000e+00
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; T245 15.982 53.091
+#&gt; phenol 1.711 5.685
+#&gt; anisole 103.784 344.763</div><div class='input'>
<span class='co'># No covariance matrix and 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'>subset</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'>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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Nov 17 22:56:55 2016
-#&gt; Date of summary: Thu Nov 17 22:56:55 2016
+#&gt; Date of fit: Fri Nov 18 15:19:35 2016
+#&gt; Date of summary: Fri Nov 18 15:19:35 2016
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +367,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.457 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.477 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 891bc18b..f6ffd21d 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -359,15 +359,15 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Nov 17 22:56:57 2016
-#&gt; Date of summary: Thu Nov 17 22:56:57 2016
+#&gt; Date of fit: Fri Nov 18 15:19:37 2016
+#&gt; Date of summary: Fri Nov 18 15:19:37 2016
#&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 0.158 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.152 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -436,7 +436,7 @@
<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; 1.168 1.260 0.924 </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; 1.220 1.184 0.904 </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
@@ -448,63 +448,2114 @@
#&gt; DT50 DT90
#&gt; parent 7.022929 23.32967
#&gt; m1 131.760712 437.69961
-#&gt; </div><div class='input'><span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span>
-<span class='co'># print(system.time(fit.deSolve &lt;- mkinfit(SFO_SFO, FOCUS_2006_D,</span>
-<span class='co'># solution_type = "deSolve")))</span>
-<span class='co'># coef(fit.deSolve)</span>
-<span class='co'># endpoints(fit.deSolve)</span>
-<span class='co'>## ---------------------------------------------</span>
+#&gt; </div><div class='input'>
+<span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span>
+<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit.deSolve</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'>"deSolve"</span>)))</div><div class='output co'>#&gt; Model cost at call 1 : 18915.53
+#&gt; Model cost at call 2 : 18915.53
+#&gt; Model cost at call 6 : 11424.02
+#&gt; Model cost at call 10 : 11424
+#&gt; Model cost at call 12 : 4094.396
+#&gt; Model cost at call 16 : 4094.396
+#&gt; Model cost at call 19 : 1340.595
+#&gt; Model cost at call 20 : 1340.593
+#&gt; Model cost at call 25 : 1072.239
+#&gt; Model cost at call 28 : 1072.236
+#&gt; Model cost at call 30 : 874.2614
+#&gt; Model cost at call 33 : 874.2611
+#&gt; Model cost at call 35 : 616.2379
+#&gt; Model cost at call 37 : 616.2374
+#&gt; Model cost at call 40 : 467.4388
+#&gt; Model cost at call 42 : 467.4382
+#&gt; Model cost at call 46 : 398.2914
+#&gt; Model cost at call 48 : 398.2914
+#&gt; Model cost at call 49 : 398.2913
+#&gt; Model cost at call 51 : 395.0712
+#&gt; Model cost at call 54 : 395.0711
+#&gt; Model cost at call 56 : 378.3298
+#&gt; Model cost at call 59 : 378.3298
+#&gt; Model cost at call 62 : 376.9812
+#&gt; Model cost at call 64 : 376.9811
+#&gt; Model cost at call 67 : 375.2085
+#&gt; Model cost at call 69 : 375.2085
+#&gt; Model cost at call 70 : 375.2085
+#&gt; Model cost at call 71 : 375.2085
+#&gt; Model cost at call 72 : 374.5723
+#&gt; Model cost at call 74 : 374.5723
+#&gt; Model cost at call 77 : 374.0075
+#&gt; Model cost at call 79 : 374.0075
+#&gt; Model cost at call 80 : 374.0075
+#&gt; Model cost at call 82 : 373.1711
+#&gt; Model cost at call 84 : 373.1711
+#&gt; Model cost at call 87 : 372.6445
+#&gt; Model cost at call 88 : 372.1614
+#&gt; Model cost at call 90 : 372.1614
+#&gt; Model cost at call 91 : 372.1614
+#&gt; Model cost at call 94 : 371.6464
+#&gt; Model cost at call 99 : 371.4299
+#&gt; Model cost at call 101 : 371.4299
+#&gt; Model cost at call 104 : 371.407
+#&gt; Model cost at call 106 : 371.407
+#&gt; Model cost at call 107 : 371.407
+#&gt; Model cost at call 109 : 371.2524
+#&gt; Model cost at call 113 : 371.2524
+#&gt; Model cost at call 114 : 371.2136
+#&gt; Model cost at call 115 : 371.2136
+#&gt; Model cost at call 116 : 371.2136
+#&gt; Model cost at call 119 : 371.2134
+#&gt; Model cost at call 120 : 371.2134
+#&gt; Model cost at call 122 : 371.2134
+#&gt; Model cost at call 123 : 371.2134
+#&gt; Model cost at call 125 : 371.2134
+#&gt; Model cost at call 126 : 371.2134
+#&gt; Model cost at call 135 : 371.2134
+#&gt; Model cost at call 147 : 371.2134
+#&gt; Model cost at call 152 : 371.2134
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; user system elapsed
+#&gt; 0.712 0.040 0.707 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</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.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt; parent_sink parent_m1 m1_sink
+#&gt; 0.485524 0.514476 1.000000
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 7.022929 23.32967
+#&gt; m1 131.760713 437.69961
+#&gt; </div><div class='input'>
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span>
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># FOMC_SFO &lt;- mkinmod(</span>
-<span class='co'># parent = mkinsub("FOMC", "m1"),</span>
-<span class='co'># m1 = mkinsub("SFO"))</span>
-<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span>
-<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D)</span>
-<span class='co'># # Use starting parameters from parent only FOMC fit</span>
-<span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span>
-<span class='co'># fit.FOMC_SFO &lt;- mkinfit(FOMC_SFO, FOCUS_2006_D,</span>
-<span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span>
-<span class='co'># </span>
-<span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
-<span class='co'># SFORB_SFO &lt;- mkinmod(</span>
-<span class='co'># parent = list(type = "SFORB", to = "m1", sink = TRUE),</span>
-<span class='co'># m1 = list(type = "SFO"))</span>
-<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span>
-<span class='co'># fit.SFORB_SFO &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D)</span>
-<span class='co'># fit.SFORB_SFO.deSolve &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")</span>
-<span class='co'># # Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
-<span class='co'># fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)</span>
-<span class='co'># fit.SFORB_SFO &lt;- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)</span>
-<span class='co'>## ---------------------------------------------</span>
-
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># # Weighted fits, including IRLS</span>
-<span class='co'># SFO_SFO.ff &lt;- mkinmod(parent = mkinsub("SFO", "m1"),</span>
-<span class='co'># m1 = mkinsub("SFO"), use_of_ff = "max")</span>
-<span class='co'># f.noweight &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span>
-<span class='co'># summary(f.noweight)</span>
-<span class='co'># f.irls &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")</span>
-<span class='co'># summary(f.irls)</span>
-<span class='co'># f.w.mean &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")</span>
-<span class='co'># summary(f.w.mean)</span>
-<span class='co'># f.w.value &lt;- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value")</span>
-<span class='co'># summary(f.w.value)</span>
-<span class='co'>## ---------------------------------------------</span>
-
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># # Manual weighting</span>
-<span class='co'># dw &lt;- FOCUS_2006_D</span>
-<span class='co'># errors &lt;- c(parent = 2, m1 = 1)</span>
-<span class='co'># dw$err.man &lt;- errors[FOCUS_2006_D$name]</span>
-<span class='co'># f.w.man &lt;- mkinfit(SFO_SFO.ff, dw, err = "err.man")</span>
-<span class='co'># summary(f.w.man)</span>
-<span class='co'># f.w.man.irls &lt;- mkinfit(SFO_SFO.ff, dw, err = "err.man",</span>
-<span class='co'># reweight.method = "obs")</span>
-<span class='co'># summary(f.w.man.irls)</span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+
+<span class='no'>FOMC_SFO</span> <span class='kw'>&lt;-</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'>"FOMC"</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='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18857.28
+#&gt; Model cost at call 4 : 18857.28
+#&gt; Model cost at call 5 : 18857.28
+#&gt; Model cost at call 8 : 15273.94
+#&gt; Model cost at call 9 : 15273.93
+#&gt; Model cost at call 12 : 15273.67
+#&gt; Model cost at call 13 : 15273.64
+#&gt; Model cost at call 14 : 12764.42
+#&gt; Model cost at call 15 : 8382.7
+#&gt; Model cost at call 20 : 8382.696
+#&gt; Model cost at call 23 : 2729.177
+#&gt; Model cost at call 24 : 2729.175
+#&gt; Model cost at call 26 : 2729.164
+#&gt; Model cost at call 30 : 2299.383
+#&gt; Model cost at call 34 : 2299.379
+#&gt; Model cost at call 35 : 2299.373
+#&gt; Model cost at call 36 : 1944.782
+#&gt; Model cost at call 40 : 1944.782
+#&gt; Model cost at call 42 : 1328.087
+#&gt; Model cost at call 43 : 908.661
+#&gt; Model cost at call 44 : 908.6604
+#&gt; Model cost at call 50 : 877.3556
+#&gt; Model cost at call 51 : 877.3554
+#&gt; Model cost at call 54 : 877.3546
+#&gt; Model cost at call 56 : 769.5186
+#&gt; Model cost at call 59 : 769.5157
+#&gt; Model cost at call 62 : 690.3426
+#&gt; Model cost at call 66 : 690.3425
+#&gt; Model cost at call 68 : 608.4032
+#&gt; Model cost at call 72 : 608.4031
+#&gt; Model cost at call 73 : 608.4031
+#&gt; Model cost at call 74 : 601.5178
+#&gt; Model cost at call 78 : 601.5174
+#&gt; Model cost at call 79 : 601.5174
+#&gt; Model cost at call 80 : 459.9885
+#&gt; Model cost at call 81 : 459.9883
+#&gt; Model cost at call 83 : 459.9878
+#&gt; Model cost at call 87 : 447.0145
+#&gt; Model cost at call 91 : 447.0145
+#&gt; Model cost at call 94 : 445.7322
+#&gt; Model cost at call 97 : 445.7322
+#&gt; Model cost at call 99 : 445.7322
+#&gt; Model cost at call 100 : 444.6965
+#&gt; Model cost at call 103 : 444.6965
+#&gt; Model cost at call 106 : 442.9742
+#&gt; Model cost at call 109 : 442.9742
+#&gt; Model cost at call 112 : 439.9665
+#&gt; Model cost at call 115 : 439.9665
+#&gt; Model cost at call 116 : 439.9664
+#&gt; Model cost at call 118 : 435.0752
+#&gt; Model cost at call 121 : 435.0751
+#&gt; Model cost at call 124 : 430.4718
+#&gt; Model cost at call 127 : 430.4717
+#&gt; Model cost at call 132 : 424.7004
+#&gt; Model cost at call 134 : 424.7003
+#&gt; Model cost at call 138 : 423.6102
+#&gt; Model cost at call 141 : 423.6102
+#&gt; Model cost at call 142 : 423.6102
+#&gt; Model cost at call 144 : 421.1786
+#&gt; Model cost at call 147 : 421.1786
+#&gt; Model cost at call 148 : 421.1786
+#&gt; Model cost at call 150 : 418.1431
+#&gt; Model cost at call 151 : 412.8665
+#&gt; Model cost at call 152 : 396.6067
+#&gt; Model cost at call 154 : 396.6067
+#&gt; Model cost at call 158 : 391.0492
+#&gt; Model cost at call 160 : 391.0492
+#&gt; Model cost at call 164 : 385.8205
+#&gt; Model cost at call 165 : 385.8205
+#&gt; Model cost at call 170 : 379.7674
+#&gt; Model cost at call 171 : 379.7674
+#&gt; Model cost at call 172 : 379.7674
+#&gt; Model cost at call 176 : 374.9389
+#&gt; Model cost at call 177 : 374.9389
+#&gt; Model cost at call 182 : 372.727
+#&gt; Model cost at call 185 : 372.727
+#&gt; Model cost at call 188 : 371.5297
+#&gt; Model cost at call 194 : 370.3738
+#&gt; Model cost at call 195 : 370.3738
+#&gt; Model cost at call 200 : 370.0182
+#&gt; Model cost at call 206 : 369.8634
+#&gt; Model cost at call 212 : 369.8188
+#&gt; Model cost at call 213 : 369.8188
+#&gt; Model cost at call 219 : 369.8114
+#&gt; Model cost at call 221 : 369.8114
+#&gt; Model cost at call 224 : 369.8114
+#&gt; Model cost at call 226 : 369.8114
+#&gt; Model cost at call 230 : 369.8105
+#&gt; Model cost at call 231 : 369.8105
+#&gt; Model cost at call 235 : 369.8105
+#&gt; Model cost at call 236 : 369.8105
+#&gt; Model cost at call 237 : 369.8105
+#&gt; Model cost at call 238 : 369.8105
+#&gt; Model cost at call 249 : 369.8105
+#&gt; Model cost at call 260 : 369.8105
+#&gt; Model cost at call 275 : 369.8105
+#&gt; Model cost at call 276 : 369.8105
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span>
+<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3237.008
+#&gt; Model cost at call 3 : 3237.007
+#&gt; Model cost at call 6 : 671.2571
+#&gt; Model cost at call 7 : 671.2559
+#&gt; Model cost at call 8 : 671.2301
+#&gt; Model cost at call 9 : 671.2249
+#&gt; Model cost at call 10 : 468.4899
+#&gt; Model cost at call 12 : 468.4899
+#&gt; Model cost at call 14 : 371.3486
+#&gt; Model cost at call 16 : 371.3485
+#&gt; Model cost at call 18 : 346.2972
+#&gt; Model cost at call 19 : 346.2971
+#&gt; Model cost at call 20 : 346.297
+#&gt; Model cost at call 21 : 346.2969
+#&gt; Model cost at call 22 : 269.7053
+#&gt; Model cost at call 23 : 269.7053
+#&gt; Model cost at call 26 : 243.9936
+#&gt; Model cost at call 27 : 235.1625
+#&gt; Model cost at call 28 : 235.1624
+#&gt; Model cost at call 30 : 235.1624
+#&gt; Model cost at call 31 : 224.2195
+#&gt; Model cost at call 35 : 218.1922
+#&gt; Model cost at call 36 : 218.1922
+#&gt; Model cost at call 38 : 218.1922
+#&gt; Model cost at call 39 : 211.5012
+#&gt; Model cost at call 41 : 211.5012
+#&gt; Model cost at call 43 : 207.9511
+#&gt; Model cost at call 44 : 207.9511
+#&gt; Model cost at call 47 : 206.5377
+#&gt; Model cost at call 51 : 205.8736
+#&gt; Model cost at call 55 : 205.5625
+#&gt; Model cost at call 59 : 205.4704
+#&gt; Model cost at call 63 : 205.4499
+#&gt; Model cost at call 67 : 205.448
+#&gt; Model cost at call 69 : 205.448
+#&gt; Model cost at call 70 : 205.448
+#&gt; Model cost at call 73 : 205.448
+#&gt; Model cost at call 74 : 205.4478
+#&gt; Model cost at call 75 : 205.4478
+#&gt; Model cost at call 77 : 205.4478
+#&gt; Model cost at call 79 : 205.4478
+#&gt; Model cost at call 84 : 205.4478
+#&gt; Model cost at call 95 : 205.4478
+#&gt; Model cost at call 98 : 205.4478
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
+ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15169.96
+#&gt; Model cost at call 2 : 15169.96
+#&gt; Model cost at call 7 : 8247.462
+#&gt; Model cost at call 14 : 6734.371
+#&gt; Model cost at call 15 : 6734.339
+#&gt; Model cost at call 16 : 6734.136
+#&gt; Model cost at call 20 : 4855.056
+#&gt; Model cost at call 24 : 4855.038
+#&gt; Model cost at call 27 : 1239.986
+#&gt; Model cost at call 29 : 1239.985
+#&gt; Model cost at call 34 : 1030.523
+#&gt; Model cost at call 38 : 1030.523
+#&gt; Model cost at call 40 : 894.2766
+#&gt; Model cost at call 43 : 894.275
+#&gt; Model cost at call 46 : 750.3629
+#&gt; Model cost at call 49 : 750.3623
+#&gt; Model cost at call 52 : 627.6819
+#&gt; Model cost at call 55 : 627.6818
+#&gt; Model cost at call 58 : 546.2947
+#&gt; Model cost at call 61 : 546.2944
+#&gt; Model cost at call 65 : 502.5529
+#&gt; Model cost at call 69 : 502.5525
+#&gt; Model cost at call 70 : 502.5525
+#&gt; Model cost at call 71 : 475.2423
+#&gt; Model cost at call 72 : 465.5298
+#&gt; Model cost at call 75 : 465.5298
+#&gt; Model cost at call 76 : 465.5297
+#&gt; Model cost at call 78 : 464.9476
+#&gt; Model cost at call 81 : 464.9476
+#&gt; Model cost at call 82 : 464.9473
+#&gt; Model cost at call 84 : 426.9626
+#&gt; Model cost at call 88 : 426.9626
+#&gt; Model cost at call 90 : 414.5235
+#&gt; Model cost at call 93 : 414.5234
+#&gt; Model cost at call 96 : 412.1478
+#&gt; Model cost at call 99 : 412.1477
+#&gt; Model cost at call 100 : 412.1477
+#&gt; Model cost at call 101 : 412.1477
+#&gt; Model cost at call 102 : 394.146
+#&gt; Model cost at call 105 : 394.146
+#&gt; Model cost at call 106 : 394.146
+#&gt; Model cost at call 107 : 394.146
+#&gt; Model cost at call 108 : 384.2002
+#&gt; Model cost at call 112 : 384.2001
+#&gt; Model cost at call 113 : 384.2001
+#&gt; Model cost at call 115 : 380.5495
+#&gt; Model cost at call 119 : 380.5494
+#&gt; Model cost at call 120 : 380.5494
+#&gt; Model cost at call 121 : 378.4803
+#&gt; Model cost at call 123 : 378.4802
+#&gt; Model cost at call 124 : 378.4792
+#&gt; Model cost at call 127 : 374.8432
+#&gt; Model cost at call 129 : 374.8431
+#&gt; Model cost at call 133 : 372.8364
+#&gt; Model cost at call 136 : 372.8364
+#&gt; Model cost at call 137 : 372.8363
+#&gt; Model cost at call 138 : 372.8363
+#&gt; Model cost at call 141 : 372.668
+#&gt; Model cost at call 145 : 372.6679
+#&gt; Model cost at call 147 : 372.5882
+#&gt; Model cost at call 150 : 372.5882
+#&gt; Model cost at call 153 : 372.4828
+#&gt; Model cost at call 156 : 372.4828
+#&gt; Model cost at call 159 : 372.3639
+#&gt; Model cost at call 162 : 372.3639
+#&gt; Model cost at call 163 : 372.3639
+#&gt; Model cost at call 164 : 372.3639
+#&gt; Model cost at call 165 : 372.1959
+#&gt; Model cost at call 168 : 372.1959
+#&gt; Model cost at call 171 : 371.9627
+#&gt; Model cost at call 172 : 371.7467
+#&gt; Model cost at call 173 : 371.1161
+#&gt; Model cost at call 174 : 370.3326
+#&gt; Model cost at call 177 : 370.3326
+#&gt; Model cost at call 178 : 370.3326
+#&gt; Model cost at call 180 : 370.3267
+#&gt; Model cost at call 186 : 370.0471
+#&gt; Model cost at call 187 : 370.0471
+#&gt; Model cost at call 193 : 369.9649
+#&gt; Model cost at call 194 : 369.9649
+#&gt; Model cost at call 196 : 369.9649
+#&gt; Model cost at call 199 : 369.8684
+#&gt; Model cost at call 200 : 369.8684
+#&gt; Model cost at call 204 : 369.8684
+#&gt; Model cost at call 206 : 369.8349
+#&gt; Model cost at call 207 : 369.8349
+#&gt; Model cost at call 209 : 369.8349
+#&gt; Model cost at call 210 : 369.8349
+#&gt; Model cost at call 211 : 369.8349
+#&gt; Model cost at call 212 : 369.8105
+#&gt; Model cost at call 214 : 369.8105
+#&gt; Model cost at call 218 : 369.8105
+#&gt; Model cost at call 220 : 369.8105
+#&gt; Model cost at call 225 : 369.8105
+#&gt; Model cost at call 229 : 369.8105
+#&gt; Model cost at call 231 : 369.8105
+#&gt; Model cost at call 232 : 369.8105
+#&gt; Model cost at call 236 : 369.8105
+#&gt; Model cost at call 239 : 369.8105
+#&gt; Model cost at call 240 : 369.8105
+#&gt; Model cost at call 255 : 369.8105
+#&gt; Model cost at call 258 : 369.8105
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
+<span class='no'>SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'># Fit the model to the FOCUS example dataset D using defaults</span>
+<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19233.21
+#&gt; Model cost at call 2 : 19233.21
+#&gt; Model cost at call 5 : 19233.21
+#&gt; Model cost at call 8 : 14482.65
+#&gt; Model cost at call 11 : 14482.51
+#&gt; Model cost at call 13 : 14482.17
+#&gt; Model cost at call 15 : 6973.814
+#&gt; Model cost at call 16 : 5161.041
+#&gt; Model cost at call 17 : 5161.029
+#&gt; Model cost at call 22 : 5161.026
+#&gt; Model cost at call 24 : 3249.595
+#&gt; Model cost at call 26 : 3249.595
+#&gt; Model cost at call 27 : 3249.519
+#&gt; Model cost at call 31 : 2615.891
+#&gt; Model cost at call 32 : 2615.888
+#&gt; Model cost at call 39 : 989.1788
+#&gt; Model cost at call 44 : 989.1772
+#&gt; Model cost at call 45 : 989.1771
+#&gt; Model cost at call 47 : 647.4307
+#&gt; Model cost at call 50 : 647.4302
+#&gt; Model cost at call 51 : 647.4261
+#&gt; Model cost at call 54 : 626.7937
+#&gt; Model cost at call 55 : 626.7935
+#&gt; Model cost at call 56 : 626.7931
+#&gt; Model cost at call 61 : 527.9042
+#&gt; Model cost at call 62 : 527.9041
+#&gt; Model cost at call 68 : 505.8828
+#&gt; Model cost at call 70 : 505.8828
+#&gt; Model cost at call 73 : 505.8827
+#&gt; Model cost at call 75 : 452.8932
+#&gt; Model cost at call 77 : 452.893
+#&gt; Model cost at call 82 : 414.4918
+#&gt; Model cost at call 83 : 414.4918
+#&gt; Model cost at call 84 : 414.4918
+#&gt; Model cost at call 88 : 414.4917
+#&gt; Model cost at call 89 : 408.2617
+#&gt; Model cost at call 90 : 408.2616
+#&gt; Model cost at call 91 : 408.2616
+#&gt; Model cost at call 95 : 408.2615
+#&gt; Model cost at call 96 : 384.4461
+#&gt; Model cost at call 102 : 384.4461
+#&gt; Model cost at call 104 : 383.4905
+#&gt; Model cost at call 105 : 383.4905
+#&gt; Model cost at call 106 : 383.4905
+#&gt; Model cost at call 109 : 383.4904
+#&gt; Model cost at call 111 : 381.8828
+#&gt; Model cost at call 112 : 381.8827
+#&gt; Model cost at call 118 : 380.8499
+#&gt; Model cost at call 120 : 380.8499
+#&gt; Model cost at call 123 : 380.8499
+#&gt; Model cost at call 125 : 379.1403
+#&gt; Model cost at call 127 : 379.1402
+#&gt; Model cost at call 132 : 376.4962
+#&gt; Model cost at call 133 : 373.0958
+#&gt; Model cost at call 134 : 365.247
+#&gt; Model cost at call 137 : 365.2469
+#&gt; Model cost at call 142 : 360.8231
+#&gt; Model cost at call 143 : 360.8231
+#&gt; Model cost at call 146 : 360.8231
+#&gt; Model cost at call 148 : 360.8231
+#&gt; Model cost at call 149 : 358.3976
+#&gt; Model cost at call 152 : 358.3976
+#&gt; Model cost at call 154 : 358.3976
+#&gt; Model cost at call 156 : 355.9066
+#&gt; Model cost at call 157 : 355.9066
+#&gt; Model cost at call 163 : 354.3386
+#&gt; Model cost at call 164 : 353.6335
+#&gt; Model cost at call 172 : 353.2094
+#&gt; Model cost at call 173 : 353.2094
+#&gt; Model cost at call 174 : 353.2093
+#&gt; Model cost at call 177 : 353.2093
+#&gt; Model cost at call 178 : 353.2093
+#&gt; Model cost at call 179 : 352.6641
+#&gt; Model cost at call 182 : 352.6641
+#&gt; Model cost at call 183 : 352.6641
+#&gt; Model cost at call 186 : 352.4908
+#&gt; Model cost at call 187 : 352.4429
+#&gt; Model cost at call 195 : 352.3246
+#&gt; Model cost at call 203 : 352.2858
+#&gt; Model cost at call 204 : 352.2858
+#&gt; Model cost at call 205 : 352.2858
+#&gt; Model cost at call 206 : 352.2858
+#&gt; Model cost at call 207 : 352.2858
+#&gt; Model cost at call 210 : 352.2332
+#&gt; Model cost at call 211 : 352.2081
+#&gt; Model cost at call 214 : 352.2081
+#&gt; Model cost at call 216 : 352.2081
+#&gt; Model cost at call 218 : 352.2049
+#&gt; Model cost at call 219 : 352.2049
+#&gt; Model cost at call 220 : 352.2049
+#&gt; Model cost at call 226 : 352.2048
+#&gt; Model cost at call 228 : 352.2048
+#&gt; Model cost at call 231 : 352.2048
+#&gt; Model cost at call 232 : 352.2048
+#&gt; Model cost at call 238 : 352.2048
+#&gt; Model cost at call 239 : 352.2048
+#&gt; Model cost at call 251 : 352.2048
+#&gt; Model cost at call 264 : 352.2048
+#&gt; Model cost at call 283 : 352.2048
+#&gt; Model cost at call 284 : 352.2048
+#&gt; Model cost at call 285 : 352.2048
+#&gt; Model cost at call 286 : 352.2048
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19233.21
+#&gt; Model cost at call 2 : 19233.21
+#&gt; Model cost at call 5 : 19233.21
+#&gt; Model cost at call 8 : 14482.65
+#&gt; Model cost at call 11 : 14482.51
+#&gt; Model cost at call 13 : 14482.17
+#&gt; Model cost at call 15 : 6973.814
+#&gt; Model cost at call 16 : 5161.041
+#&gt; Model cost at call 17 : 5161.029
+#&gt; Model cost at call 22 : 5161.026
+#&gt; Model cost at call 24 : 3249.595
+#&gt; Model cost at call 26 : 3249.595
+#&gt; Model cost at call 27 : 3249.519
+#&gt; Model cost at call 31 : 2615.891
+#&gt; Model cost at call 32 : 2615.888
+#&gt; Model cost at call 39 : 989.1788
+#&gt; Model cost at call 44 : 989.1772
+#&gt; Model cost at call 45 : 989.1771
+#&gt; Model cost at call 47 : 647.4307
+#&gt; Model cost at call 50 : 647.4302
+#&gt; Model cost at call 51 : 647.4261
+#&gt; Model cost at call 54 : 626.7937
+#&gt; Model cost at call 55 : 626.7935
+#&gt; Model cost at call 56 : 626.7931
+#&gt; Model cost at call 61 : 527.9042
+#&gt; Model cost at call 62 : 527.9041
+#&gt; Model cost at call 68 : 505.8828
+#&gt; Model cost at call 70 : 505.8828
+#&gt; Model cost at call 73 : 505.8827
+#&gt; Model cost at call 75 : 452.8932
+#&gt; Model cost at call 77 : 452.893
+#&gt; Model cost at call 82 : 414.4918
+#&gt; Model cost at call 83 : 414.4918
+#&gt; Model cost at call 84 : 414.4918
+#&gt; Model cost at call 88 : 414.4917
+#&gt; Model cost at call 89 : 408.2617
+#&gt; Model cost at call 90 : 408.2616
+#&gt; Model cost at call 91 : 408.2616
+#&gt; Model cost at call 95 : 408.2615
+#&gt; Model cost at call 96 : 384.4461
+#&gt; Model cost at call 102 : 384.4461
+#&gt; Model cost at call 104 : 383.4905
+#&gt; Model cost at call 105 : 383.4905
+#&gt; Model cost at call 106 : 383.4905
+#&gt; Model cost at call 109 : 383.4904
+#&gt; Model cost at call 111 : 381.8828
+#&gt; Model cost at call 112 : 381.8827
+#&gt; Model cost at call 118 : 380.8499
+#&gt; Model cost at call 120 : 380.8499
+#&gt; Model cost at call 123 : 380.8499
+#&gt; Model cost at call 125 : 379.1403
+#&gt; Model cost at call 127 : 379.1402
+#&gt; Model cost at call 132 : 376.4962
+#&gt; Model cost at call 133 : 373.0958
+#&gt; Model cost at call 134 : 365.247
+#&gt; Model cost at call 137 : 365.2469
+#&gt; Model cost at call 142 : 360.8231
+#&gt; Model cost at call 143 : 360.8231
+#&gt; Model cost at call 146 : 360.8231
+#&gt; Model cost at call 148 : 360.8231
+#&gt; Model cost at call 149 : 358.3976
+#&gt; Model cost at call 152 : 358.3976
+#&gt; Model cost at call 154 : 358.3976
+#&gt; Model cost at call 156 : 355.9066
+#&gt; Model cost at call 157 : 355.9066
+#&gt; Model cost at call 163 : 354.3386
+#&gt; Model cost at call 164 : 353.6335
+#&gt; Model cost at call 172 : 353.2094
+#&gt; Model cost at call 173 : 353.2094
+#&gt; Model cost at call 174 : 353.2093
+#&gt; Model cost at call 177 : 353.2093
+#&gt; Model cost at call 178 : 353.2093
+#&gt; Model cost at call 179 : 352.6641
+#&gt; Model cost at call 182 : 352.6641
+#&gt; Model cost at call 183 : 352.6641
+#&gt; Model cost at call 186 : 352.4908
+#&gt; Model cost at call 187 : 352.4429
+#&gt; Model cost at call 195 : 352.3246
+#&gt; Model cost at call 203 : 352.2858
+#&gt; Model cost at call 204 : 352.2858
+#&gt; Model cost at call 205 : 352.2858
+#&gt; Model cost at call 206 : 352.2858
+#&gt; Model cost at call 207 : 352.2858
+#&gt; Model cost at call 210 : 352.2332
+#&gt; Model cost at call 211 : 352.2081
+#&gt; Model cost at call 214 : 352.2081
+#&gt; Model cost at call 216 : 352.2081
+#&gt; Model cost at call 218 : 352.2049
+#&gt; Model cost at call 219 : 352.2049
+#&gt; Model cost at call 220 : 352.2049
+#&gt; Model cost at call 226 : 352.2048
+#&gt; Model cost at call 228 : 352.2048
+#&gt; Model cost at call 231 : 352.2048
+#&gt; Model cost at call 232 : 352.2048
+#&gt; Model cost at call 238 : 352.2048
+#&gt; Model cost at call 239 : 352.2048
+#&gt; Model cost at call 251 : 352.2048
+#&gt; Model cost at call 264 : 352.2048
+#&gt; Model cost at call 283 : 352.2048
+#&gt; Model cost at call 284 : 352.2048
+#&gt; Model cost at call 285 : 352.2048
+#&gt; Model cost at call 286 : 352.2048
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
+<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 10426.65
+#&gt; Model cost at call 3 : 10426.65
+#&gt; Model cost at call 6 : 1995.326
+#&gt; Model cost at call 7 : 1995.322
+#&gt; Model cost at call 8 : 1995.14
+#&gt; Model cost at call 11 : 718.5568
+#&gt; Model cost at call 12 : 718.5566
+#&gt; Model cost at call 13 : 718.5563
+#&gt; Model cost at call 16 : 408.9208
+#&gt; Model cost at call 17 : 408.9204
+#&gt; Model cost at call 18 : 408.9204
+#&gt; Model cost at call 20 : 408.9203
+#&gt; Model cost at call 21 : 402.7935
+#&gt; Model cost at call 22 : 402.793
+#&gt; Model cost at call 26 : 202.0443
+#&gt; Model cost at call 28 : 202.0443
+#&gt; Model cost at call 30 : 202.0443
+#&gt; Model cost at call 31 : 196.438
+#&gt; Model cost at call 36 : 196.1947
+#&gt; Model cost at call 37 : 196.1947
+#&gt; Model cost at call 41 : 192.9338
+#&gt; Model cost at call 43 : 192.9338
+#&gt; Model cost at call 45 : 192.9338
+#&gt; Model cost at call 46 : 191.6452
+#&gt; Model cost at call 47 : 191.6452
+#&gt; Model cost at call 51 : 188.9328
+#&gt; Model cost at call 54 : 188.9328
+#&gt; Model cost at call 55 : 188.9328
+#&gt; Model cost at call 56 : 183.6499
+#&gt; Model cost at call 59 : 183.6499
+#&gt; Model cost at call 62 : 181.9039
+#&gt; Model cost at call 67 : 179.0543
+#&gt; Model cost at call 68 : 179.0543
+#&gt; Model cost at call 69 : 179.0543
+#&gt; Model cost at call 70 : 179.0543
+#&gt; Model cost at call 72 : 176.749
+#&gt; Model cost at call 73 : 176.2321
+#&gt; Model cost at call 74 : 176.232
+#&gt; Model cost at call 75 : 176.232
+#&gt; Model cost at call 76 : 176.232
+#&gt; Model cost at call 78 : 175.3914
+#&gt; Model cost at call 79 : 175.3914
+#&gt; Model cost at call 81 : 175.3913
+#&gt; Model cost at call 83 : 174.6257
+#&gt; Model cost at call 84 : 174.6257
+#&gt; Model cost at call 89 : 174.1476
+#&gt; Model cost at call 92 : 174.1476
+#&gt; Model cost at call 93 : 174.1476
+#&gt; Model cost at call 94 : 173.8512
+#&gt; Model cost at call 99 : 173.6987
+#&gt; Model cost at call 104 : 173.6813
+#&gt; Model cost at call 105 : 173.6813
+#&gt; Model cost at call 106 : 173.6813
+#&gt; Model cost at call 107 : 173.6813
+#&gt; Model cost at call 108 : 173.6813
+#&gt; Model cost at call 109 : 173.6802
+#&gt; Model cost at call 110 : 173.6802
+#&gt; Model cost at call 111 : 173.6802
+#&gt; Model cost at call 112 : 173.6802
+#&gt; Model cost at call 113 : 173.6802
+#&gt; Model cost at call 114 : 173.6799
+#&gt; Model cost at call 116 : 173.6799
+#&gt; Model cost at call 118 : 173.6799
+#&gt; Model cost at call 119 : 173.6799
+#&gt; Model cost at call 120 : 173.6799
+#&gt; Model cost at call 129 : 173.6799
+#&gt; Model cost at call 141 : 173.6799
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18365.33
+#&gt; Model cost at call 2 : 18365.33
+#&gt; Model cost at call 8 : 11666.4
+#&gt; Model cost at call 9 : 10992.15
+#&gt; Model cost at call 10 : 10992.13
+#&gt; Model cost at call 11 : 10991.95
+#&gt; Model cost at call 12 : 10991.17
+#&gt; Model cost at call 14 : 10990.65
+#&gt; Model cost at call 17 : 3940.801
+#&gt; Model cost at call 20 : 3940.8
+#&gt; Model cost at call 22 : 3940.798
+#&gt; Model cost at call 24 : 3241.199
+#&gt; Model cost at call 27 : 3241.198
+#&gt; Model cost at call 30 : 3241.192
+#&gt; Model cost at call 31 : 1518.749
+#&gt; Model cost at call 37 : 1518.747
+#&gt; Model cost at call 39 : 1091.836
+#&gt; Model cost at call 42 : 1091.835
+#&gt; Model cost at call 43 : 1091.835
+#&gt; Model cost at call 44 : 1091.804
+#&gt; Model cost at call 46 : 927.8538
+#&gt; Model cost at call 49 : 927.8529
+#&gt; Model cost at call 53 : 638.102
+#&gt; Model cost at call 56 : 638.1019
+#&gt; Model cost at call 58 : 638.1018
+#&gt; Model cost at call 61 : 560.4352
+#&gt; Model cost at call 62 : 560.435
+#&gt; Model cost at call 63 : 560.4327
+#&gt; Model cost at call 68 : 423.9629
+#&gt; Model cost at call 69 : 423.9629
+#&gt; Model cost at call 70 : 423.9629
+#&gt; Model cost at call 71 : 423.9628
+#&gt; Model cost at call 73 : 423.9628
+#&gt; Model cost at call 75 : 395.8015
+#&gt; Model cost at call 78 : 395.8013
+#&gt; Model cost at call 79 : 395.8013
+#&gt; Model cost at call 83 : 365.6975
+#&gt; Model cost at call 84 : 365.6975
+#&gt; Model cost at call 88 : 365.6975
+#&gt; Model cost at call 91 : 362.9843
+#&gt; Model cost at call 93 : 362.9843
+#&gt; Model cost at call 98 : 361.5506
+#&gt; Model cost at call 99 : 361.5506
+#&gt; Model cost at call 100 : 361.5505
+#&gt; Model cost at call 105 : 359.0492
+#&gt; Model cost at call 106 : 359.0492
+#&gt; Model cost at call 112 : 357.6574
+#&gt; Model cost at call 113 : 357.6574
+#&gt; Model cost at call 114 : 357.6574
+#&gt; Model cost at call 115 : 357.6574
+#&gt; Model cost at call 119 : 355.4518
+#&gt; Model cost at call 120 : 355.4518
+#&gt; Model cost at call 127 : 354.9045
+#&gt; Model cost at call 129 : 354.9045
+#&gt; Model cost at call 131 : 354.9045
+#&gt; Model cost at call 134 : 354.4168
+#&gt; Model cost at call 135 : 354.4168
+#&gt; Model cost at call 137 : 354.4167
+#&gt; Model cost at call 141 : 353.7901
+#&gt; Model cost at call 142 : 353.7901
+#&gt; Model cost at call 143 : 353.7899
+#&gt; Model cost at call 149 : 353.3233
+#&gt; Model cost at call 151 : 353.3233
+#&gt; Model cost at call 154 : 353.3233
+#&gt; Model cost at call 156 : 353.2939
+#&gt; Model cost at call 158 : 353.2938
+#&gt; Model cost at call 159 : 353.2938
+#&gt; Model cost at call 160 : 353.2938
+#&gt; Model cost at call 163 : 353.0571
+#&gt; Model cost at call 165 : 353.0571
+#&gt; Model cost at call 170 : 352.9457
+#&gt; Model cost at call 171 : 352.7458
+#&gt; Model cost at call 173 : 352.7457
+#&gt; Model cost at call 178 : 352.6377
+#&gt; Model cost at call 180 : 352.6377
+#&gt; Model cost at call 183 : 352.6377
+#&gt; Model cost at call 185 : 352.5377
+#&gt; Model cost at call 187 : 352.5377
+#&gt; Model cost at call 188 : 352.5377
+#&gt; Model cost at call 191 : 352.5377
+#&gt; Model cost at call 193 : 352.4479
+#&gt; Model cost at call 195 : 352.4479
+#&gt; Model cost at call 198 : 352.4479
+#&gt; Model cost at call 200 : 352.4021
+#&gt; Model cost at call 202 : 352.4021
+#&gt; Model cost at call 205 : 352.4021
+#&gt; Model cost at call 207 : 352.3465
+#&gt; Model cost at call 210 : 352.3465
+#&gt; Model cost at call 214 : 352.3031
+#&gt; Model cost at call 216 : 352.3031
+#&gt; Model cost at call 221 : 352.2632
+#&gt; Model cost at call 223 : 352.2632
+#&gt; Model cost at call 228 : 352.2367
+#&gt; Model cost at call 230 : 352.2367
+#&gt; Model cost at call 231 : 352.2367
+#&gt; Model cost at call 233 : 352.2367
+#&gt; Model cost at call 235 : 352.215
+#&gt; Model cost at call 238 : 352.215
+#&gt; Model cost at call 239 : 352.215
+#&gt; Model cost at call 242 : 352.207
+#&gt; Model cost at call 245 : 352.207
+#&gt; Model cost at call 250 : 352.2053
+#&gt; Model cost at call 251 : 352.2053
+#&gt; Model cost at call 253 : 352.2053
+#&gt; Model cost at call 256 : 352.2053
+#&gt; Model cost at call 258 : 352.2053
+#&gt; Model cost at call 259 : 352.2052
+#&gt; Model cost at call 260 : 352.2052
+#&gt; Model cost at call 263 : 352.2052
+#&gt; Model cost at call 271 : 352.2048
+#&gt; Model cost at call 273 : 352.2048
+#&gt; Model cost at call 274 : 352.2048
+#&gt; Model cost at call 281 : 352.2048
+#&gt; Model cost at call 282 : 352.2048
+#&gt; Model cost at call 286 : 352.2048
+#&gt; Model cost at call 289 : 352.2048
+#&gt; Model cost at call 294 : 352.2048
+#&gt; Model cost at call 296 : 352.2048
+#&gt; Model cost at call 300 : 352.2048
+#&gt; Model cost at call 307 : 352.2048
+#&gt; Model cost at call 325 : 352.2048
+#&gt; Model cost at call 331 : 352.2048
+#&gt; Model cost at call 333 : 352.2048
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+
+
+<span class='co'># Weighted fits, including IRLS</span>
+<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</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='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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15156.12
+#&gt; Model cost at call 2 : 15156.12
+#&gt; Model cost at call 6 : 8243.644
+#&gt; Model cost at call 12 : 6290.714
+#&gt; Model cost at call 13 : 6290.684
+#&gt; Model cost at call 15 : 6290.453
+#&gt; Model cost at call 18 : 1700.75
+#&gt; Model cost at call 20 : 1700.612
+#&gt; Model cost at call 24 : 1190.923
+#&gt; Model cost at call 26 : 1190.922
+#&gt; Model cost at call 29 : 1017.417
+#&gt; Model cost at call 31 : 1017.417
+#&gt; Model cost at call 33 : 1017.416
+#&gt; Model cost at call 34 : 644.0471
+#&gt; Model cost at call 36 : 644.0469
+#&gt; Model cost at call 38 : 644.0468
+#&gt; Model cost at call 39 : 590.5024
+#&gt; Model cost at call 41 : 590.5021
+#&gt; Model cost at call 43 : 590.5015
+#&gt; Model cost at call 44 : 543.2187
+#&gt; Model cost at call 45 : 543.2183
+#&gt; Model cost at call 46 : 543.2182
+#&gt; Model cost at call 50 : 391.348
+#&gt; Model cost at call 51 : 391.3479
+#&gt; Model cost at call 56 : 386.4789
+#&gt; Model cost at call 58 : 386.4789
+#&gt; Model cost at call 60 : 386.4779
+#&gt; Model cost at call 61 : 384.0686
+#&gt; Model cost at call 63 : 384.0686
+#&gt; Model cost at call 66 : 382.7812
+#&gt; Model cost at call 68 : 382.7812
+#&gt; Model cost at call 70 : 382.7812
+#&gt; Model cost at call 71 : 378.9272
+#&gt; Model cost at call 73 : 378.9272
+#&gt; Model cost at call 75 : 378.9272
+#&gt; Model cost at call 76 : 377.4846
+#&gt; Model cost at call 78 : 377.4846
+#&gt; Model cost at call 81 : 375.9738
+#&gt; Model cost at call 83 : 375.9738
+#&gt; Model cost at call 86 : 375.3387
+#&gt; Model cost at call 88 : 375.3387
+#&gt; Model cost at call 91 : 374.5774
+#&gt; Model cost at call 93 : 374.5774
+#&gt; Model cost at call 95 : 374.5774
+#&gt; Model cost at call 96 : 373.5447
+#&gt; Model cost at call 100 : 373.5446
+#&gt; Model cost at call 102 : 373.2643
+#&gt; Model cost at call 104 : 373.2643
+#&gt; Model cost at call 107 : 372.6799
+#&gt; Model cost at call 111 : 372.6798
+#&gt; Model cost at call 114 : 372.6325
+#&gt; Model cost at call 116 : 372.6325
+#&gt; Model cost at call 119 : 372.6159
+#&gt; Model cost at call 121 : 372.6159
+#&gt; Model cost at call 123 : 372.6159
+#&gt; Model cost at call 124 : 372.5845
+#&gt; Model cost at call 126 : 372.5845
+#&gt; Model cost at call 129 : 372.5375
+#&gt; Model cost at call 130 : 372.4771
+#&gt; Model cost at call 131 : 372.2008
+#&gt; Model cost at call 132 : 371.4923
+#&gt; Model cost at call 134 : 371.4923
+#&gt; Model cost at call 137 : 371.3022
+#&gt; Model cost at call 139 : 371.3022
+#&gt; Model cost at call 143 : 371.2271
+#&gt; Model cost at call 144 : 371.2271
+#&gt; Model cost at call 148 : 371.2202
+#&gt; Model cost at call 149 : 371.215
+#&gt; Model cost at call 152 : 371.215
+#&gt; Model cost at call 154 : 371.2136
+#&gt; Model cost at call 155 : 371.2136
+#&gt; Model cost at call 156 : 371.2136
+#&gt; Model cost at call 160 : 371.2134
+#&gt; Model cost at call 164 : 371.2134
+#&gt; Model cost at call 167 : 371.2134
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:47 2016
+#&gt; Date of summary: Fri Nov 18 15:19:47 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 185 model solutions performed in 0.748 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
+#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
+#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
+#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
+#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
+#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
+#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent 0.098700 23.880 5.701e-24 0.090660 1.074e-01
+#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
+#&gt; f_parent_to_m1 0.514500 22.490 4.374e-23 0.468100 5.606e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.459 2 7
+#&gt; m1 4.690 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5145
+#&gt; parent_sink 0.4855
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 99.46 9.960e+01 -1.385e-01
+#&gt; 0 parent 102.04 9.960e+01 2.442e+00
+#&gt; 1 parent 93.50 9.024e+01 3.262e+00
+#&gt; 1 parent 92.50 9.024e+01 2.262e+00
+#&gt; 3 parent 63.23 7.407e+01 -1.084e+01
+#&gt; 3 parent 68.99 7.407e+01 -5.083e+00
+#&gt; 7 parent 52.32 4.991e+01 2.408e+00
+#&gt; 7 parent 55.13 4.991e+01 5.218e+00
+#&gt; 14 parent 27.27 2.501e+01 2.257e+00
+#&gt; 14 parent 26.64 2.501e+01 1.627e+00
+#&gt; 21 parent 11.50 1.253e+01 -1.035e+00
+#&gt; 21 parent 11.64 1.253e+01 -8.946e-01
+#&gt; 35 parent 2.85 3.148e+00 -2.979e-01
+#&gt; 35 parent 2.91 3.148e+00 -2.379e-01
+#&gt; 50 parent 0.69 7.162e-01 -2.624e-02
+#&gt; 50 parent 0.63 7.162e-01 -8.624e-02
+#&gt; 75 parent 0.05 6.074e-02 -1.074e-02
+#&gt; 75 parent 0.06 6.074e-02 -7.381e-04
+#&gt; 100 parent NA 5.151e-03 NA
+#&gt; 100 parent NA 5.151e-03 NA
+#&gt; 120 parent NA 7.155e-04 NA
+#&gt; 120 parent NA 7.155e-04 NA
+#&gt; 0 m1 0.00 0.000e+00 0.000e+00
+#&gt; 0 m1 0.00 0.000e+00 0.000e+00
+#&gt; 1 m1 4.84 4.803e+00 3.704e-02
+#&gt; 1 m1 5.64 4.803e+00 8.370e-01
+#&gt; 3 m1 12.91 1.302e+01 -1.140e-01
+#&gt; 3 m1 12.96 1.302e+01 -6.400e-02
+#&gt; 7 m1 22.97 2.504e+01 -2.075e+00
+#&gt; 7 m1 24.47 2.504e+01 -5.748e-01
+#&gt; 14 m1 41.69 3.669e+01 5.000e+00
+#&gt; 14 m1 33.21 3.669e+01 -3.480e+00
+#&gt; 21 m1 44.37 4.165e+01 2.717e+00
+#&gt; 21 m1 46.44 4.165e+01 4.787e+00
+#&gt; 35 m1 41.22 4.331e+01 -2.093e+00
+#&gt; 35 m1 37.95 4.331e+01 -5.363e+00
+#&gt; 50 m1 41.19 4.122e+01 -2.831e-02
+#&gt; 50 m1 40.01 4.122e+01 -1.208e+00
+#&gt; 75 m1 40.09 3.645e+01 3.643e+00
+#&gt; 75 m1 33.85 3.645e+01 -2.597e+00
+#&gt; 100 m1 31.04 3.198e+01 -9.416e-01
+#&gt; 100 m1 33.13 3.198e+01 1.148e+00
+#&gt; 120 m1 25.15 2.879e+01 -3.640e+00
+#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15156.12
+#&gt; Model cost at call 2 : 15156.12
+#&gt; Model cost at call 6 : 8243.644
+#&gt; Model cost at call 12 : 6290.714
+#&gt; Model cost at call 13 : 6290.684
+#&gt; Model cost at call 15 : 6290.453
+#&gt; Model cost at call 18 : 1700.75
+#&gt; Model cost at call 20 : 1700.612
+#&gt; Model cost at call 24 : 1190.923
+#&gt; Model cost at call 26 : 1190.922
+#&gt; Model cost at call 29 : 1017.417
+#&gt; Model cost at call 31 : 1017.417
+#&gt; Model cost at call 33 : 1017.416
+#&gt; Model cost at call 34 : 644.0471
+#&gt; Model cost at call 36 : 644.0469
+#&gt; Model cost at call 38 : 644.0468
+#&gt; Model cost at call 39 : 590.5024
+#&gt; Model cost at call 41 : 590.5021
+#&gt; Model cost at call 43 : 590.5015
+#&gt; Model cost at call 44 : 543.2187
+#&gt; Model cost at call 45 : 543.2183
+#&gt; Model cost at call 46 : 543.2182
+#&gt; Model cost at call 50 : 391.348
+#&gt; Model cost at call 51 : 391.3479
+#&gt; Model cost at call 56 : 386.4789
+#&gt; Model cost at call 58 : 386.4789
+#&gt; Model cost at call 60 : 386.4779
+#&gt; Model cost at call 61 : 384.0686
+#&gt; Model cost at call 63 : 384.0686
+#&gt; Model cost at call 66 : 382.7812
+#&gt; Model cost at call 68 : 382.7812
+#&gt; Model cost at call 70 : 382.7812
+#&gt; Model cost at call 71 : 378.9272
+#&gt; Model cost at call 73 : 378.9272
+#&gt; Model cost at call 75 : 378.9272
+#&gt; Model cost at call 76 : 377.4846
+#&gt; Model cost at call 78 : 377.4846
+#&gt; Model cost at call 81 : 375.9738
+#&gt; Model cost at call 83 : 375.9738
+#&gt; Model cost at call 86 : 375.3387
+#&gt; Model cost at call 88 : 375.3387
+#&gt; Model cost at call 91 : 374.5774
+#&gt; Model cost at call 93 : 374.5774
+#&gt; Model cost at call 95 : 374.5774
+#&gt; Model cost at call 96 : 373.5447
+#&gt; Model cost at call 100 : 373.5446
+#&gt; Model cost at call 102 : 373.2643
+#&gt; Model cost at call 104 : 373.2643
+#&gt; Model cost at call 107 : 372.6799
+#&gt; Model cost at call 111 : 372.6798
+#&gt; Model cost at call 114 : 372.6325
+#&gt; Model cost at call 116 : 372.6325
+#&gt; Model cost at call 119 : 372.6159
+#&gt; Model cost at call 121 : 372.6159
+#&gt; Model cost at call 123 : 372.6159
+#&gt; Model cost at call 124 : 372.5845
+#&gt; Model cost at call 126 : 372.5845
+#&gt; Model cost at call 129 : 372.5375
+#&gt; Model cost at call 130 : 372.4771
+#&gt; Model cost at call 131 : 372.2008
+#&gt; Model cost at call 132 : 371.4923
+#&gt; Model cost at call 134 : 371.4923
+#&gt; Model cost at call 137 : 371.3022
+#&gt; Model cost at call 139 : 371.3022
+#&gt; Model cost at call 143 : 371.2271
+#&gt; Model cost at call 144 : 371.2271
+#&gt; Model cost at call 148 : 371.2202
+#&gt; Model cost at call 149 : 371.215
+#&gt; Model cost at call 152 : 371.215
+#&gt; Model cost at call 154 : 371.2136
+#&gt; Model cost at call 155 : 371.2136
+#&gt; Model cost at call 156 : 371.2136
+#&gt; Model cost at call 160 : 371.2134
+#&gt; Model cost at call 164 : 371.2134
+#&gt; Model cost at call 167 : 371.2134
+#&gt; IRLS based on variance estimates for each observed variable
+#&gt; Initial variance estimates are:
+#&gt; parent m1
+#&gt; 11.552581 7.421226
+#&gt; Model cost at call 186 : 40
+#&gt; Model cost at call 188 : 40
+#&gt; Model cost at call 194 : 39.99562
+#&gt; Model cost at call 195 : 39.99562
+#&gt; Model cost at call 201 : 39.9956
+#&gt; Model cost at call 203 : 39.99528
+#&gt; Model cost at call 205 : 39.99528
+#&gt; Model cost at call 207 : 39.99528
+#&gt; Model cost at call 209 : 39.99515
+#&gt; Model cost at call 211 : 39.99515
+#&gt; Model cost at call 214 : 39.99515
+#&gt; Model cost at call 215 : 39.99505
+#&gt; Model cost at call 217 : 39.99505
+#&gt; Model cost at call 219 : 39.99505
+#&gt; Model cost at call 220 : 39.99489
+#&gt; Model cost at call 222 : 39.99489
+#&gt; Model cost at call 224 : 39.99489
+#&gt; Model cost at call 225 : 39.99479
+#&gt; Model cost at call 227 : 39.99479
+#&gt; Model cost at call 231 : 39.99467
+#&gt; Model cost at call 234 : 39.99467
+#&gt; Model cost at call 235 : 39.99467
+#&gt; Model cost at call 236 : 39.99458
+#&gt; Model cost at call 238 : 39.99458
+#&gt; Model cost at call 239 : 39.99458
+#&gt; Model cost at call 241 : 39.99452
+#&gt; Model cost at call 242 : 39.99444
+#&gt; Model cost at call 243 : 39.99433
+#&gt; Model cost at call 245 : 39.99433
+#&gt; Model cost at call 248 : 39.99383
+#&gt; Model cost at call 250 : 39.99383
+#&gt; Model cost at call 251 : 39.99383
+#&gt; Model cost at call 252 : 39.99383
+#&gt; Model cost at call 253 : 39.9935
+#&gt; Model cost at call 254 : 39.99309
+#&gt; Model cost at call 256 : 39.99309
+#&gt; Model cost at call 261 : 39.99295
+#&gt; Model cost at call 264 : 39.99295
+#&gt; Model cost at call 267 : 39.99281
+#&gt; Model cost at call 272 : 39.99281
+#&gt; Model cost at call 273 : 39.99278
+#&gt; Model cost at call 276 : 39.99278
+#&gt; Model cost at call 278 : 39.99278
+#&gt; Model cost at call 279 : 39.99278
+#&gt; Model cost at call 281 : 39.99278
+#&gt; Model cost at call 283 : 39.99278
+#&gt; Model cost at call 286 : 39.99278
+#&gt; Model cost at call 289 : 39.99278
+#&gt; Model cost at call 290 : 39.99278
+#&gt; Iteration 1 yields variance estimates:
+#&gt; parent m1
+#&gt; 11.573172 7.407968
+#&gt; Sum of squared differences to last variance estimates: 1.5e-05
+#&gt; Iteration 2 yields variance estimates:
+#&gt; parent m1
+#&gt; 11.573405 7.407846
+#&gt; Sum of squared differences to last variance estimates: 1.7e-09
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:50 2016
+#&gt; Date of summary: Fri Nov 18 15:19:50 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 486 model solutions performed in 2.052 s
+#&gt;
+#&gt; Weighting: none then iterative reweighting method obs
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.67000 1.79200 96.04000 103.300
+#&gt; log_k_parent -2.31200 0.04560 -2.40400 -2.220
+#&gt; log_k_m1 -5.25100 0.12510 -5.50500 -4.998
+#&gt; f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6148
+#&gt; log_k_parent 0.5083 1.0000 -0.3894 -0.6062
+#&gt; log_k_m1 -0.1979 -0.3894 1.0000 0.7417
+#&gt; f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000
+#&gt;
+#&gt; Residual standard error: 1.054 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.67000 55.630 8.183e-37 96.040000 1.033e+02
+#&gt; k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01
+#&gt; k_m1 0.00524 7.996 8.487e-10 0.004066 6.753e-03
+#&gt; f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.399 4 15
+#&gt; parent 6.466 2 7
+#&gt; m1 4.679 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5134
+#&gt; parent_sink 0.4866
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.997 23.24
+#&gt; m1 132.282 439.43
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err
+#&gt; 0 parent 99.46 9.967e+01 -2.122e-01 3.402
+#&gt; 0 parent 102.04 9.967e+01 2.368e+00 3.402
+#&gt; 1 parent 93.50 9.027e+01 3.228e+00 3.402
+#&gt; 1 parent 92.50 9.027e+01 2.228e+00 3.402
+#&gt; 3 parent 63.23 7.405e+01 -1.082e+01 3.402
+#&gt; 3 parent 68.99 7.405e+01 -5.056e+00 3.402
+#&gt; 7 parent 52.32 4.982e+01 2.499e+00 3.402
+#&gt; 7 parent 55.13 4.982e+01 5.309e+00 3.402
+#&gt; 14 parent 27.27 2.490e+01 2.367e+00 3.402
+#&gt; 14 parent 26.64 2.490e+01 1.737e+00 3.402
+#&gt; 21 parent 11.50 1.245e+01 -9.477e-01 3.402
+#&gt; 21 parent 11.64 1.245e+01 -8.077e-01 3.402
+#&gt; 35 parent 2.85 3.110e+00 -2.600e-01 3.402
+#&gt; 35 parent 2.91 3.110e+00 -2.000e-01 3.402
+#&gt; 50 parent 0.69 7.037e-01 -1.375e-02 3.402
+#&gt; 50 parent 0.63 7.037e-01 -7.375e-02 3.402
+#&gt; 75 parent 0.05 5.913e-02 -9.134e-03 3.402
+#&gt; 75 parent 0.06 5.913e-02 8.661e-04 3.402
+#&gt; 100 parent NA 4.969e-03 NA 3.402
+#&gt; 100 parent NA 4.969e-03 NA 3.402
+#&gt; 120 parent NA 6.852e-04 NA 3.402
+#&gt; 120 parent NA 6.852e-04 NA 3.402
+#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2.722
+#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2.722
+#&gt; 1 m1 4.84 4.813e+00 2.672e-02 2.722
+#&gt; 1 m1 5.64 4.813e+00 8.267e-01 2.722
+#&gt; 3 m1 12.91 1.305e+01 -1.378e-01 2.722
+#&gt; 3 m1 12.96 1.305e+01 -8.779e-02 2.722
+#&gt; 7 m1 22.97 2.508e+01 -2.106e+00 2.722
+#&gt; 7 m1 24.47 2.508e+01 -6.061e-01 2.722
+#&gt; 14 m1 41.69 3.671e+01 4.983e+00 2.722
+#&gt; 14 m1 33.21 3.671e+01 -3.497e+00 2.722
+#&gt; 21 m1 44.37 4.165e+01 2.719e+00 2.722
+#&gt; 21 m1 46.44 4.165e+01 4.789e+00 2.722
+#&gt; 35 m1 41.22 4.329e+01 -2.069e+00 2.722
+#&gt; 35 m1 37.95 4.329e+01 -5.339e+00 2.722
+#&gt; 50 m1 41.19 4.119e+01 -3.388e-03 2.722
+#&gt; 50 m1 40.01 4.119e+01 -1.183e+00 2.722
+#&gt; 75 m1 40.09 3.644e+01 3.652e+00 2.722
+#&gt; 75 m1 33.85 3.644e+01 -2.588e+00 2.722
+#&gt; 100 m1 31.04 3.199e+01 -9.497e-01 2.722
+#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2.722
+#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2.722
+#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19.80132
+#&gt; Model cost at call 2 : 19.80132
+#&gt; Model cost at call 6 : 10.68776
+#&gt; Model cost at call 12 : 7.14353
+#&gt; Model cost at call 13 : 7.143529
+#&gt; Model cost at call 15 : 7.143511
+#&gt; Model cost at call 18 : 2.189024
+#&gt; Model cost at call 20 : 2.189019
+#&gt; Model cost at call 23 : 1.587262
+#&gt; Model cost at call 25 : 1.587261
+#&gt; Model cost at call 26 : 1.58726
+#&gt; Model cost at call 28 : 1.036794
+#&gt; Model cost at call 29 : 1.036794
+#&gt; Model cost at call 30 : 1.036793
+#&gt; Model cost at call 34 : 0.4939937
+#&gt; Model cost at call 35 : 0.4939937
+#&gt; Model cost at call 38 : 0.4939936
+#&gt; Model cost at call 39 : 0.4018506
+#&gt; Model cost at call 43 : 0.4018505
+#&gt; Model cost at call 45 : 0.3797853
+#&gt; Model cost at call 51 : 0.3669779
+#&gt; Model cost at call 55 : 0.3669778
+#&gt; Model cost at call 56 : 0.3585654
+#&gt; Model cost at call 57 : 0.3533252
+#&gt; Model cost at call 62 : 0.3502505
+#&gt; Model cost at call 64 : 0.3502505
+#&gt; Model cost at call 66 : 0.3502505
+#&gt; Model cost at call 67 : 0.3501535
+#&gt; Model cost at call 72 : 0.3501187
+#&gt; Model cost at call 74 : 0.3501187
+#&gt; Model cost at call 75 : 0.3501187
+#&gt; Model cost at call 77 : 0.3500378
+#&gt; Model cost at call 79 : 0.3500378
+#&gt; Model cost at call 83 : 0.349831
+#&gt; Model cost at call 88 : 0.3494286
+#&gt; Model cost at call 93 : 0.3488101
+#&gt; Model cost at call 98 : 0.3481444
+#&gt; Model cost at call 103 : 0.3478528
+#&gt; Model cost at call 108 : 0.3478092
+#&gt; Model cost at call 109 : 0.3478092
+#&gt; Model cost at call 113 : 0.347807
+#&gt; Model cost at call 116 : 0.347807
+#&gt; Model cost at call 117 : 0.347807
+#&gt; Model cost at call 119 : 0.347807
+#&gt; Model cost at call 120 : 0.347807
+#&gt; Model cost at call 125 : 0.347807
+#&gt; Model cost at call 126 : 0.347807
+#&gt; Model cost at call 128 : 0.347807
+#&gt; Model cost at call 137 : 0.347807
+#&gt; Model cost at call 148 : 0.347807
+#&gt; Model cost at call 152 : 0.347807
+#&gt; Model cost at call 154 : 0.347807
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:50 2016
+#&gt; Date of summary: Fri Nov 18 15:19:50 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 155 model solutions performed in 0.636 s
+#&gt;
+#&gt; Weighting: mean
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.7300 1.93200 95.81000 103.6000
+#&gt; log_k_parent -2.3090 0.04837 -2.40700 -2.2110
+#&gt; log_k_m1 -5.2550 0.12070 -5.49900 -5.0100
+#&gt; f_parent_ilr_1 0.0354 0.06344 -0.09327 0.1641
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5004 -0.2143 -0.6514
+#&gt; log_k_parent 0.5004 1.0000 -0.4282 -0.6383
+#&gt; log_k_m1 -0.2143 -0.4282 1.0000 0.7390
+#&gt; f_parent_ilr_1 -0.6514 -0.6383 0.7390 1.0000
+#&gt;
+#&gt; Residual standard error: 0.09829 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.730000 51.630 1.166e-35 95.81000 1.036e+02
+#&gt; k_parent 0.099360 20.670 7.304e-22 0.09007 1.096e-01
+#&gt; k_m1 0.005224 8.287 3.649e-10 0.00409 6.672e-03
+#&gt; f_parent_to_m1 0.512500 22.860 2.497e-23 0.46710 5.578e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.401 4 15
+#&gt; parent 6.473 2 7
+#&gt; m1 4.671 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5125
+#&gt; parent_sink 0.4875
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.976 23.18
+#&gt; m1 132.696 440.81
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 99.46 99.730570 -0.270570
+#&gt; 0 parent 102.04 99.730570 2.309430
+#&gt; 1 parent 93.50 90.298055 3.201945
+#&gt; 1 parent 92.50 90.298055 2.201945
+#&gt; 3 parent 63.23 74.025028 -10.795028
+#&gt; 3 parent 68.99 74.025028 -5.035028
+#&gt; 7 parent 52.32 49.748382 2.571618
+#&gt; 7 parent 55.13 49.748382 5.381618
+#&gt; 14 parent 27.27 24.815876 2.454124
+#&gt; 14 parent 26.64 24.815876 1.824124
+#&gt; 21 parent 11.50 12.378849 -0.878849
+#&gt; 21 parent 11.64 12.378849 -0.738849
+#&gt; 35 parent 2.85 3.080219 -0.230219
+#&gt; 35 parent 2.91 3.080219 -0.170219
+#&gt; 50 parent 0.69 0.693958 -0.003958
+#&gt; 50 parent 0.63 0.693958 -0.063958
+#&gt; 75 parent 0.05 0.057888 -0.007888
+#&gt; 75 parent 0.06 0.057888 0.002112
+#&gt; 100 parent NA 0.004829 NA
+#&gt; 100 parent NA 0.004829 NA
+#&gt; 120 parent NA 0.000662 NA
+#&gt; 120 parent NA 0.000662 NA
+#&gt; 0 m1 0.00 0.000000 0.000000
+#&gt; 0 m1 0.00 0.000000 0.000000
+#&gt; 1 m1 4.84 4.821488 0.018512
+#&gt; 1 m1 5.64 4.821488 0.818512
+#&gt; 3 m1 12.91 13.066692 -0.156692
+#&gt; 3 m1 12.96 13.066692 -0.106692
+#&gt; 7 m1 22.97 25.101058 -2.131058
+#&gt; 7 m1 24.47 25.101058 -0.631058
+#&gt; 14 m1 41.69 36.720923 4.969077
+#&gt; 14 m1 33.21 36.720923 -3.510923
+#&gt; 21 m1 44.37 41.648353 2.721647
+#&gt; 21 m1 46.44 41.648353 4.791647
+#&gt; 35 m1 41.22 43.269225 -2.049225
+#&gt; 35 m1 37.95 43.269225 -5.319225
+#&gt; 50 m1 41.19 41.173639 0.016361
+#&gt; 50 m1 40.01 41.173639 -1.163639
+#&gt; 75 m1 40.09 36.431224 3.658776
+#&gt; 75 m1 33.85 36.431224 -2.581224
+#&gt; 100 m1 31.04 31.996124 -0.956124
+#&gt; 100 m1 33.13 31.996124 1.133876
+#&gt; 120 m1 25.15 28.824128 -3.674128
+#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 11.21571
+#&gt; Model cost at call 2 : 11.21571
+#&gt; Model cost at call 3 : 11.21571
+#&gt; Model cost at call 8 : 11.12803
+#&gt; Model cost at call 10 : 11.128
+#&gt; Model cost at call 13 : 10.88016
+#&gt; Model cost at call 15 : 10.88016
+#&gt; Model cost at call 18 : 10.58819
+#&gt; Model cost at call 20 : 10.58819
+#&gt; Model cost at call 23 : 9.71699
+#&gt; Model cost at call 24 : 7.794026
+#&gt; Model cost at call 26 : 7.794026
+#&gt; Model cost at call 31 : 6.89734
+#&gt; Model cost at call 33 : 6.897337
+#&gt; Model cost at call 36 : 5.2239
+#&gt; Model cost at call 37 : 3.357735
+#&gt; Model cost at call 41 : 3.357733
+#&gt; Model cost at call 44 : 2.982323
+#&gt; Model cost at call 46 : 2.982322
+#&gt; Model cost at call 49 : 2.703946
+#&gt; Model cost at call 50 : 2.080395
+#&gt; Model cost at call 55 : 0.5307591
+#&gt; Model cost at call 56 : 0.5307591
+#&gt; Model cost at call 57 : 0.5307591
+#&gt; Model cost at call 59 : 0.5307584
+#&gt; Model cost at call 60 : 0.3240066
+#&gt; Model cost at call 61 : 0.3240066
+#&gt; Model cost at call 64 : 0.3240066
+#&gt; Model cost at call 65 : 0.2601108
+#&gt; Model cost at call 70 : 0.2414055
+#&gt; Model cost at call 74 : 0.2414055
+#&gt; Model cost at call 75 : 0.2404251
+#&gt; Model cost at call 80 : 0.2404087
+#&gt; Model cost at call 82 : 0.2404087
+#&gt; Model cost at call 85 : 0.2404054
+#&gt; Model cost at call 88 : 0.2404054
+#&gt; Model cost at call 92 : 0.2403931
+#&gt; Model cost at call 93 : 0.2403784
+#&gt; Model cost at call 98 : 0.2403784
+#&gt; Model cost at call 99 : 0.2403322
+#&gt; Model cost at call 104 : 0.2402188
+#&gt; Model cost at call 109 : 0.2400275
+#&gt; Model cost at call 114 : 0.239844
+#&gt; Model cost at call 119 : 0.2397153
+#&gt; Model cost at call 120 : 0.2397153
+#&gt; Model cost at call 124 : 0.2396978
+#&gt; Model cost at call 126 : 0.2396978
+#&gt; Model cost at call 130 : 0.239697
+#&gt; Model cost at call 131 : 0.2396963
+#&gt; Model cost at call 133 : 0.2396963
+#&gt; Model cost at call 138 : 0.2396962
+#&gt; Model cost at call 139 : 0.2396962
+#&gt; Model cost at call 141 : 0.2396962
+#&gt; Model cost at call 144 : 0.2396962
+#&gt; Model cost at call 147 : 0.2396962
+#&gt; Model cost at call 156 : 0.2396962
+#&gt; Model cost at call 167 : 0.2396962
+#&gt; Model cost at call 169 : 0.2396962
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:51 2016
+#&gt; Date of summary: Fri Nov 18 15:19:51 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 174 model solutions performed in 0.789 s
+#&gt;
+#&gt; Weighting: manual
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.6600 2.712000 94.14000 105.2000
+#&gt; log_k_parent -2.2980 0.008118 -2.31500 -2.2820
+#&gt; log_k_m1 -5.2410 0.096690 -5.43800 -5.0450
+#&gt; f_parent_ilr_1 0.0231 0.057990 -0.09474 0.1409
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.00000 0.6844 -0.08687 -0.7564
+#&gt; log_k_parent 0.68435 1.0000 -0.12694 -0.5812
+#&gt; log_k_m1 -0.08687 -0.1269 1.00000 0.5195
+#&gt; f_parent_ilr_1 -0.75644 -0.5812 0.51951 1.0000
+#&gt;
+#&gt; Residual standard error: 0.08396 on 34 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.660000 36.75 2.957e-29 94.14000 1.052e+02
+#&gt; k_parent 0.100400 123.20 5.927e-47 0.09878 1.021e-01
+#&gt; k_m1 0.005295 10.34 2.447e-12 0.00435 6.444e-03
+#&gt; f_parent_to_m1 0.508200 24.79 1.184e-23 0.46660 5.497e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.461 4 15
+#&gt; parent 6.520 2 7
+#&gt; m1 4.744 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5082
+#&gt; parent_sink 0.4918
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.902 22.93
+#&gt; m1 130.916 434.89
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err
+#&gt; 0 parent 99.46 99.65571 -0.195714 99.46
+#&gt; 0 parent 102.04 99.65571 2.384286 102.04
+#&gt; 1 parent 93.50 90.13383 3.366170 93.50
+#&gt; 1 parent 92.50 90.13383 2.366170 92.50
+#&gt; 3 parent 63.23 73.73252 -10.502518 63.23
+#&gt; 3 parent 68.99 73.73252 -4.742518 68.99
+#&gt; 7 parent 52.32 49.34027 2.979728 52.32
+#&gt; 7 parent 55.13 49.34027 5.789728 55.13
+#&gt; 14 parent 27.27 24.42873 2.841271 27.27
+#&gt; 14 parent 26.64 24.42873 2.211271 26.64
+#&gt; 21 parent 11.50 12.09484 -0.594842 11.50
+#&gt; 21 parent 11.64 12.09484 -0.454842 11.64
+#&gt; 35 parent 2.85 2.96482 -0.114824 2.85
+#&gt; 35 parent 2.91 2.96482 -0.054824 2.91
+#&gt; 50 parent 0.69 0.65733 0.032670 0.69
+#&gt; 50 parent 0.63 0.65733 -0.027330 0.63
+#&gt; 75 parent 0.05 0.05339 -0.003386 0.05
+#&gt; 75 parent 0.06 0.05339 0.006614 0.06
+#&gt; 1 m1 4.84 4.82570 0.014301 4.84
+#&gt; 1 m1 5.64 4.82570 0.814301 5.64
+#&gt; 3 m1 12.91 13.06402 -0.154020 12.91
+#&gt; 3 m1 12.96 13.06402 -0.104020 12.96
+#&gt; 7 m1 22.97 25.04656 -2.076564 22.97
+#&gt; 7 m1 24.47 25.04656 -0.576564 24.47
+#&gt; 14 m1 41.69 36.53601 5.153988 41.69
+#&gt; 14 m1 33.21 36.53601 -3.326012 33.21
+#&gt; 21 m1 44.37 41.34639 3.023609 44.37
+#&gt; 21 m1 46.44 41.34639 5.093609 46.44
+#&gt; 35 m1 41.22 42.82669 -1.606690 41.22
+#&gt; 35 m1 37.95 42.82669 -4.876690 37.95
+#&gt; 50 m1 41.19 40.67342 0.516578 41.19
+#&gt; 50 m1 40.01 40.67342 -0.663422 40.01
+#&gt; 75 m1 40.09 35.91105 4.178947 40.09
+#&gt; 75 m1 33.85 35.91105 -2.061053 33.85
+#&gt; 100 m1 31.04 31.48161 -0.441612 31.04
+#&gt; 100 m1 33.13 31.48161 1.648388 33.13
+#&gt; 120 m1 25.15 28.32018 -3.170181 25.15
+#&gt; 120 m1 33.31 28.32018 4.989819 33.31</div><div class='input'>
+
+
+<span class='co'># Manual weighting</span>
+<span class='no'>dw</span> <span class='kw'>&lt;-</span> <span class='no'>FOCUS_2006_D</span>
+<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
+<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3949.676
+#&gt; Model cost at call 2 : 3949.676
+#&gt; Model cost at call 5 : 3949.676
+#&gt; Model cost at call 6 : 2252.859
+#&gt; Model cost at call 8 : 2252.858
+#&gt; Model cost at call 9 : 2252.826
+#&gt; Model cost at call 13 : 1567.343
+#&gt; Model cost at call 14 : 1567.342
+#&gt; Model cost at call 15 : 1567.333
+#&gt; Model cost at call 18 : 1041.524
+#&gt; Model cost at call 19 : 1041.522
+#&gt; Model cost at call 24 : 840.4649
+#&gt; Model cost at call 26 : 840.4646
+#&gt; Model cost at call 29 : 782.303
+#&gt; Model cost at call 31 : 782.3028
+#&gt; Model cost at call 34 : 664.539
+#&gt; Model cost at call 36 : 664.5389
+#&gt; Model cost at call 40 : 615.7908
+#&gt; Model cost at call 42 : 615.7907
+#&gt; Model cost at call 45 : 569.5971
+#&gt; Model cost at call 47 : 569.597
+#&gt; Model cost at call 50 : 517.3175
+#&gt; Model cost at call 52 : 517.3173
+#&gt; Model cost at call 56 : 464.8158
+#&gt; Model cost at call 58 : 464.8157
+#&gt; Model cost at call 62 : 433.0031
+#&gt; Model cost at call 64 : 433.003
+#&gt; Model cost at call 67 : 423.7407
+#&gt; Model cost at call 69 : 423.7406
+#&gt; Model cost at call 70 : 423.7392
+#&gt; Model cost at call 72 : 346.2781
+#&gt; Model cost at call 74 : 346.278
+#&gt; Model cost at call 75 : 346.2779
+#&gt; Model cost at call 78 : 334.5399
+#&gt; Model cost at call 80 : 334.5398
+#&gt; Model cost at call 83 : 324.139
+#&gt; Model cost at call 85 : 324.1389
+#&gt; Model cost at call 88 : 319.7514
+#&gt; Model cost at call 90 : 319.7514
+#&gt; Model cost at call 94 : 300.9426
+#&gt; Model cost at call 96 : 300.9425
+#&gt; Model cost at call 100 : 295.8803
+#&gt; Model cost at call 102 : 295.8803
+#&gt; Model cost at call 105 : 290.3288
+#&gt; Model cost at call 107 : 290.3287
+#&gt; Model cost at call 111 : 284.3257
+#&gt; Model cost at call 113 : 284.3257
+#&gt; Model cost at call 116 : 282.3972
+#&gt; Model cost at call 118 : 282.3972
+#&gt; Model cost at call 122 : 273.7385
+#&gt; Model cost at call 124 : 273.7385
+#&gt; Model cost at call 128 : 271.8379
+#&gt; Model cost at call 130 : 271.8379
+#&gt; Model cost at call 133 : 270.064
+#&gt; Model cost at call 135 : 270.064
+#&gt; Model cost at call 138 : 268.0107
+#&gt; Model cost at call 140 : 268.0107
+#&gt; Model cost at call 144 : 265.6194
+#&gt; Model cost at call 146 : 265.6194
+#&gt; Model cost at call 148 : 265.6194
+#&gt; Model cost at call 149 : 263.4825
+#&gt; Model cost at call 151 : 263.4825
+#&gt; Model cost at call 153 : 263.4824
+#&gt; Model cost at call 154 : 262.0988
+#&gt; Model cost at call 156 : 262.0988
+#&gt; Model cost at call 160 : 260.7078
+#&gt; Model cost at call 162 : 260.7078
+#&gt; Model cost at call 165 : 259.9453
+#&gt; Model cost at call 167 : 259.9453
+#&gt; Model cost at call 170 : 258.9623
+#&gt; Model cost at call 172 : 258.9623
+#&gt; Model cost at call 174 : 258.962
+#&gt; Model cost at call 176 : 258.0119
+#&gt; Model cost at call 178 : 258.0119
+#&gt; Model cost at call 180 : 258.0119
+#&gt; Model cost at call 181 : 257.8698
+#&gt; Model cost at call 183 : 257.8698
+#&gt; Model cost at call 186 : 256.8608
+#&gt; Model cost at call 188 : 256.8608
+#&gt; Model cost at call 190 : 256.8608
+#&gt; Model cost at call 191 : 256.2306
+#&gt; Model cost at call 193 : 256.2306
+#&gt; Model cost at call 195 : 256.2305
+#&gt; Model cost at call 196 : 255.7119
+#&gt; Model cost at call 198 : 255.7118
+#&gt; Model cost at call 201 : 255.3323
+#&gt; Model cost at call 203 : 255.3323
+#&gt; Model cost at call 205 : 255.3323
+#&gt; Model cost at call 206 : 254.6653
+#&gt; Model cost at call 208 : 254.6653
+#&gt; Model cost at call 211 : 254.3984
+#&gt; Model cost at call 213 : 254.3984
+#&gt; Model cost at call 216 : 253.3199
+#&gt; Model cost at call 218 : 253.3199
+#&gt; Model cost at call 220 : 253.3198
+#&gt; Model cost at call 221 : 252.4845
+#&gt; Model cost at call 223 : 252.4845
+#&gt; Model cost at call 225 : 252.4845
+#&gt; Model cost at call 226 : 251.6917
+#&gt; Model cost at call 229 : 251.6917
+#&gt; Model cost at call 230 : 251.6917
+#&gt; Model cost at call 233 : 251.0189
+#&gt; Model cost at call 235 : 251.0189
+#&gt; Model cost at call 238 : 250.6912
+#&gt; Model cost at call 240 : 250.6912
+#&gt; Model cost at call 243 : 250.5546
+#&gt; Model cost at call 245 : 250.5546
+#&gt; Model cost at call 248 : 250.466
+#&gt; Model cost at call 249 : 250.3744
+#&gt; Model cost at call 250 : 249.9681
+#&gt; Model cost at call 251 : 249.2215
+#&gt; Model cost at call 260 : 248.919
+#&gt; Model cost at call 264 : 248.919
+#&gt; Model cost at call 265 : 248.8876
+#&gt; Model cost at call 267 : 248.8876
+#&gt; Model cost at call 270 : 248.8521
+#&gt; Model cost at call 271 : 248.8178
+#&gt; Model cost at call 272 : 248.6837
+#&gt; Model cost at call 273 : 248.5989
+#&gt; Model cost at call 276 : 248.5989
+#&gt; Model cost at call 278 : 248.5935
+#&gt; Model cost at call 280 : 248.5935
+#&gt; Model cost at call 282 : 248.5935
+#&gt; Model cost at call 283 : 248.5902
+#&gt; Model cost at call 284 : 248.5902
+#&gt; Model cost at call 289 : 248.5902
+#&gt; Model cost at call 298 : 248.5902
+#&gt; Model cost at call 309 : 248.5902
+#&gt; Model cost at call 311 : 248.5902
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:53 2016
+#&gt; Date of summary: Fri Nov 18 15:19:53 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 316 model solutions performed in 1.337 s
+#&gt;
+#&gt; Weighting: manual
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.49000 1.33200 96.7800 102.2000
+#&gt; log_k_parent -2.32100 0.03550 -2.3930 -2.2490
+#&gt; log_k_m1 -5.24100 0.21280 -5.6730 -4.8100
+#&gt; f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.00000 0.5312 -0.09455 -0.3351
+#&gt; log_k_parent 0.53123 1.0000 -0.17800 -0.3360
+#&gt; log_k_m1 -0.09455 -0.1780 1.00000 0.7616
+#&gt; f_parent_ilr_1 -0.33513 -0.3360 0.76156 1.0000
+#&gt;
+#&gt; Residual standard error: 2.628 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.490000 74.69 2.222e-41 96.780000 1.022e+02
+#&gt; k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01
+#&gt; k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03
+#&gt; f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.400 4 15
+#&gt; parent 6.454 2 7
+#&gt; m1 4.708 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5162
+#&gt; parent_sink 0.4838
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.063 23.46
+#&gt; m1 130.971 435.08
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err
+#&gt; 0 parent 99.46 99.485977 -0.025977 1
+#&gt; 0 parent 102.04 99.485977 2.554023 1
+#&gt; 1 parent 93.50 90.186118 3.313882 1
+#&gt; 1 parent 92.50 90.186118 2.313882 1
+#&gt; 3 parent 63.23 74.113162 -10.883162 1
+#&gt; 3 parent 68.99 74.113162 -5.123162 1
+#&gt; 7 parent 52.32 50.050295 2.269705 1
+#&gt; 7 parent 55.13 50.050295 5.079705 1
+#&gt; 14 parent 27.27 25.179750 2.090250 1
+#&gt; 14 parent 26.64 25.179750 1.460250 1
+#&gt; 21 parent 11.50 12.667654 -1.167654 1
+#&gt; 21 parent 11.64 12.667654 -1.027654 1
+#&gt; 35 parent 2.85 3.206164 -0.356164 1
+#&gt; 35 parent 2.91 3.206164 -0.296164 1
+#&gt; 50 parent 0.69 0.735619 -0.045619 1
+#&gt; 50 parent 0.63 0.735619 -0.105619 1
+#&gt; 75 parent 0.05 0.063256 -0.013256 1
+#&gt; 75 parent 0.06 0.063256 -0.003256 1
+#&gt; 100 parent NA 0.005439 NA 1
+#&gt; 100 parent NA 0.005439 NA 1
+#&gt; 120 parent NA 0.000764 NA 1
+#&gt; 120 parent NA 0.000764 NA 1
+#&gt; 0 m1 0.00 0.000000 0.000000 2
+#&gt; 0 m1 0.00 0.000000 0.000000 2
+#&gt; 1 m1 4.84 4.787287 0.052713 2
+#&gt; 1 m1 5.64 4.787287 0.852713 2
+#&gt; 3 m1 12.91 12.987848 -0.077848 2
+#&gt; 3 m1 12.96 12.987848 -0.027848 2
+#&gt; 7 m1 22.97 24.996945 -2.026945 2
+#&gt; 7 m1 24.47 24.996945 -0.526945 2
+#&gt; 14 m1 41.69 36.663527 5.026473 2
+#&gt; 14 m1 33.21 36.663527 -3.453527 2
+#&gt; 21 m1 44.37 41.656812 2.713188 2
+#&gt; 21 m1 46.44 41.656812 4.783188 2
+#&gt; 35 m1 41.22 43.350311 -2.130311 2
+#&gt; 35 m1 37.95 43.350311 -5.400311 2
+#&gt; 50 m1 41.19 41.256364 -0.066364 2
+#&gt; 50 m1 40.01 41.256364 -1.246364 2
+#&gt; 75 m1 40.09 36.460566 3.629434 2
+#&gt; 75 m1 33.85 36.460566 -2.610566 2
+#&gt; 100 m1 31.04 31.969288 -0.929288 2
+#&gt; 100 m1 33.13 31.969288 1.160712 2
+#&gt; 120 m1 25.15 28.760615 -3.610615 2
+#&gt; 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>,
+ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3949.676
+#&gt; Model cost at call 2 : 3949.676
+#&gt; Model cost at call 5 : 3949.676
+#&gt; Model cost at call 6 : 2252.859
+#&gt; Model cost at call 8 : 2252.858
+#&gt; Model cost at call 9 : 2252.826
+#&gt; Model cost at call 13 : 1567.343
+#&gt; Model cost at call 14 : 1567.342
+#&gt; Model cost at call 15 : 1567.333
+#&gt; Model cost at call 18 : 1041.524
+#&gt; Model cost at call 19 : 1041.522
+#&gt; Model cost at call 24 : 840.4649
+#&gt; Model cost at call 26 : 840.4646
+#&gt; Model cost at call 29 : 782.303
+#&gt; Model cost at call 31 : 782.3028
+#&gt; Model cost at call 34 : 664.539
+#&gt; Model cost at call 36 : 664.5389
+#&gt; Model cost at call 40 : 615.7908
+#&gt; Model cost at call 42 : 615.7907
+#&gt; Model cost at call 45 : 569.5971
+#&gt; Model cost at call 47 : 569.597
+#&gt; Model cost at call 50 : 517.3175
+#&gt; Model cost at call 52 : 517.3173
+#&gt; Model cost at call 56 : 464.8158
+#&gt; Model cost at call 58 : 464.8157
+#&gt; Model cost at call 62 : 433.0031
+#&gt; Model cost at call 64 : 433.003
+#&gt; Model cost at call 67 : 423.7407
+#&gt; Model cost at call 69 : 423.7406
+#&gt; Model cost at call 70 : 423.7392
+#&gt; Model cost at call 72 : 346.2781
+#&gt; Model cost at call 74 : 346.278
+#&gt; Model cost at call 75 : 346.2779
+#&gt; Model cost at call 78 : 334.5399
+#&gt; Model cost at call 80 : 334.5398
+#&gt; Model cost at call 83 : 324.139
+#&gt; Model cost at call 85 : 324.1389
+#&gt; Model cost at call 88 : 319.7514
+#&gt; Model cost at call 90 : 319.7514
+#&gt; Model cost at call 94 : 300.9426
+#&gt; Model cost at call 96 : 300.9425
+#&gt; Model cost at call 100 : 295.8803
+#&gt; Model cost at call 102 : 295.8803
+#&gt; Model cost at call 105 : 290.3288
+#&gt; Model cost at call 107 : 290.3287
+#&gt; Model cost at call 111 : 284.3257
+#&gt; Model cost at call 113 : 284.3257
+#&gt; Model cost at call 116 : 282.3972
+#&gt; Model cost at call 118 : 282.3972
+#&gt; Model cost at call 122 : 273.7385
+#&gt; Model cost at call 124 : 273.7385
+#&gt; Model cost at call 128 : 271.8379
+#&gt; Model cost at call 130 : 271.8379
+#&gt; Model cost at call 133 : 270.064
+#&gt; Model cost at call 135 : 270.064
+#&gt; Model cost at call 138 : 268.0107
+#&gt; Model cost at call 140 : 268.0107
+#&gt; Model cost at call 144 : 265.6194
+#&gt; Model cost at call 146 : 265.6194
+#&gt; Model cost at call 148 : 265.6194
+#&gt; Model cost at call 149 : 263.4825
+#&gt; Model cost at call 151 : 263.4825
+#&gt; Model cost at call 153 : 263.4824
+#&gt; Model cost at call 154 : 262.0988
+#&gt; Model cost at call 156 : 262.0988
+#&gt; Model cost at call 160 : 260.7078
+#&gt; Model cost at call 162 : 260.7078
+#&gt; Model cost at call 165 : 259.9453
+#&gt; Model cost at call 167 : 259.9453
+#&gt; Model cost at call 170 : 258.9623
+#&gt; Model cost at call 172 : 258.9623
+#&gt; Model cost at call 174 : 258.962
+#&gt; Model cost at call 176 : 258.0119
+#&gt; Model cost at call 178 : 258.0119
+#&gt; Model cost at call 180 : 258.0119
+#&gt; Model cost at call 181 : 257.8698
+#&gt; Model cost at call 183 : 257.8698
+#&gt; Model cost at call 186 : 256.8608
+#&gt; Model cost at call 188 : 256.8608
+#&gt; Model cost at call 190 : 256.8608
+#&gt; Model cost at call 191 : 256.2306
+#&gt; Model cost at call 193 : 256.2306
+#&gt; Model cost at call 195 : 256.2305
+#&gt; Model cost at call 196 : 255.7119
+#&gt; Model cost at call 198 : 255.7118
+#&gt; Model cost at call 201 : 255.3323
+#&gt; Model cost at call 203 : 255.3323
+#&gt; Model cost at call 205 : 255.3323
+#&gt; Model cost at call 206 : 254.6653
+#&gt; Model cost at call 208 : 254.6653
+#&gt; Model cost at call 211 : 254.3984
+#&gt; Model cost at call 213 : 254.3984
+#&gt; Model cost at call 216 : 253.3199
+#&gt; Model cost at call 218 : 253.3199
+#&gt; Model cost at call 220 : 253.3198
+#&gt; Model cost at call 221 : 252.4845
+#&gt; Model cost at call 223 : 252.4845
+#&gt; Model cost at call 225 : 252.4845
+#&gt; Model cost at call 226 : 251.6917
+#&gt; Model cost at call 229 : 251.6917
+#&gt; Model cost at call 230 : 251.6917
+#&gt; Model cost at call 233 : 251.0189
+#&gt; Model cost at call 235 : 251.0189
+#&gt; Model cost at call 238 : 250.6912
+#&gt; Model cost at call 240 : 250.6912
+#&gt; Model cost at call 243 : 250.5546
+#&gt; Model cost at call 245 : 250.5546
+#&gt; Model cost at call 248 : 250.466
+#&gt; Model cost at call 249 : 250.3744
+#&gt; Model cost at call 250 : 249.9681
+#&gt; Model cost at call 251 : 249.2215
+#&gt; Model cost at call 260 : 248.919
+#&gt; Model cost at call 264 : 248.919
+#&gt; Model cost at call 265 : 248.8876
+#&gt; Model cost at call 267 : 248.8876
+#&gt; Model cost at call 270 : 248.8521
+#&gt; Model cost at call 271 : 248.8178
+#&gt; Model cost at call 272 : 248.6837
+#&gt; Model cost at call 273 : 248.5989
+#&gt; Model cost at call 276 : 248.5989
+#&gt; Model cost at call 278 : 248.5935
+#&gt; Model cost at call 280 : 248.5935
+#&gt; Model cost at call 282 : 248.5935
+#&gt; Model cost at call 283 : 248.5902
+#&gt; Model cost at call 284 : 248.5902
+#&gt; Model cost at call 289 : 248.5902
+#&gt; Model cost at call 298 : 248.5902
+#&gt; Model cost at call 309 : 248.5902
+#&gt; Model cost at call 311 : 248.5902
+#&gt; IRLS based on variance estimates for each observed variable
+#&gt; Initial variance estimates are:
+#&gt; parent m1
+#&gt; 11.536305 7.443046
+#&gt; Model cost at call 317 : 40
+#&gt; Model cost at call 319 : 40
+#&gt; Model cost at call 324 : 39.98891
+#&gt; Model cost at call 325 : 39.9889
+#&gt; Model cost at call 327 : 39.98886
+#&gt; Model cost at call 331 : 39.98871
+#&gt; Model cost at call 333 : 39.97254
+#&gt; Model cost at call 336 : 39.97253
+#&gt; Model cost at call 338 : 39.96929
+#&gt; Model cost at call 340 : 39.96929
+#&gt; Model cost at call 344 : 39.96849
+#&gt; Model cost at call 346 : 39.96849
+#&gt; Model cost at call 348 : 39.96849
+#&gt; Model cost at call 349 : 39.96774
+#&gt; Model cost at call 351 : 39.96774
+#&gt; Model cost at call 353 : 39.96774
+#&gt; Model cost at call 354 : 39.96714
+#&gt; Model cost at call 356 : 39.96714
+#&gt; Model cost at call 359 : 39.96617
+#&gt; Model cost at call 361 : 39.96617
+#&gt; Model cost at call 364 : 39.96606
+#&gt; Model cost at call 366 : 39.96606
+#&gt; Model cost at call 369 : 39.96551
+#&gt; Model cost at call 371 : 39.96551
+#&gt; Model cost at call 372 : 39.96551
+#&gt; Model cost at call 375 : 39.96527
+#&gt; Model cost at call 378 : 39.96527
+#&gt; Model cost at call 379 : 39.96527
+#&gt; Model cost at call 380 : 39.96525
+#&gt; Model cost at call 382 : 39.96525
+#&gt; Model cost at call 385 : 39.9651
+#&gt; Model cost at call 387 : 39.9651
+#&gt; Model cost at call 388 : 39.9651
+#&gt; Model cost at call 390 : 39.96502
+#&gt; Model cost at call 393 : 39.96502
+#&gt; Model cost at call 396 : 39.96502
+#&gt; Model cost at call 397 : 39.96467
+#&gt; Model cost at call 398 : 39.96422
+#&gt; Model cost at call 399 : 39.9624
+#&gt; Model cost at call 400 : 39.95909
+#&gt; Model cost at call 402 : 39.95909
+#&gt; Model cost at call 405 : 39.9571
+#&gt; Model cost at call 407 : 39.95709
+#&gt; Model cost at call 413 : 39.95479
+#&gt; Model cost at call 414 : 39.95479
+#&gt; Model cost at call 415 : 39.95479
+#&gt; Model cost at call 417 : 39.95479
+#&gt; Model cost at call 419 : 39.95398
+#&gt; Model cost at call 422 : 39.95398
+#&gt; Model cost at call 424 : 39.95387
+#&gt; Model cost at call 429 : 39.95384
+#&gt; Model cost at call 432 : 39.95384
+#&gt; Model cost at call 435 : 39.95384
+#&gt; Model cost at call 437 : 39.95384
+#&gt; Model cost at call 438 : 39.95384
+#&gt; Model cost at call 446 : 39.95384
+#&gt; Model cost at call 455 : 39.95384
+#&gt; Model cost at call 469 : 39.95384
+#&gt; Model cost at call 473 : 39.95384
+#&gt; Iteration 1 yields variance estimates:
+#&gt; parent m1
+#&gt; 11.572891 7.408116
+#&gt; Sum of squared differences to last variance estimates: 7e-05
+#&gt; Iteration 2 yields variance estimates:
+#&gt; parent m1
+#&gt; 11.573402 7.407847
+#&gt; Sum of squared differences to last variance estimates: 8.1e-09
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:55 2016
+#&gt; Date of summary: Fri Nov 18 15:19:55 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 648 model solutions performed in 2.716 s
+#&gt;
+#&gt; Weighting: manual then iterative reweighting method obs
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.67000 1.79200 96.04000 103.300
+#&gt; log_k_parent -2.31200 0.04560 -2.40400 -2.220
+#&gt; log_k_m1 -5.25100 0.12510 -5.50500 -4.998
+#&gt; f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5083 -0.1979 -0.6147
+#&gt; log_k_parent 0.5083 1.0000 -0.3894 -0.6062
+#&gt; log_k_m1 -0.1979 -0.3894 1.0000 0.7417
+#&gt; f_parent_ilr_1 -0.6147 -0.6062 0.7417 1.0000
+#&gt;
+#&gt; Residual standard error: 1.054 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.67000 55.630 8.178e-37 96.040000 1.033e+02
+#&gt; k_parent 0.09906 21.930 1.015e-22 0.090310 1.087e-01
+#&gt; k_m1 0.00524 7.996 8.488e-10 0.004066 6.753e-03
+#&gt; f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.399 4 15
+#&gt; parent 6.466 2 7
+#&gt; m1 4.679 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5134
+#&gt; parent_sink 0.4866
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 6.997 23.24
+#&gt; m1 132.281 439.43
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual err.ini err
+#&gt; 0 parent 99.46 9.967e+01 -2.122e-01 1 3.402
+#&gt; 0 parent 102.04 9.967e+01 2.368e+00 1 3.402
+#&gt; 1 parent 93.50 9.027e+01 3.228e+00 1 3.402
+#&gt; 1 parent 92.50 9.027e+01 2.228e+00 1 3.402
+#&gt; 3 parent 63.23 7.405e+01 -1.082e+01 1 3.402
+#&gt; 3 parent 68.99 7.405e+01 -5.056e+00 1 3.402
+#&gt; 7 parent 52.32 4.982e+01 2.499e+00 1 3.402
+#&gt; 7 parent 55.13 4.982e+01 5.309e+00 1 3.402
+#&gt; 14 parent 27.27 2.490e+01 2.367e+00 1 3.402
+#&gt; 14 parent 26.64 2.490e+01 1.737e+00 1 3.402
+#&gt; 21 parent 11.50 1.245e+01 -9.477e-01 1 3.402
+#&gt; 21 parent 11.64 1.245e+01 -8.077e-01 1 3.402
+#&gt; 35 parent 2.85 3.110e+00 -2.600e-01 1 3.402
+#&gt; 35 parent 2.91 3.110e+00 -2.000e-01 1 3.402
+#&gt; 50 parent 0.69 7.037e-01 -1.375e-02 1 3.402
+#&gt; 50 parent 0.63 7.037e-01 -7.375e-02 1 3.402
+#&gt; 75 parent 0.05 5.913e-02 -9.134e-03 1 3.402
+#&gt; 75 parent 0.06 5.913e-02 8.659e-04 1 3.402
+#&gt; 100 parent NA 4.969e-03 NA 1 3.402
+#&gt; 100 parent NA 4.969e-03 NA 1 3.402
+#&gt; 120 parent NA 6.852e-04 NA 1 3.402
+#&gt; 120 parent NA 6.852e-04 NA 1 3.402
+#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2 2.722
+#&gt; 0 m1 0.00 0.000e+00 0.000e+00 2 2.722
+#&gt; 1 m1 4.84 4.813e+00 2.672e-02 2 2.722
+#&gt; 1 m1 5.64 4.813e+00 8.267e-01 2 2.722
+#&gt; 3 m1 12.91 1.305e+01 -1.378e-01 2 2.722
+#&gt; 3 m1 12.96 1.305e+01 -8.778e-02 2 2.722
+#&gt; 7 m1 22.97 2.508e+01 -2.106e+00 2 2.722
+#&gt; 7 m1 24.47 2.508e+01 -6.061e-01 2 2.722
+#&gt; 14 m1 41.69 3.671e+01 4.983e+00 2 2.722
+#&gt; 14 m1 33.21 3.671e+01 -3.497e+00 2 2.722
+#&gt; 21 m1 44.37 4.165e+01 2.719e+00 2 2.722
+#&gt; 21 m1 46.44 4.165e+01 4.789e+00 2 2.722
+#&gt; 35 m1 41.22 4.329e+01 -2.069e+00 2 2.722
+#&gt; 35 m1 37.95 4.329e+01 -5.339e+00 2 2.722
+#&gt; 50 m1 41.19 4.119e+01 -3.394e-03 2 2.722
+#&gt; 50 m1 40.01 4.119e+01 -1.183e+00 2 2.722
+#&gt; 75 m1 40.09 3.644e+01 3.652e+00 2 2.722
+#&gt; 75 m1 33.85 3.644e+01 -2.588e+00 2 2.722
+#&gt; 100 m1 31.04 3.199e+01 -9.497e-01 2 2.722
+#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2 2.722
+#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2 2.722
+#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2 2.722</div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 9c78d78a..546d7c88 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -275,17 +275,17 @@
<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; 0.024 0.004 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.008 0.024 0.004 </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
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.016 0.004 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.020 0.000 0.002 </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='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; 0.032 0.000 0.035 </div></pre>
+#&gt; 0.032 0.000 0.034 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mmkin-14.png b/docs/reference/mmkin-14.png
new file mode 100644
index 00000000..9e40d451
--- /dev/null
+++ b/docs/reference/mmkin-14.png
Binary files differ
diff --git a/docs/reference/mmkin-16.png b/docs/reference/mmkin-16.png
new file mode 100644
index 00000000..72cfc5e7
--- /dev/null
+++ b/docs/reference/mmkin-16.png
Binary files differ
diff --git a/docs/reference/mmkin-18.png b/docs/reference/mmkin-18.png
new file mode 100644
index 00000000..0b315b1a
--- /dev/null
+++ b/docs/reference/mmkin-18.png
Binary files differ
diff --git a/docs/reference/mmkin-20.png b/docs/reference/mmkin-20.png
new file mode 100644
index 00000000..b98940ff
--- /dev/null
+++ b/docs/reference/mmkin-20.png
Binary files differ
diff --git a/docs/reference/mmkin-22.png b/docs/reference/mmkin-22.png
new file mode 100644
index 00000000..c2e9e5ae
--- /dev/null
+++ b/docs/reference/mmkin-22.png
Binary files differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index f7f56164..0e39dac0 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -128,38 +128,1103 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># m_synth_SFO_lin &lt;- mkinmod(parent = mkinsub("SFO", "M1"),</span>
-<span class='co'># M1 = mkinsub("SFO", "M2"),</span>
-<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># m_synth_FOMC_lin &lt;- mkinmod(parent = mkinsub("FOMC", "M1"),</span>
-<span class='co'># M1 = mkinsub("SFO", "M2"),</span>
-<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># models &lt;- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span>
-<span class='co'># datasets &lt;- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span>
-<span class='co'># names(datasets) &lt;- paste("Dataset", 1:3)</span>
-<span class='co'># </span>
-<span class='co'># time_default &lt;- system.time(fits.0 &lt;- mmkin(models, datasets))</span>
-<span class='co'># time_1 &lt;- system.time(fits.1 &lt;- mmkin(models, datasets, cores = 1))</span>
-<span class='co'># </span>
-<span class='co'># time_default</span>
-<span class='co'># time_1</span>
-<span class='co'># </span>
-<span class='co'># endpoints(fits[["SFO_lin", 2]])</span>
-<span class='co'># </span>
-<span class='co'># # Plot.mkinfit handles rows or columns of mmkin result objects</span>
-<span class='co'># plot(fits.0[1, ])</span>
-<span class='co'># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span>
-<span class='co'># plot(fits.0[, 1])</span>
-<span class='co'># # Use double brackets to extract a single mkinfit object, which will be plotted</span>
-<span class='co'># # by plot.mkinfit</span>
-<span class='co'># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span>
-<span class='co'># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
-<span class='co'># # allow to plot the observed variables separately</span>
-<span class='co'># plot(fits.0[1, 1])</span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+ <pre class="examples"><div class='input'>
+<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</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='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='st'>"M2"</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>)</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='no'>m_synth_FOMC_lin</span> <span class='kw'>&lt;-</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'>"FOMC"</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='st'>"M2"</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>)</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='no'>models</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>)
+<span class='no'>datasets</span> <span class='kw'>&lt;-</span> <span class='fu'>lapply</span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>)
+<span class='fu'>names</span>(<span class='no'>datasets</span>) <span class='kw'>&lt;-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)
+
+<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>))
+<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.1</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>))</div><div class='output co'>#&gt; Model cost at call 1 : 31054.59
+#&gt; Model cost at call 3 : 31054.59
+#&gt; Model cost at call 8 : 15089.57
+#&gt; Model cost at call 9 : 11464.3
+#&gt; Model cost at call 11 : 11464.1
+#&gt; Model cost at call 16 : 5723.32
+#&gt; Model cost at call 17 : 5723.318
+#&gt; Model cost at call 19 : 5723.304
+#&gt; Model cost at call 21 : 5723.304
+#&gt; Model cost at call 24 : 3968.126
+#&gt; Model cost at call 25 : 3968.124
+#&gt; Model cost at call 28 : 3968.119
+#&gt; Model cost at call 31 : 3416.421
+#&gt; Model cost at call 32 : 3416.42
+#&gt; Model cost at call 36 : 3416.418
+#&gt; Model cost at call 38 : 866.5564
+#&gt; Model cost at call 42 : 866.5557
+#&gt; Model cost at call 45 : 670.4833
+#&gt; Model cost at call 47 : 670.476
+#&gt; Model cost at call 53 : 312.9905
+#&gt; Model cost at call 57 : 312.9904
+#&gt; Model cost at call 58 : 312.9904
+#&gt; Model cost at call 61 : 287.8916
+#&gt; Model cost at call 63 : 287.8916
+#&gt; Model cost at call 66 : 287.8916
+#&gt; Model cost at call 69 : 284.5441
+#&gt; Model cost at call 71 : 284.5441
+#&gt; Model cost at call 73 : 284.5441
+#&gt; Model cost at call 76 : 283.4533
+#&gt; Model cost at call 78 : 283.4533
+#&gt; Model cost at call 83 : 282.1356
+#&gt; Model cost at call 85 : 282.1356
+#&gt; Model cost at call 88 : 282.1356
+#&gt; Model cost at call 90 : 280.7846
+#&gt; Model cost at call 92 : 280.7846
+#&gt; Model cost at call 95 : 280.7846
+#&gt; Model cost at call 97 : 278.4856
+#&gt; Model cost at call 98 : 274.5025
+#&gt; Model cost at call 99 : 269.2866
+#&gt; Model cost at call 101 : 269.2866
+#&gt; Model cost at call 102 : 269.2866
+#&gt; Model cost at call 103 : 269.2866
+#&gt; Model cost at call 106 : 254.1284
+#&gt; Model cost at call 108 : 254.1283
+#&gt; Model cost at call 109 : 254.1283
+#&gt; Model cost at call 112 : 254.128
+#&gt; Model cost at call 114 : 233.1376
+#&gt; Model cost at call 116 : 233.1376
+#&gt; Model cost at call 118 : 233.1375
+#&gt; Model cost at call 121 : 227.5879
+#&gt; Model cost at call 124 : 227.5879
+#&gt; Model cost at call 125 : 227.5878
+#&gt; Model cost at call 129 : 217.0041
+#&gt; Model cost at call 133 : 217.0041
+#&gt; Model cost at call 135 : 217.0041
+#&gt; Model cost at call 136 : 215.1367
+#&gt; Model cost at call 138 : 215.1367
+#&gt; Model cost at call 143 : 213.3794
+#&gt; Model cost at call 145 : 213.3794
+#&gt; Model cost at call 150 : 211.0201
+#&gt; Model cost at call 152 : 211.0201
+#&gt; Model cost at call 154 : 211.0201
+#&gt; Model cost at call 155 : 211.0201
+#&gt; Model cost at call 157 : 210.6426
+#&gt; Model cost at call 159 : 210.6426
+#&gt; Model cost at call 160 : 210.6425
+#&gt; Model cost at call 164 : 207.6331
+#&gt; Model cost at call 167 : 207.6331
+#&gt; Model cost at call 171 : 206.2366
+#&gt; Model cost at call 173 : 206.2366
+#&gt; Model cost at call 174 : 206.2366
+#&gt; Model cost at call 178 : 204.8117
+#&gt; Model cost at call 180 : 204.8117
+#&gt; Model cost at call 185 : 204.7988
+#&gt; Model cost at call 187 : 204.7988
+#&gt; Model cost at call 190 : 204.7988
+#&gt; Model cost at call 192 : 203.5122
+#&gt; Model cost at call 194 : 203.5122
+#&gt; Model cost at call 197 : 203.5122
+#&gt; Model cost at call 198 : 203.5122
+#&gt; Model cost at call 199 : 203.354
+#&gt; Model cost at call 201 : 203.354
+#&gt; Model cost at call 204 : 203.354
+#&gt; Model cost at call 206 : 202.6825
+#&gt; Model cost at call 208 : 202.6825
+#&gt; Model cost at call 209 : 202.6825
+#&gt; Model cost at call 212 : 202.6825
+#&gt; Model cost at call 213 : 202.4582
+#&gt; Model cost at call 215 : 202.4582
+#&gt; Model cost at call 220 : 202.3261
+#&gt; Model cost at call 222 : 202.3261
+#&gt; Model cost at call 227 : 202.2306
+#&gt; Model cost at call 229 : 202.2306
+#&gt; Model cost at call 231 : 202.2306
+#&gt; Model cost at call 234 : 202.115
+#&gt; Model cost at call 236 : 202.115
+#&gt; Model cost at call 238 : 202.115
+#&gt; Model cost at call 241 : 202.0397
+#&gt; Model cost at call 243 : 202.0397
+#&gt; Model cost at call 248 : 201.8989
+#&gt; Model cost at call 249 : 201.8551
+#&gt; Model cost at call 252 : 201.8551
+#&gt; Model cost at call 257 : 201.676
+#&gt; Model cost at call 259 : 201.676
+#&gt; Model cost at call 264 : 201.6285
+#&gt; Model cost at call 266 : 201.6285
+#&gt; Model cost at call 270 : 201.6284
+#&gt; Model cost at call 271 : 201.5876
+#&gt; Model cost at call 272 : 201.5876
+#&gt; Model cost at call 278 : 201.5317
+#&gt; Model cost at call 279 : 201.5317
+#&gt; Model cost at call 286 : 201.5207
+#&gt; Model cost at call 287 : 201.5207
+#&gt; Model cost at call 289 : 201.5207
+#&gt; Model cost at call 293 : 201.5207
+#&gt; Model cost at call 294 : 201.5207
+#&gt; Model cost at call 296 : 201.5174
+#&gt; Model cost at call 301 : 201.5174
+#&gt; Model cost at call 304 : 201.5169
+#&gt; Model cost at call 305 : 201.5169
+#&gt; Model cost at call 306 : 201.5169
+#&gt; Model cost at call 309 : 201.5169
+#&gt; Model cost at call 312 : 201.5169
+#&gt; Model cost at call 314 : 201.5169
+#&gt; Model cost at call 322 : 201.5169
+#&gt; Model cost at call 325 : 201.5169
+#&gt; Model cost at call 340 : 201.5169
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; Model cost at call 1 : 35974.4
+#&gt; Model cost at call 3 : 35974.4
+#&gt; Model cost at call 5 : 35974.4
+#&gt; Model cost at call 7 : 35974.4
+#&gt; Model cost at call 9 : 13270.14
+#&gt; Model cost at call 10 : 12432.22
+#&gt; Model cost at call 14 : 12432.12
+#&gt; Model cost at call 16 : 12431.88
+#&gt; Model cost at call 18 : 5356.271
+#&gt; Model cost at call 19 : 5356.268
+#&gt; Model cost at call 20 : 5356.251
+#&gt; Model cost at call 22 : 5356.245
+#&gt; Model cost at call 27 : 1507.839
+#&gt; Model cost at call 33 : 1507.839
+#&gt; Model cost at call 35 : 582.0818
+#&gt; Model cost at call 36 : 582.0813
+#&gt; Model cost at call 38 : 582.0802
+#&gt; Model cost at call 40 : 582.0799
+#&gt; Model cost at call 44 : 328.9337
+#&gt; Model cost at call 45 : 328.9335
+#&gt; Model cost at call 51 : 328.9328
+#&gt; Model cost at call 53 : 313.4901
+#&gt; Model cost at call 59 : 313.49
+#&gt; Model cost at call 60 : 313.4899
+#&gt; Model cost at call 61 : 308.6268
+#&gt; Model cost at call 63 : 308.6267
+#&gt; Model cost at call 69 : 302.4454
+#&gt; Model cost at call 73 : 302.4453
+#&gt; Model cost at call 77 : 298.0751
+#&gt; Model cost at call 79 : 298.075
+#&gt; Model cost at call 85 : 293.1404
+#&gt; Model cost at call 86 : 289.6645
+#&gt; Model cost at call 88 : 289.6645
+#&gt; Model cost at call 95 : 288.1617
+#&gt; Model cost at call 101 : 288.1616
+#&gt; Model cost at call 102 : 288.1615
+#&gt; Model cost at call 103 : 286.7649
+#&gt; Model cost at call 109 : 286.7649
+#&gt; Model cost at call 111 : 284.5224
+#&gt; Model cost at call 117 : 284.5224
+#&gt; Model cost at call 118 : 284.5224
+#&gt; Model cost at call 119 : 281.3466
+#&gt; Model cost at call 125 : 281.3466
+#&gt; Model cost at call 127 : 274.0924
+#&gt; Model cost at call 128 : 264.929
+#&gt; Model cost at call 133 : 264.929
+#&gt; Model cost at call 136 : 251.3329
+#&gt; Model cost at call 137 : 251.3329
+#&gt; Model cost at call 140 : 251.3329
+#&gt; Model cost at call 141 : 251.3329
+#&gt; Model cost at call 146 : 247.7019
+#&gt; Model cost at call 147 : 247.7019
+#&gt; Model cost at call 149 : 247.7018
+#&gt; Model cost at call 154 : 247.3465
+#&gt; Model cost at call 158 : 247.3465
+#&gt; Model cost at call 160 : 247.3464
+#&gt; Model cost at call 162 : 244.622
+#&gt; Model cost at call 166 : 244.622
+#&gt; Model cost at call 170 : 242.5961
+#&gt; Model cost at call 171 : 241.6973
+#&gt; Model cost at call 173 : 241.6973
+#&gt; Model cost at call 174 : 241.6973
+#&gt; Model cost at call 175 : 241.6973
+#&gt; Model cost at call 179 : 238.8924
+#&gt; Model cost at call 181 : 238.8923
+#&gt; Model cost at call 187 : 236.0921
+#&gt; Model cost at call 190 : 236.0921
+#&gt; Model cost at call 192 : 236.092
+#&gt; Model cost at call 195 : 233.9082
+#&gt; Model cost at call 197 : 233.9082
+#&gt; Model cost at call 201 : 233.9082
+#&gt; Model cost at call 202 : 233.9082
+#&gt; Model cost at call 203 : 228.1486
+#&gt; Model cost at call 205 : 228.1486
+#&gt; Model cost at call 206 : 228.1485
+#&gt; Model cost at call 207 : 228.1485
+#&gt; Model cost at call 211 : 225.0879
+#&gt; Model cost at call 214 : 225.0879
+#&gt; Model cost at call 216 : 225.0879
+#&gt; Model cost at call 218 : 225.0879
+#&gt; Model cost at call 219 : 220.9928
+#&gt; Model cost at call 221 : 220.9928
+#&gt; Model cost at call 227 : 219.1889
+#&gt; Model cost at call 229 : 219.1888
+#&gt; Model cost at call 233 : 219.1888
+#&gt; Model cost at call 235 : 218.6966
+#&gt; Model cost at call 238 : 218.6966
+#&gt; Model cost at call 239 : 218.6966
+#&gt; Model cost at call 240 : 218.6966
+#&gt; Model cost at call 241 : 218.6966
+#&gt; Model cost at call 242 : 218.6966
+#&gt; Model cost at call 243 : 214.4307
+#&gt; Model cost at call 247 : 214.4307
+#&gt; Model cost at call 251 : 213.6076
+#&gt; Model cost at call 253 : 213.6076
+#&gt; Model cost at call 254 : 213.6076
+#&gt; Model cost at call 256 : 213.6076
+#&gt; Model cost at call 259 : 211.0287
+#&gt; Model cost at call 262 : 211.0287
+#&gt; Model cost at call 263 : 211.0287
+#&gt; Model cost at call 267 : 209.6141
+#&gt; Model cost at call 270 : 209.6141
+#&gt; Model cost at call 271 : 209.6141
+#&gt; Model cost at call 276 : 207.896
+#&gt; Model cost at call 278 : 207.896
+#&gt; Model cost at call 284 : 206.4468
+#&gt; Model cost at call 286 : 206.4468
+#&gt; Model cost at call 289 : 206.4468
+#&gt; Model cost at call 292 : 205.8789
+#&gt; Model cost at call 296 : 205.8789
+#&gt; Model cost at call 298 : 205.8789
+#&gt; Model cost at call 299 : 205.8789
+#&gt; Model cost at call 300 : 204.2634
+#&gt; Model cost at call 301 : 204.2634
+#&gt; Model cost at call 303 : 204.2634
+#&gt; Model cost at call 305 : 204.2634
+#&gt; Model cost at call 308 : 203.5453
+#&gt; Model cost at call 309 : 203.338
+#&gt; Model cost at call 310 : 203.338
+#&gt; Model cost at call 313 : 203.338
+#&gt; Model cost at call 314 : 203.338
+#&gt; Model cost at call 316 : 203.338
+#&gt; Model cost at call 318 : 202.797
+#&gt; Model cost at call 321 : 202.797
+#&gt; Model cost at call 326 : 202.4377
+#&gt; Model cost at call 327 : 202.4377
+#&gt; Model cost at call 334 : 202.0027
+#&gt; Model cost at call 335 : 202.0027
+#&gt; Model cost at call 342 : 201.8249
+#&gt; Model cost at call 344 : 201.8249
+#&gt; Model cost at call 349 : 201.8249
+#&gt; Model cost at call 351 : 201.7123
+#&gt; Model cost at call 352 : 201.7123
+#&gt; Model cost at call 359 : 201.6476
+#&gt; Model cost at call 361 : 201.6476
+#&gt; Model cost at call 365 : 201.6476
+#&gt; Model cost at call 368 : 201.5827
+#&gt; Model cost at call 371 : 201.5827
+#&gt; Model cost at call 378 : 201.5531
+#&gt; Model cost at call 379 : 201.5531
+#&gt; Model cost at call 386 : 201.5531
+#&gt; Model cost at call 390 : 201.537
+#&gt; Model cost at call 391 : 201.537
+#&gt; Model cost at call 401 : 201.5281
+#&gt; Model cost at call 402 : 201.5281
+#&gt; Model cost at call 404 : 201.5281
+#&gt; Model cost at call 407 : 201.5281
+#&gt; Model cost at call 413 : 201.5231
+#&gt; Model cost at call 417 : 201.5231
+#&gt; Model cost at call 418 : 201.5231
+#&gt; Model cost at call 420 : 201.5231
+#&gt; Model cost at call 426 : 201.5199
+#&gt; Model cost at call 428 : 201.5199
+#&gt; Model cost at call 439 : 201.5184
+#&gt; Model cost at call 443 : 201.5184
+#&gt; Model cost at call 444 : 201.5184
+#&gt; Model cost at call 446 : 201.5184
+#&gt; Model cost at call 454 : 201.5177
+#&gt; Model cost at call 457 : 201.5177
+#&gt; Model cost at call 469 : 201.5174
+#&gt; Model cost at call 473 : 201.5174
+#&gt; Model cost at call 476 : 201.5174
+#&gt; Model cost at call 480 : 201.5174
+#&gt; Model cost at call 483 : 201.5174
+#&gt; Model cost at call 484 : 201.5171
+#&gt; Model cost at call 487 : 201.5171
+#&gt; Model cost at call 499 : 201.517
+#&gt; Model cost at call 506 : 201.517
+#&gt; Model cost at call 510 : 201.517
+#&gt; Model cost at call 514 : 201.517
+#&gt; Model cost at call 522 : 201.517
+#&gt; Model cost at call 526 : 201.517
+#&gt; Model cost at call 527 : 201.517
+#&gt; Model cost at call 529 : 201.5169
+#&gt; Model cost at call 536 : 201.5169
+#&gt; Model cost at call 540 : 201.5169
+#&gt; Model cost at call 544 : 201.5169
+#&gt; Model cost at call 556 : 201.5169
+#&gt; Model cost at call 557 : 201.5169
+#&gt; Model cost at call 559 : 201.5169
+#&gt; Model cost at call 574 : 201.5169
+#&gt; Model cost at call 575 : 201.5169
+#&gt; Model cost at call 578 : 201.5169
+#&gt; Model cost at call 582 : 201.5169
+#&gt; Model cost at call 586 : 201.5169
+#&gt; Model cost at call 589 : 201.5169
+#&gt; Model cost at call 590 : 201.5169
+#&gt; Model cost at call 601 : 201.5169
+#&gt; Model cost at call 604 : 201.5169
+#&gt; Model cost at call 617 : 201.5169
+#&gt; Model cost at call 632 : 201.5169
+#&gt; Model cost at call 647 : 201.5169
+#&gt; Model cost at call 662 : 201.5169
+#&gt; Model cost at call 680 : 201.5169
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; Model cost at call 1 : 30689.89
+#&gt; Model cost at call 3 : 30689.89
+#&gt; Model cost at call 8 : 16294.04
+#&gt; Model cost at call 9 : 12699.33
+#&gt; Model cost at call 11 : 12699.26
+#&gt; Model cost at call 14 : 12699.05
+#&gt; Model cost at call 17 : 9202.163
+#&gt; Model cost at call 18 : 9202.16
+#&gt; Model cost at call 20 : 9202.147
+#&gt; Model cost at call 22 : 9202.147
+#&gt; Model cost at call 25 : 6601.043
+#&gt; Model cost at call 26 : 6601.041
+#&gt; Model cost at call 30 : 6601.04
+#&gt; Model cost at call 32 : 4223.705
+#&gt; Model cost at call 34 : 4223.703
+#&gt; Model cost at call 39 : 4223.703
+#&gt; Model cost at call 40 : 1443.507
+#&gt; Model cost at call 45 : 1443.507
+#&gt; Model cost at call 49 : 1191.267
+#&gt; Model cost at call 51 : 1191.267
+#&gt; Model cost at call 56 : 1186.498
+#&gt; Model cost at call 57 : 1186.498
+#&gt; Model cost at call 58 : 1186.497
+#&gt; Model cost at call 59 : 1186.497
+#&gt; Model cost at call 61 : 1186.496
+#&gt; Model cost at call 62 : 1186.494
+#&gt; Model cost at call 63 : 1130.799
+#&gt; Model cost at call 64 : 1130.799
+#&gt; Model cost at call 71 : 1126.363
+#&gt; Model cost at call 73 : 1126.363
+#&gt; Model cost at call 78 : 1122.848
+#&gt; Model cost at call 80 : 1122.848
+#&gt; Model cost at call 82 : 1122.848
+#&gt; Model cost at call 85 : 1120.954
+#&gt; Model cost at call 87 : 1120.954
+#&gt; Model cost at call 88 : 1120.954
+#&gt; Model cost at call 89 : 1120.954
+#&gt; Model cost at call 92 : 1117.156
+#&gt; Model cost at call 95 : 1117.156
+#&gt; Model cost at call 96 : 1117.156
+#&gt; Model cost at call 99 : 1116.894
+#&gt; Model cost at call 101 : 1116.894
+#&gt; Model cost at call 104 : 1116.894
+#&gt; Model cost at call 106 : 1113.955
+#&gt; Model cost at call 108 : 1113.955
+#&gt; Model cost at call 112 : 1113.955
+#&gt; Model cost at call 113 : 1113.03
+#&gt; Model cost at call 115 : 1113.03
+#&gt; Model cost at call 120 : 1111.643
+#&gt; Model cost at call 122 : 1111.643
+#&gt; Model cost at call 127 : 1109.657
+#&gt; Model cost at call 129 : 1109.657
+#&gt; Model cost at call 131 : 1109.657
+#&gt; Model cost at call 134 : 1106.725
+#&gt; Model cost at call 136 : 1106.725
+#&gt; Model cost at call 137 : 1106.725
+#&gt; Model cost at call 142 : 1106.005
+#&gt; Model cost at call 144 : 1106.005
+#&gt; Model cost at call 145 : 1106.005
+#&gt; Model cost at call 147 : 1106.005
+#&gt; Model cost at call 149 : 1105.268
+#&gt; Model cost at call 151 : 1105.268
+#&gt; Model cost at call 153 : 1105.268
+#&gt; Model cost at call 156 : 1104.247
+#&gt; Model cost at call 158 : 1104.247
+#&gt; Model cost at call 159 : 1104.247
+#&gt; Model cost at call 161 : 1104.247
+#&gt; Model cost at call 163 : 1103.813
+#&gt; Model cost at call 165 : 1103.813
+#&gt; Model cost at call 167 : 1103.813
+#&gt; Model cost at call 170 : 1103.075
+#&gt; Model cost at call 172 : 1103.075
+#&gt; Model cost at call 173 : 1103.075
+#&gt; Model cost at call 177 : 1102.447
+#&gt; Model cost at call 179 : 1102.447
+#&gt; Model cost at call 180 : 1102.447
+#&gt; Model cost at call 183 : 1102.447
+#&gt; Model cost at call 184 : 1102.038
+#&gt; Model cost at call 185 : 1101.712
+#&gt; Model cost at call 186 : 1101.337
+#&gt; Model cost at call 188 : 1101.337
+#&gt; Model cost at call 193 : 1100.37
+#&gt; Model cost at call 195 : 1100.37
+#&gt; Model cost at call 197 : 1100.37
+#&gt; Model cost at call 200 : 1099.46
+#&gt; Model cost at call 202 : 1099.46
+#&gt; Model cost at call 207 : 1099.262
+#&gt; Model cost at call 209 : 1099.262
+#&gt; Model cost at call 211 : 1099.262
+#&gt; Model cost at call 212 : 1099.261
+#&gt; Model cost at call 214 : 1099.227
+#&gt; Model cost at call 216 : 1099.227
+#&gt; Model cost at call 217 : 1099.227
+#&gt; Model cost at call 218 : 1099.227
+#&gt; Model cost at call 221 : 1098.331
+#&gt; Model cost at call 223 : 1098.331
+#&gt; Model cost at call 224 : 1098.331
+#&gt; Model cost at call 230 : 1098.24
+#&gt; Model cost at call 235 : 1098.24
+#&gt; Model cost at call 236 : 1098.24
+#&gt; Model cost at call 238 : 1098.231
+#&gt; Model cost at call 240 : 1098.231
+#&gt; Model cost at call 245 : 1098.228
+#&gt; Model cost at call 247 : 1098.228
+#&gt; Model cost at call 252 : 1098.221
+#&gt; Model cost at call 254 : 1098.221
+#&gt; Model cost at call 255 : 1098.221
+#&gt; Model cost at call 258 : 1098.221
+#&gt; Model cost at call 261 : 1098.214
+#&gt; Model cost at call 263 : 1098.214
+#&gt; Model cost at call 268 : 1098.204
+#&gt; Model cost at call 269 : 1098.196
+#&gt; Model cost at call 270 : 1098.187
+#&gt; Model cost at call 272 : 1098.187
+#&gt; Model cost at call 273 : 1098.187
+#&gt; Model cost at call 279 : 1098.181
+#&gt; Model cost at call 281 : 1098.181
+#&gt; Model cost at call 282 : 1098.181
+#&gt; Model cost at call 284 : 1098.181
+#&gt; Model cost at call 285 : 1098.181
+#&gt; Model cost at call 287 : 1098.172
+#&gt; Model cost at call 291 : 1098.172
+#&gt; Model cost at call 293 : 1098.172
+#&gt; Model cost at call 294 : 1098.169
+#&gt; Model cost at call 295 : 1098.169
+#&gt; Model cost at call 296 : 1098.169
+#&gt; Model cost at call 301 : 1098.169
+#&gt; Model cost at call 305 : 1098.169
+#&gt; Model cost at call 306 : 1098.169
+#&gt; Model cost at call 309 : 1098.169
+#&gt; Model cost at call 314 : 1098.169
+#&gt; Model cost at call 318 : 1098.169
+#&gt; Model cost at call 319 : 1098.169
+#&gt; Model cost at call 321 : 1098.169
+#&gt; Model cost at call 324 : 1098.169
+#&gt; Model cost at call 325 : 1098.169
+#&gt; Model cost at call 331 : 1098.169
+#&gt; Model cost at call 333 : 1098.169
+#&gt; Model cost at call 336 : 1098.169
+#&gt; Model cost at call 342 : 1098.169
+#&gt; Model cost at call 344 : 1098.169
+#&gt; Model cost at call 348 : 1098.169
+#&gt; Model cost at call 352 : 1098.169
+#&gt; Model cost at call 357 : 1098.169
+#&gt; Model cost at call 370 : 1098.169
+#&gt; Model cost at call 385 : 1098.169
+#&gt; Model cost at call 386 : 1098.169
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; Model cost at call 1 : 34499.23
+#&gt; Model cost at call 3 : 34499.23
+#&gt; Model cost at call 5 : 34499.23
+#&gt; Model cost at call 7 : 34499.23
+#&gt; Model cost at call 9 : 14274.95
+#&gt; Model cost at call 10 : 14162.89
+#&gt; Model cost at call 14 : 14162.68
+#&gt; Model cost at call 18 : 13341.49
+#&gt; Model cost at call 19 : 13341.48
+#&gt; Model cost at call 20 : 13341.47
+#&gt; Model cost at call 22 : 13341.44
+#&gt; Model cost at call 27 : 10055.95
+#&gt; Model cost at call 28 : 10055.95
+#&gt; Model cost at call 30 : 10055.95
+#&gt; Model cost at call 35 : 7732.384
+#&gt; Model cost at call 36 : 7732.381
+#&gt; Model cost at call 39 : 7732.381
+#&gt; Model cost at call 44 : 6325.124
+#&gt; Model cost at call 45 : 6325.122
+#&gt; Model cost at call 47 : 6325.117
+#&gt; Model cost at call 52 : 3732.612
+#&gt; Model cost at call 54 : 3732.611
+#&gt; Model cost at call 61 : 1371.768
+#&gt; Model cost at call 64 : 1371.768
+#&gt; Model cost at call 67 : 1371.768
+#&gt; Model cost at call 70 : 1302.633
+#&gt; Model cost at call 74 : 1302.633
+#&gt; Model cost at call 75 : 1302.633
+#&gt; Model cost at call 78 : 1298.854
+#&gt; Model cost at call 82 : 1298.854
+#&gt; Model cost at call 84 : 1298.854
+#&gt; Model cost at call 86 : 1245.775
+#&gt; Model cost at call 91 : 1245.775
+#&gt; Model cost at call 94 : 1230.679
+#&gt; Model cost at call 96 : 1230.679
+#&gt; Model cost at call 100 : 1230.679
+#&gt; Model cost at call 103 : 1227.471
+#&gt; Model cost at call 105 : 1227.471
+#&gt; Model cost at call 109 : 1227.471
+#&gt; Model cost at call 111 : 1225.318
+#&gt; Model cost at call 113 : 1225.318
+#&gt; Model cost at call 117 : 1225.318
+#&gt; Model cost at call 118 : 1225.318
+#&gt; Model cost at call 119 : 1221.478
+#&gt; Model cost at call 121 : 1221.478
+#&gt; Model cost at call 127 : 1214.191
+#&gt; Model cost at call 128 : 1203.986
+#&gt; Model cost at call 129 : 1164.433
+#&gt; Model cost at call 135 : 1164.433
+#&gt; Model cost at call 140 : 1158.843
+#&gt; Model cost at call 145 : 1158.843
+#&gt; Model cost at call 148 : 1156.585
+#&gt; Model cost at call 154 : 1156.585
+#&gt; Model cost at call 156 : 1155.177
+#&gt; Model cost at call 159 : 1155.177
+#&gt; Model cost at call 161 : 1155.176
+#&gt; Model cost at call 164 : 1151.603
+#&gt; Model cost at call 166 : 1151.603
+#&gt; Model cost at call 167 : 1151.603
+#&gt; Model cost at call 169 : 1151.603
+#&gt; Model cost at call 173 : 1150.467
+#&gt; Model cost at call 175 : 1150.467
+#&gt; Model cost at call 176 : 1150.467
+#&gt; Model cost at call 181 : 1150.117
+#&gt; Model cost at call 184 : 1150.117
+#&gt; Model cost at call 185 : 1150.117
+#&gt; Model cost at call 187 : 1150.117
+#&gt; Model cost at call 188 : 1150.117
+#&gt; Model cost at call 189 : 1149.03
+#&gt; Model cost at call 193 : 1149.03
+#&gt; Model cost at call 195 : 1149.03
+#&gt; Model cost at call 197 : 1148.468
+#&gt; Model cost at call 199 : 1148.468
+#&gt; Model cost at call 205 : 1147.297
+#&gt; Model cost at call 207 : 1147.297
+#&gt; Model cost at call 211 : 1147.297
+#&gt; Model cost at call 213 : 1146.841
+#&gt; Model cost at call 216 : 1146.841
+#&gt; Model cost at call 217 : 1146.841
+#&gt; Model cost at call 219 : 1146.841
+#&gt; Model cost at call 221 : 1144.548
+#&gt; Model cost at call 223 : 1144.548
+#&gt; Model cost at call 229 : 1143.258
+#&gt; Model cost at call 231 : 1143.258
+#&gt; Model cost at call 237 : 1141.772
+#&gt; Model cost at call 239 : 1141.772
+#&gt; Model cost at call 240 : 1141.772
+#&gt; Model cost at call 241 : 1141.772
+#&gt; Model cost at call 243 : 1141.772
+#&gt; Model cost at call 245 : 1140.849
+#&gt; Model cost at call 251 : 1140.849
+#&gt; Model cost at call 252 : 1140.849
+#&gt; Model cost at call 253 : 1139.456
+#&gt; Model cost at call 259 : 1139.456
+#&gt; Model cost at call 261 : 1137.678
+#&gt; Model cost at call 263 : 1137.678
+#&gt; Model cost at call 269 : 1135.358
+#&gt; Model cost at call 270 : 1134.128
+#&gt; Model cost at call 272 : 1134.128
+#&gt; Model cost at call 280 : 1133.342
+#&gt; Model cost at call 283 : 1133.342
+#&gt; Model cost at call 286 : 1133.342
+#&gt; Model cost at call 288 : 1133.229
+#&gt; Model cost at call 292 : 1133.229
+#&gt; Model cost at call 294 : 1133.229
+#&gt; Model cost at call 295 : 1133.229
+#&gt; Model cost at call 296 : 1132.641
+#&gt; Model cost at call 300 : 1132.641
+#&gt; Model cost at call 304 : 1132.126
+#&gt; Model cost at call 310 : 1132.126
+#&gt; Model cost at call 312 : 1131.169
+#&gt; Model cost at call 318 : 1131.169
+#&gt; Model cost at call 320 : 1130.405
+#&gt; Model cost at call 324 : 1130.405
+#&gt; Model cost at call 328 : 1129.635
+#&gt; Model cost at call 330 : 1129.635
+#&gt; Model cost at call 332 : 1129.635
+#&gt; Model cost at call 334 : 1129.635
+#&gt; Model cost at call 336 : 1128.526
+#&gt; Model cost at call 338 : 1128.526
+#&gt; Model cost at call 343 : 1128.526
+#&gt; Model cost at call 344 : 1127.498
+#&gt; Model cost at call 346 : 1127.498
+#&gt; Model cost at call 350 : 1127.498
+#&gt; Model cost at call 352 : 1126.06
+#&gt; Model cost at call 353 : 1124.911
+#&gt; Model cost at call 356 : 1124.911
+#&gt; Model cost at call 362 : 1120.309
+#&gt; Model cost at call 366 : 1120.309
+#&gt; Model cost at call 368 : 1120.308
+#&gt; Model cost at call 369 : 1120.308
+#&gt; Model cost at call 370 : 1117.687
+#&gt; Model cost at call 374 : 1117.687
+#&gt; Model cost at call 375 : 1117.687
+#&gt; Model cost at call 378 : 1112.013
+#&gt; Model cost at call 379 : 1112.013
+#&gt; Model cost at call 381 : 1112.013
+#&gt; Model cost at call 386 : 1108.648
+#&gt; Model cost at call 387 : 1108.251
+#&gt; Model cost at call 388 : 1108.251
+#&gt; Model cost at call 391 : 1108.251
+#&gt; Model cost at call 392 : 1108.251
+#&gt; Model cost at call 395 : 1104.73
+#&gt; Model cost at call 396 : 1104.73
+#&gt; Model cost at call 397 : 1104.73
+#&gt; Model cost at call 403 : 1103.277
+#&gt; Model cost at call 404 : 1103.277
+#&gt; Model cost at call 411 : 1101.351
+#&gt; Model cost at call 414 : 1101.351
+#&gt; Model cost at call 416 : 1101.351
+#&gt; Model cost at call 417 : 1101.351
+#&gt; Model cost at call 419 : 1100.36
+#&gt; Model cost at call 420 : 1100.36
+#&gt; Model cost at call 421 : 1100.36
+#&gt; Model cost at call 427 : 1099.596
+#&gt; Model cost at call 431 : 1099.596
+#&gt; Model cost at call 432 : 1099.596
+#&gt; Model cost at call 435 : 1099.029
+#&gt; Model cost at call 437 : 1099.029
+#&gt; Model cost at call 444 : 1098.722
+#&gt; Model cost at call 447 : 1098.722
+#&gt; Model cost at call 448 : 1098.722
+#&gt; Model cost at call 453 : 1098.441
+#&gt; Model cost at call 455 : 1098.441
+#&gt; Model cost at call 458 : 1098.441
+#&gt; Model cost at call 463 : 1098.314
+#&gt; Model cost at call 464 : 1098.314
+#&gt; Model cost at call 469 : 1098.314
+#&gt; Model cost at call 471 : 1098.314
+#&gt; Model cost at call 475 : 1098.245
+#&gt; Model cost at call 477 : 1098.245
+#&gt; Model cost at call 480 : 1098.245
+#&gt; Model cost at call 486 : 1098.209
+#&gt; Model cost at call 487 : 1098.209
+#&gt; Model cost at call 489 : 1098.209
+#&gt; Model cost at call 493 : 1098.209
+#&gt; Model cost at call 505 : 1098.209
+#&gt; Model cost at call 506 : 1098.209
+#&gt; Model cost at call 510 : 1098.209
+#&gt; Model cost at call 518 : 1098.209
+#&gt; Model cost at call 519 : 1098.209
+#&gt; Model cost at call 522 : 1098.209
+#&gt; Model cost at call 526 : 1098.209
+#&gt; Model cost at call 528 : 1098.209
+#&gt; Model cost at call 530 : 1098.209
+#&gt; Model cost at call 533 : 1098.209
+#&gt; Model cost at call 534 : 1098.209
+#&gt; Model cost at call 536 : 1098.209
+#&gt; Model cost at call 542 : 1098.209
+#&gt; Model cost at call 549 : 1098.207
+#&gt; Model cost at call 551 : 1098.207
+#&gt; Model cost at call 552 : 1098.207
+#&gt; Model cost at call 555 : 1098.207
+#&gt; Model cost at call 564 : 1098.205
+#&gt; Model cost at call 566 : 1098.205
+#&gt; Model cost at call 567 : 1098.205
+#&gt; Model cost at call 570 : 1098.205
+#&gt; Model cost at call 579 : 1098.2
+#&gt; Model cost at call 580 : 1098.191
+#&gt; Model cost at call 581 : 1098.191
+#&gt; Model cost at call 583 : 1098.191
+#&gt; Model cost at call 586 : 1098.191
+#&gt; Model cost at call 587 : 1098.191
+#&gt; Model cost at call 589 : 1098.191
+#&gt; Model cost at call 595 : 1098.186
+#&gt; Model cost at call 596 : 1098.186
+#&gt; Model cost at call 606 : 1098.18
+#&gt; Model cost at call 609 : 1098.18
+#&gt; Model cost at call 610 : 1098.18
+#&gt; Model cost at call 616 : 1098.177
+#&gt; Model cost at call 619 : 1098.177
+#&gt; Model cost at call 620 : 1098.177
+#&gt; Model cost at call 627 : 1098.173
+#&gt; Model cost at call 630 : 1098.173
+#&gt; Model cost at call 631 : 1098.173
+#&gt; Model cost at call 636 : 1098.173
+#&gt; Model cost at call 641 : 1098.172
+#&gt; Model cost at call 642 : 1098.172
+#&gt; Model cost at call 653 : 1098.172
+#&gt; Model cost at call 654 : 1098.172
+#&gt; Model cost at call 664 : 1098.172
+#&gt; Model cost at call 669 : 1098.172
+#&gt; Model cost at call 671 : 1098.172
+#&gt; Model cost at call 675 : 1098.172
+#&gt; Model cost at call 678 : 1098.172
+#&gt; Model cost at call 680 : 1098.172
+#&gt; Model cost at call 683 : 1098.172
+#&gt; Model cost at call 684 : 1098.172
+#&gt; Model cost at call 686 : 1098.172
+#&gt; Model cost at call 690 : 1098.172
+#&gt; Model cost at call 702 : 1098.172
+#&gt; Model cost at call 704 : 1098.172
+#&gt; Model cost at call 708 : 1098.172
+#&gt; Model cost at call 721 : 1098.172
+#&gt; Model cost at call 723 : 1098.172
+#&gt; Model cost at call 736 : 1098.172
+#&gt; Model cost at call 738 : 1098.172
+#&gt; Model cost at call 751 : 1098.172
+#&gt; Model cost at call 753 : 1098.172
+#&gt; Model cost at call 766 : 1098.172
+#&gt; Model cost at call 767 : 1098.172
+#&gt; Model cost at call 768 : 1098.172
+#&gt; Model cost at call 770 : 1098.172
+#&gt; Model cost at call 783 : 1098.172
+#&gt; Model cost at call 784 : 1098.172
+#&gt; Model cost at call 785 : 1098.172
+#&gt; Model cost at call 799 : 1098.172
+#&gt; Model cost at call 800 : 1098.172
+#&gt; Model cost at call 814 : 1098.172
+#&gt; Model cost at call 815 : 1098.172
+#&gt; Model cost at call 816 : 1098.172
+#&gt; Model cost at call 822 : 1098.172
+#&gt; Model cost at call 830 : 1098.172
+#&gt; Model cost at call 831 : 1098.172
+#&gt; Model cost at call 834 : 1098.172
+#&gt; Model cost at call 845 : 1098.172
+#&gt; Model cost at call 846 : 1098.172
+#&gt; Model cost at call 849 : 1098.172
+#&gt; Model cost at call 860 : 1098.171
+#&gt; Model cost at call 861 : 1098.171
+#&gt; Model cost at call 864 : 1098.171
+#&gt; Model cost at call 875 : 1098.171
+#&gt; Model cost at call 876 : 1098.171
+#&gt; Model cost at call 879 : 1098.171
+#&gt; Model cost at call 890 : 1098.17
+#&gt; Model cost at call 891 : 1098.17
+#&gt; Model cost at call 894 : 1098.17
+#&gt; Model cost at call 904 : 1098.169
+#&gt; Model cost at call 905 : 1098.169
+#&gt; Model cost at call 908 : 1098.169
+#&gt; Model cost at call 909 : 1098.169
+#&gt; Model cost at call 919 : 1098.169
+#&gt; Model cost at call 921 : 1098.169
+#&gt; Model cost at call 931 : 1098.169
+#&gt; Model cost at call 932 : 1098.169
+#&gt; Model cost at call 934 : 1098.169
+#&gt; Model cost at call 936 : 1098.169
+#&gt; Model cost at call 937 : 1098.169
+#&gt; Model cost at call 944 : 1098.169
+#&gt; Model cost at call 947 : 1098.169
+#&gt; Model cost at call 949 : 1098.169
+#&gt; Model cost at call 951 : 1098.169
+#&gt; Model cost at call 952 : 1098.169
+#&gt; Model cost at call 954 : 1098.169
+#&gt; Model cost at call 964 : 1098.169
+#&gt; Model cost at call 967 : 1098.169
+#&gt; Model cost at call 969 : 1098.169
+#&gt; Model cost at call 982 : 1098.169
+#&gt; Model cost at call 1017 : 1098.169
+#&gt; Model cost at call 1018 : 1098.169
+#&gt; Model cost at call 1022 : 1098.169
+#&gt; Model cost at call 1029 : 1098.169
+#&gt; Model cost at call 1033 : 1098.169
+#&gt; Model cost at call 1038 : 1098.169
+#&gt; Model cost at call 1048 : 1098.169
+#&gt; Model cost at call 1049 : 1098.169
+#&gt; Model cost at call 1055 : 1098.169
+#&gt; Model cost at call 1063 : 1098.169
+#&gt; Model cost at call 1074 : 1098.169
+#&gt; Model cost at call 1079 : 1098.169
+#&gt; Model cost at call 1089 : 1098.169
+#&gt; Model cost at call 1120 : 1098.169
+#&gt; Model cost at call 1124 : 1098.169
+#&gt; Model cost at call 1139 : 1098.169
+#&gt; Model cost at call 1154 : 1098.169
+#&gt; Model cost at call 1170 : 1098.169
+#&gt; Model cost at call 1185 : 1098.169
+#&gt; Model cost at call 1200 : 1098.169
+#&gt; Model cost at call 1215 : 1098.169
+#&gt; Model cost at call 1231 : 1098.169
+#&gt; Model cost at call 1246 : 1098.169
+#&gt; Model cost at call 1247 : 1098.169
+#&gt; Model cost at call 1248 : 1098.169
+#&gt; Model cost at call 1258 : 1098.169
+#&gt; Model cost at call 1263 : 1098.169
+#&gt; Model cost at call 1278 : 1098.169
+#&gt; Model cost at call 1295 : 1098.169
+#&gt; Model cost at call 1296 : 1098.169
+#&gt; Model cost at call 1297 : 1098.169
+#&gt; Model cost at call 1298 : 1098.169
+#&gt; Model cost at call 1306 : 1098.169
+#&gt; Model cost at call 1308 : 1098.169
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; Model cost at call 1 : 31389.19
+#&gt; Model cost at call 3 : 31389.19
+#&gt; Model cost at call 8 : 15003.41
+#&gt; Model cost at call 9 : 11136.21
+#&gt; Model cost at call 11 : 11135.87
+#&gt; Model cost at call 16 : 4800.182
+#&gt; Model cost at call 17 : 4800.181
+#&gt; Model cost at call 19 : 4800.163
+#&gt; Model cost at call 24 : 3036.068
+#&gt; Model cost at call 25 : 3036.068
+#&gt; Model cost at call 26 : 3036.052
+#&gt; Model cost at call 31 : 1361.371
+#&gt; Model cost at call 33 : 1361.371
+#&gt; Model cost at call 40 : 494.6738
+#&gt; Model cost at call 41 : 494.6736
+#&gt; Model cost at call 45 : 494.6734
+#&gt; Model cost at call 48 : 260.2631
+#&gt; Model cost at call 49 : 260.2629
+#&gt; Model cost at call 55 : 248.3035
+#&gt; Model cost at call 56 : 248.3034
+#&gt; Model cost at call 57 : 248.3023
+#&gt; Model cost at call 62 : 171.6337
+#&gt; Model cost at call 63 : 171.6337
+#&gt; Model cost at call 70 : 167.3473
+#&gt; Model cost at call 72 : 167.3473
+#&gt; Model cost at call 73 : 167.3473
+#&gt; Model cost at call 78 : 165.9868
+#&gt; Model cost at call 80 : 165.9868
+#&gt; Model cost at call 83 : 165.9868
+#&gt; Model cost at call 85 : 165.2025
+#&gt; Model cost at call 87 : 165.2024
+#&gt; Model cost at call 92 : 163.5932
+#&gt; Model cost at call 94 : 163.5932
+#&gt; Model cost at call 96 : 163.5932
+#&gt; Model cost at call 99 : 159.4289
+#&gt; Model cost at call 100 : 147.5939
+#&gt; Model cost at call 105 : 147.5939
+#&gt; Model cost at call 108 : 139.3925
+#&gt; Model cost at call 113 : 139.3925
+#&gt; Model cost at call 115 : 139.392
+#&gt; Model cost at call 116 : 123.9799
+#&gt; Model cost at call 117 : 123.9798
+#&gt; Model cost at call 118 : 123.9795
+#&gt; Model cost at call 124 : 103.8653
+#&gt; Model cost at call 125 : 103.8653
+#&gt; Model cost at call 126 : 103.8652
+#&gt; Model cost at call 131 : 96.14276
+#&gt; Model cost at call 134 : 96.14275
+#&gt; Model cost at call 135 : 96.14274
+#&gt; Model cost at call 139 : 95.96056
+#&gt; Model cost at call 141 : 95.96056
+#&gt; Model cost at call 142 : 95.96056
+#&gt; Model cost at call 145 : 95.96056
+#&gt; Model cost at call 146 : 95.90851
+#&gt; Model cost at call 148 : 95.9085
+#&gt; Model cost at call 153 : 95.84671
+#&gt; Model cost at call 155 : 95.8467
+#&gt; Model cost at call 161 : 95.82479
+#&gt; Model cost at call 163 : 95.82479
+#&gt; Model cost at call 166 : 95.82479
+#&gt; Model cost at call 168 : 95.81938
+#&gt; Model cost at call 170 : 95.81938
+#&gt; Model cost at call 174 : 95.81938
+#&gt; Model cost at call 175 : 95.81558
+#&gt; Model cost at call 177 : 95.81558
+#&gt; Model cost at call 178 : 95.81558
+#&gt; Model cost at call 180 : 95.81558
+#&gt; Model cost at call 181 : 95.81558
+#&gt; Model cost at call 183 : 95.81558
+#&gt; Model cost at call 184 : 95.8118
+#&gt; Model cost at call 186 : 95.8118
+#&gt; Model cost at call 188 : 95.8118
+#&gt; Model cost at call 191 : 95.80885
+#&gt; Model cost at call 192 : 95.80353
+#&gt; Model cost at call 193 : 95.78121
+#&gt; Model cost at call 194 : 95.72164
+#&gt; Model cost at call 197 : 95.72164
+#&gt; Model cost at call 201 : 95.72163
+#&gt; Model cost at call 206 : 95.71206
+#&gt; Model cost at call 208 : 95.71205
+#&gt; Model cost at call 213 : 95.70874
+#&gt; Model cost at call 215 : 95.70874
+#&gt; Model cost at call 219 : 95.70874
+#&gt; Model cost at call 221 : 95.70751
+#&gt; Model cost at call 222 : 95.70404
+#&gt; Model cost at call 223 : 95.69259
+#&gt; Model cost at call 224 : 95.68092
+#&gt; Model cost at call 226 : 95.68092
+#&gt; Model cost at call 227 : 95.68092
+#&gt; Model cost at call 233 : 95.67595
+#&gt; Model cost at call 235 : 95.67595
+#&gt; Model cost at call 236 : 95.67595
+#&gt; Model cost at call 242 : 95.67219
+#&gt; Model cost at call 244 : 95.67219
+#&gt; Model cost at call 245 : 95.67219
+#&gt; Model cost at call 249 : 95.66939
+#&gt; Model cost at call 251 : 95.66939
+#&gt; Model cost at call 253 : 95.66939
+#&gt; Model cost at call 254 : 95.66939
+#&gt; Model cost at call 256 : 95.66904
+#&gt; Model cost at call 257 : 95.66904
+#&gt; Model cost at call 260 : 95.66904
+#&gt; Model cost at call 265 : 95.66857
+#&gt; Model cost at call 267 : 95.66856
+#&gt; Model cost at call 273 : 95.66822
+#&gt; Model cost at call 275 : 95.66822
+#&gt; Model cost at call 276 : 95.66822
+#&gt; Model cost at call 282 : 95.66809
+#&gt; Model cost at call 283 : 95.66809
+#&gt; Model cost at call 291 : 95.66805
+#&gt; Model cost at call 293 : 95.66805
+#&gt; Model cost at call 295 : 95.66805
+#&gt; Model cost at call 297 : 95.66805
+#&gt; Model cost at call 298 : 95.66805
+#&gt; Model cost at call 302 : 95.66805
+#&gt; Model cost at call 304 : 95.66805
+#&gt; Model cost at call 306 : 95.66805
+#&gt; Model cost at call 309 : 95.66805
+#&gt; Model cost at call 314 : 95.66805
+#&gt; Model cost at call 315 : 95.66805
+#&gt; Model cost at call 328 : 95.66805
+#&gt; Optimisation by method Port successfully terminated.
+#&gt; Model cost at call 1 : 36597.78
+#&gt; Model cost at call 3 : 36597.78
+#&gt; Model cost at call 5 : 36597.78
+#&gt; Model cost at call 7 : 36597.78
+#&gt; Model cost at call 9 : 13188.26
+#&gt; Model cost at call 10 : 12648.25
+#&gt; Model cost at call 14 : 12648.13
+#&gt; Model cost at call 16 : 12647.92
+#&gt; Model cost at call 18 : 6148.715
+#&gt; Model cost at call 19 : 6148.712
+#&gt; Model cost at call 20 : 6148.695
+#&gt; Model cost at call 22 : 6148.683
+#&gt; Model cost at call 27 : 1490.597
+#&gt; Model cost at call 33 : 1490.597
+#&gt; Model cost at call 35 : 594.2031
+#&gt; Model cost at call 36 : 594.2023
+#&gt; Model cost at call 38 : 594.201
+#&gt; Model cost at call 40 : 594.2009
+#&gt; Model cost at call 44 : 230.6504
+#&gt; Model cost at call 45 : 230.6503
+#&gt; Model cost at call 48 : 230.6503
+#&gt; Model cost at call 50 : 230.6495
+#&gt; Model cost at call 51 : 230.6494
+#&gt; Model cost at call 53 : 186.2336
+#&gt; Model cost at call 57 : 186.2336
+#&gt; Model cost at call 59 : 186.2336
+#&gt; Model cost at call 60 : 186.2336
+#&gt; Model cost at call 62 : 181.3507
+#&gt; Model cost at call 66 : 181.3507
+#&gt; Model cost at call 70 : 180.733
+#&gt; Model cost at call 74 : 180.733
+#&gt; Model cost at call 76 : 180.7329
+#&gt; Model cost at call 77 : 180.7329
+#&gt; Model cost at call 78 : 175.5254
+#&gt; Model cost at call 80 : 175.5253
+#&gt; Model cost at call 86 : 173.1139
+#&gt; Model cost at call 88 : 173.1139
+#&gt; Model cost at call 94 : 168.0503
+#&gt; Model cost at call 96 : 168.0502
+#&gt; Model cost at call 102 : 164.9084
+#&gt; Model cost at call 104 : 164.9084
+#&gt; Model cost at call 105 : 164.9084
+#&gt; Model cost at call 110 : 159.7912
+#&gt; Model cost at call 112 : 159.7912
+#&gt; Model cost at call 113 : 159.7912
+#&gt; Model cost at call 116 : 159.7911
+#&gt; Model cost at call 117 : 159.7911
+#&gt; Model cost at call 118 : 158.6003
+#&gt; Model cost at call 122 : 158.6002
+#&gt; Model cost at call 124 : 158.6002
+#&gt; Model cost at call 126 : 150.4132
+#&gt; Model cost at call 132 : 150.4132
+#&gt; Model cost at call 133 : 150.4132
+#&gt; Model cost at call 134 : 146.5123
+#&gt; Model cost at call 140 : 146.5122
+#&gt; Model cost at call 142 : 136.6018
+#&gt; Model cost at call 145 : 136.6018
+#&gt; Model cost at call 149 : 136.6018
+#&gt; Model cost at call 150 : 133.91
+#&gt; Model cost at call 153 : 133.91
+#&gt; Model cost at call 155 : 133.91
+#&gt; Model cost at call 156 : 133.91
+#&gt; Model cost at call 158 : 124.7878
+#&gt; Model cost at call 162 : 124.7878
+#&gt; Model cost at call 163 : 124.7878
+#&gt; Model cost at call 167 : 124.2615
+#&gt; Model cost at call 169 : 124.2614
+#&gt; Model cost at call 170 : 124.2614
+#&gt; Model cost at call 175 : 123.2425
+#&gt; Model cost at call 179 : 123.2425
+#&gt; Model cost at call 180 : 123.2425
+#&gt; Model cost at call 181 : 123.2425
+#&gt; Model cost at call 182 : 123.2425
+#&gt; Model cost at call 183 : 120.7214
+#&gt; Model cost at call 185 : 120.7214
+#&gt; Model cost at call 191 : 119.2706
+#&gt; Model cost at call 192 : 117.872
+#&gt; Model cost at call 193 : 114.6257
+#&gt; Model cost at call 198 : 114.6257
+#&gt; Model cost at call 201 : 111.8985
+#&gt; Model cost at call 203 : 111.8985
+#&gt; Model cost at call 206 : 111.8984
+#&gt; Model cost at call 209 : 111.6987
+#&gt; Model cost at call 212 : 111.6987
+#&gt; Model cost at call 213 : 111.6986
+#&gt; Model cost at call 217 : 107.9995
+#&gt; Model cost at call 219 : 107.9995
+#&gt; Model cost at call 225 : 106.1322
+#&gt; Model cost at call 226 : 104.6907
+#&gt; Model cost at call 227 : 104.6316
+#&gt; Model cost at call 229 : 104.6316
+#&gt; Model cost at call 232 : 104.6315
+#&gt; Model cost at call 239 : 103.3421
+#&gt; Model cost at call 245 : 103.3421
+#&gt; Model cost at call 246 : 103.3421
+#&gt; Model cost at call 247 : 103.1772
+#&gt; Model cost at call 248 : 103.1772
+#&gt; Model cost at call 249 : 103.1772
+#&gt; Model cost at call 250 : 103.1772
+#&gt; Model cost at call 253 : 103.1772
+#&gt; Model cost at call 255 : 102.8623
+#&gt; Model cost at call 256 : 102.8623
+#&gt; Model cost at call 262 : 102.8623
+#&gt; Model cost at call 263 : 102.6013
+#&gt; Model cost at call 266 : 102.6013
+#&gt; Model cost at call 271 : 102.0341
+#&gt; Model cost at call 272 : 101.25
+#&gt; Model cost at call 273 : 99.17557
+#&gt; Model cost at call 274 : 99.17556
+#&gt; Model cost at call 282 : 99.06481
+#&gt; Model cost at call 284 : 99.06479
+#&gt; Model cost at call 290 : 98.57515
+#&gt; Model cost at call 294 : 98.57514
+#&gt; Model cost at call 296 : 98.57514
+#&gt; Model cost at call 298 : 98.05781
+#&gt; Model cost at call 304 : 98.05781
+#&gt; Model cost at call 305 : 98.05781
+#&gt; Model cost at call 306 : 97.81766
+#&gt; Model cost at call 307 : 97.63972
+#&gt; Model cost at call 308 : 97.63971
+#&gt; Model cost at call 315 : 97.15447
+#&gt; Model cost at call 317 : 97.15447
+#&gt; Model cost at call 321 : 97.15446
+#&gt; Model cost at call 323 : 96.25231
+#&gt; Model cost at call 324 : 96.25231
+#&gt; Model cost at call 328 : 96.25231
+#&gt; Model cost at call 331 : 95.48051
+#&gt; Model cost at call 334 : 95.4805
+#&gt; Model cost at call 339 : 95.08754
+#&gt; Model cost at call 341 : 95.08754
+#&gt; Model cost at call 347 : 94.9916
+#&gt; Model cost at call 348 : 94.9916
+#&gt; Model cost at call 350 : 94.9916
+#&gt; Model cost at call 355 : 94.93856
+#&gt; Model cost at call 356 : 94.93856
+#&gt; Model cost at call 357 : 94.93856
+#&gt; Model cost at call 363 : 94.92067
+#&gt; Model cost at call 366 : 94.92067
+#&gt; Model cost at call 367 : 94.92067
+#&gt; Model cost at call 369 : 94.92067
+#&gt; Model cost at call 370 : 94.92067
+#&gt; Model cost at call 371 : 94.91762
+#&gt; Model cost at call 372 : 94.91762
+#&gt; Model cost at call 373 : 94.91762
+#&gt; Model cost at call 379 : 94.91744
+#&gt; Model cost at call 380 : 94.91744
+#&gt; Model cost at call 385 : 94.91744
+#&gt; Model cost at call 387 : 94.91744
+#&gt; Model cost at call 393 : 94.91743
+#&gt; Model cost at call 394 : 94.91743
+#&gt; Model cost at call 404 : 94.91743
+#&gt; Model cost at call 407 : 94.91743
+#&gt; Model cost at call 408 : 94.91743
+#&gt; Model cost at call 423 : 94.91743
+#&gt; Model cost at call 442 : 94.91743
+#&gt; Model cost at call 446 : 94.91743
+#&gt; Model cost at call 447 : 94.91743
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 16.180 0.132 9.130 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 22.856 0.000 22.858 </div><div class='input'>
+<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; <span class='error'>Error in endpoints(fits[[&quot;SFO_lin&quot;, 2]]): Objekt &#39;fits&#39; nicht gefunden</span></div><div class='input'>
+<span class='co'># Plot.mkinfit handles rows or columns of mmkin result objects</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-18.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
+<span class='co'># by plot.mkinfit</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
+<span class='co'># allow to plot the observed variables separately</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-22.png' alt='' width='540' height='400' /><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index e2f845d9..9bb6d4ee 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -116,7 +116,1059 @@
<span class='kw'>A1</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'>"A2"</span>),
<span class='kw'>B1</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'>C1</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'>A2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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: mkinfit(model, data, plot=TRUE)</span></div></pre>
+ <span class='kw'>A2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 2511.655
+#&gt; Model cost at call 2 : 2511.655
+#&gt; Model cost at call 11 : 1436.639
+#&gt; Model cost at call 12 : 1436.638
+#&gt; Model cost at call 13 : 1436.566
+#&gt; Model cost at call 21 : 643.6583
+#&gt; Model cost at call 22 : 643.6583
+#&gt; Model cost at call 23 : 643.6582
+#&gt; Model cost at call 29 : 643.6576
+#&gt; Model cost at call 31 : 454.0244
+#&gt; Model cost at call 32 : 454.0241
+#&gt; Model cost at call 34 : 454.0229
+#&gt; Model cost at call 43 : 378.1144
+#&gt; Model cost at call 45 : 378.1143
+#&gt; Model cost at call 53 : 357.245
+#&gt; Model cost at call 55 : 357.2449
+#&gt; Model cost at call 56 : 357.2447
+#&gt; Model cost at call 63 : 354.3415
+#&gt; Model cost at call 64 : 354.3415
+#&gt; Model cost at call 65 : 354.3413
+#&gt; Model cost at call 73 : 332.49
+#&gt; Model cost at call 74 : 332.49
+#&gt; Model cost at call 81 : 332.4899
+#&gt; Model cost at call 83 : 315.2962
+#&gt; Model cost at call 84 : 306.3085
+#&gt; Model cost at call 86 : 306.3084
+#&gt; Model cost at call 87 : 306.3084
+#&gt; Model cost at call 92 : 306.3083
+#&gt; Model cost at call 94 : 290.6377
+#&gt; Model cost at call 96 : 290.6375
+#&gt; Model cost at call 98 : 290.6375
+#&gt; Model cost at call 101 : 290.6371
+#&gt; Model cost at call 105 : 269.09
+#&gt; Model cost at call 107 : 269.0899
+#&gt; Model cost at call 115 : 259.7551
+#&gt; Model cost at call 120 : 259.7549
+#&gt; Model cost at call 123 : 259.7547
+#&gt; Model cost at call 126 : 253.7973
+#&gt; Model cost at call 128 : 253.7972
+#&gt; Model cost at call 137 : 251.7358
+#&gt; Model cost at call 139 : 251.7358
+#&gt; Model cost at call 147 : 250.7394
+#&gt; Model cost at call 149 : 250.7393
+#&gt; Model cost at call 157 : 249.1148
+#&gt; Model cost at call 159 : 249.1148
+#&gt; Model cost at call 167 : 246.8768
+#&gt; Model cost at call 169 : 246.8768
+#&gt; Model cost at call 177 : 244.9758
+#&gt; Model cost at call 179 : 244.9758
+#&gt; Model cost at call 187 : 243.2914
+#&gt; Model cost at call 189 : 243.2914
+#&gt; Model cost at call 190 : 243.2914
+#&gt; Model cost at call 194 : 243.2914
+#&gt; Model cost at call 199 : 242.9202
+#&gt; Model cost at call 201 : 242.9202
+#&gt; Model cost at call 202 : 242.9202
+#&gt; Model cost at call 209 : 242.7695
+#&gt; Model cost at call 211 : 242.7695
+#&gt; Model cost at call 216 : 242.7695
+#&gt; Model cost at call 219 : 242.5771
+#&gt; Model cost at call 221 : 242.5771
+#&gt; Model cost at call 229 : 242.4402
+#&gt; Model cost at call 231 : 242.4402
+#&gt; Model cost at call 239 : 242.1878
+#&gt; Model cost at call 241 : 242.1878
+#&gt; Model cost at call 249 : 242.0553
+#&gt; Model cost at call 251 : 242.0553
+#&gt; Model cost at call 256 : 242.0553
+#&gt; Model cost at call 259 : 241.8761
+#&gt; Model cost at call 260 : 241.7412
+#&gt; Model cost at call 261 : 241.6954
+#&gt; Model cost at call 264 : 241.6954
+#&gt; Model cost at call 275 : 241.5982
+#&gt; Model cost at call 277 : 241.5982
+#&gt; Model cost at call 285 : 241.5459
+#&gt; Model cost at call 287 : 241.5459
+#&gt; Model cost at call 295 : 241.4837
+#&gt; Model cost at call 297 : 241.4837
+#&gt; Model cost at call 305 : 241.3882
+#&gt; Model cost at call 306 : 241.3161
+#&gt; Model cost at call 307 : 241.2315
+#&gt; Model cost at call 309 : 241.2315
+#&gt; Model cost at call 314 : 241.2315
+#&gt; Model cost at call 317 : 240.9738
+#&gt; Model cost at call 322 : 240.9738
+#&gt; Model cost at call 327 : 240.8244
+#&gt; Model cost at call 329 : 240.8244
+#&gt; Model cost at call 337 : 240.7005
+#&gt; Model cost at call 339 : 240.7005
+#&gt; Model cost at call 342 : 240.7005
+#&gt; Model cost at call 347 : 240.629
+#&gt; Model cost at call 350 : 240.629
+#&gt; Model cost at call 357 : 240.6193
+#&gt; Model cost at call 358 : 240.6193
+#&gt; Model cost at call 364 : 240.6193
+#&gt; Model cost at call 367 : 240.6193
+#&gt; Model cost at call 369 : 240.5873
+#&gt; Model cost at call 374 : 240.5873
+#&gt; Model cost at call 380 : 240.578
+#&gt; Model cost at call 382 : 240.578
+#&gt; Model cost at call 390 : 240.5723
+#&gt; Model cost at call 393 : 240.5723
+#&gt; Model cost at call 403 : 240.569
+#&gt; Model cost at call 404 : 240.569
+#&gt; Model cost at call 413 : 240.569
+#&gt; Model cost at call 415 : 240.5688
+#&gt; Model cost at call 416 : 240.5688
+#&gt; Model cost at call 417 : 240.5688
+#&gt; Model cost at call 431 : 240.5686
+#&gt; Model cost at call 432 : 240.5686
+#&gt; Model cost at call 434 : 240.5686
+#&gt; Model cost at call 443 : 240.5686
+#&gt; Model cost at call 444 : 240.5686
+#&gt; Model cost at call 447 : 240.5686
+#&gt; Model cost at call 449 : 240.5686
+#&gt; Model cost at call 450 : 240.5686
+#&gt; Model cost at call 466 : 240.5686
+#&gt; Model cost at call 470 : 240.5686
+#&gt; Model cost at call 485 : 240.5686
+#&gt; Model cost at call 509 : 240.5686
+#&gt; Optimisation by method Port successfully terminated.</div><div class='output co'>#&gt; $par
+#&gt; parent_0 log_k_parent log_k_A1 log_k_B1 log_k_C1
+#&gt; 91.9181598 -3.0020485 -4.2735924 -3.9846764 -2.7852180
+#&gt; log_k_A2 f_parent_ilr_1 f_parent_ilr_2 f_A1_ilr_1
+#&gt; -3.7166415 0.4718588 -0.3589948 -0.1477244
+#&gt;
+#&gt; $ssr
+#&gt; [1] 240.5686
+#&gt;
+#&gt; $convergence
+#&gt; [1] 0
+#&gt;
+#&gt; $iterations
+#&gt; [1] 43
+#&gt;
+#&gt; $evaluations
+#&gt; function gradient
+#&gt; 62 441
+#&gt;
+#&gt; $counts
+#&gt; [1] &quot;relative convergence (4)&quot;
+#&gt;
+#&gt; $hessian
+#&gt; parent_0 log_k_parent log_k_A1 log_k_B1
+#&gt; parent_0 7.3650812 -92.141920 -1.001134e+01 -2.432415e+00
+#&gt; log_k_parent -92.1419204 6632.673492 -4.316240e+01 -1.320833e+01
+#&gt; log_k_A1 -10.0113364 -43.162398 6.071628e+02 0.000000e+00
+#&gt; log_k_B1 -2.4324147 -13.208329 0.000000e+00 1.572303e+02
+#&gt; log_k_C1 -4.7153201 -118.288037 -5.878291e-05 -3.073041e-06
+#&gt; log_k_A2 -0.4360727 -5.304259 -1.977980e+01 0.000000e+00
+#&gt; f_parent_ilr_1 10.5460899 271.145438 -5.299954e+02 1.874235e+02
+#&gt; f_parent_ilr_2 11.6409409 222.570696 -4.773816e+02 -1.159875e+02
+#&gt; f_A1_ilr_1 0.5572072 10.374810 2.850173e+01 0.000000e+00
+#&gt; log_k_C1 log_k_A2 f_parent_ilr_1 f_parent_ilr_2
+#&gt; parent_0 -4.715320e+00 -4.360727e-01 10.54609 11.64094
+#&gt; log_k_parent -1.182880e+02 -5.304259e+00 271.14544 222.57070
+#&gt; log_k_A1 -5.878291e-05 -1.977980e+01 -529.99537 -477.38164
+#&gt; log_k_B1 -3.073041e-06 0.000000e+00 187.42348 -115.98754
+#&gt; log_k_C1 3.372749e+02 -2.395674e-06 56.85184 305.98862
+#&gt; log_k_A2 -2.395674e-06 2.749192e+01 -23.08549 -20.79373
+#&gt; f_parent_ilr_1 5.685184e+01 -2.308549e+01 1256.24941 632.09769
+#&gt; f_parent_ilr_2 3.059886e+02 -2.079373e+01 632.09769 1250.65147
+#&gt; f_A1_ilr_1 3.158891e-06 -3.129286e+01 29.49830 26.56991
+#&gt; f_A1_ilr_1
+#&gt; parent_0 5.572072e-01
+#&gt; log_k_parent 1.037481e+01
+#&gt; log_k_A1 2.850173e+01
+#&gt; log_k_B1 0.000000e+00
+#&gt; log_k_C1 3.158891e-06
+#&gt; log_k_A2 -3.129286e+01
+#&gt; f_parent_ilr_1 2.949830e+01
+#&gt; f_parent_ilr_2 2.656991e+01
+#&gt; f_A1_ilr_1 3.998554e+01
+#&gt;
+#&gt; $residuals
+#&gt; parent parent parent parent parent parent parent
+#&gt; -1.2818402 -1.9372115 -0.5105519 3.8165318 -2.3531716 4.8043342 -2.2775432
+#&gt; parent A1 A1 A1 A1 A1 A1
+#&gt; -5.3608524 4.1967522 2.9032987 -1.3124875 -0.6021093 2.5092324 -1.8861396
+#&gt; B1 B1 B1 B1 B1 C1 C1
+#&gt; 4.3801768 5.5002481 -5.7917184 1.3852658 0.5313301 1.2796458 1.7105311
+#&gt; C1 C1 C1 C1 C1 A2 A2
+#&gt; 3.7116712 -0.1182953 0.5228429 -0.8570298 -3.5476556 -0.5447276 -1.3652404
+#&gt; A2 A2 A2 A2 A2
+#&gt; -0.3330261 -0.5802059 0.1285850 0.2119280 -0.1381990
+#&gt;
+#&gt; $ms
+#&gt; [1] 7.289956
+#&gt;
+#&gt; $var_ms
+#&gt; parent A1 B1 C1 A2
+#&gt; 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002
+#&gt;
+#&gt; $var_ms_unscaled
+#&gt; parent A1 B1 C1 A2
+#&gt; 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002
+#&gt;
+#&gt; $var_ms_unweighted
+#&gt; parent A1 B1 C1 A2
+#&gt; 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002
+#&gt;
+#&gt; $rank
+#&gt; [1] 9
+#&gt;
+#&gt; $df.residual
+#&gt; [1] 24
+#&gt;
+#&gt; $solution_type
+#&gt; [1] &quot;deSolve&quot;
+#&gt;
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt;
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt;
+#&gt; $method.modFit
+#&gt; [1] &quot;Port&quot;
+#&gt;
+#&gt; $maxit.modFit
+#&gt; [1] &quot;auto&quot;
+#&gt;
+#&gt; $calls
+#&gt; [1] 523
+#&gt;
+#&gt; $time
+#&gt; user system elapsed
+#&gt; 5.004 0.000 5.004
+#&gt;
+#&gt; $mkinmod
+#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: max
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: SFO; $to: A1, B1, C1; $sink: FALSE
+#&gt; $A1
+#&gt; $type: SFO; $to: A2; $sink: TRUE
+#&gt; $B1
+#&gt; $type: SFO; $sink: TRUE
+#&gt; $C1
+#&gt; $type: SFO; $sink: TRUE
+#&gt; $A2
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt; Compiled model $cf available
+#&gt;
+#&gt; $observed
+#&gt; name time value
+#&gt; 1 parent 0 93.20
+#&gt; 2 parent 1 89.40
+#&gt; 3 parent 3 79.70
+#&gt; 4 parent 7 61.10
+#&gt; 5 parent 14 48.20
+#&gt; 6 parent 30 15.90
+#&gt; 7 parent 62 6.50
+#&gt; 8 parent 100 6.00
+#&gt; 9 A1 0 NA
+#&gt; 10 A1 1 NA
+#&gt; 11 A1 3 0.55
+#&gt; 12 A1 7 6.87
+#&gt; 13 A1 14 17.08
+#&gt; 14 A1 30 21.68
+#&gt; 15 A1 62 15.77
+#&gt; 16 A1 100 13.63
+#&gt; 17 B1 0 NA
+#&gt; 18 B1 1 NA
+#&gt; 19 B1 3 NA
+#&gt; 20 B1 7 0.55
+#&gt; 21 B1 14 2.31
+#&gt; 22 B1 30 15.76
+#&gt; 23 B1 62 6.36
+#&gt; 24 B1 100 3.74
+#&gt; 25 C1 0 NA
+#&gt; 26 C1 1 0.55
+#&gt; 27 C1 3 3.20
+#&gt; 28 C1 7 5.46
+#&gt; 29 C1 14 12.55
+#&gt; 30 C1 30 10.45
+#&gt; 31 C1 62 4.74
+#&gt; 32 C1 100 4.33
+#&gt; 33 A2 0 NA
+#&gt; 34 A2 1 0.55
+#&gt; 35 A2 3 1.41
+#&gt; 36 A2 7 0.55
+#&gt; 37 A2 14 1.29
+#&gt; 38 A2 30 1.95
+#&gt; 39 A2 62 3.54
+#&gt; 40 A2 100 3.86
+#&gt;
+#&gt; $obs_vars
+#&gt; [1] &quot;parent&quot; &quot;A1&quot; &quot;B1&quot; &quot;C1&quot; &quot;A2&quot;
+#&gt;
+#&gt; $predicted
+#&gt; name time value
+#&gt; 1 parent 0.000000 91.918159794
+#&gt; 2 parent 1.000000 87.462788491
+#&gt; 3 parent 1.010101 87.418904506
+#&gt; 4 parent 2.020202 83.139880984
+#&gt; 5 parent 3.000000 79.189448055
+#&gt; 6 parent 3.030303 79.070309209
+#&gt; 7 parent 4.040404 75.199936833
+#&gt; 8 parent 5.050505 71.519013349
+#&gt; 9 parent 6.060606 68.018265517
+#&gt; 10 parent 7.000000 64.916531757
+#&gt; 11 parent 7.070707 64.688874011
+#&gt; 12 parent 8.080808 61.522451197
+#&gt; 13 parent 9.090909 58.511020005
+#&gt; 14 parent 10.101010 55.646993828
+#&gt; 15 parent 11.111111 52.923157412
+#&gt; 16 parent 12.121212 50.332648680
+#&gt; 17 parent 13.131313 47.868941444
+#&gt; 18 parent 14.000000 45.846828365
+#&gt; 19 parent 14.141414 45.525828960
+#&gt; 20 parent 15.151515 43.297408299
+#&gt; 21 parent 16.161616 41.178065468
+#&gt; 22 parent 17.171717 39.162461272
+#&gt; 23 parent 18.181818 37.245517861
+#&gt; 24 parent 19.191919 35.422405939
+#&gt; 25 parent 20.202020 33.688532595
+#&gt; 26 parent 21.212121 32.039529737
+#&gt; 27 parent 22.222222 30.471243081
+#&gt; 28 parent 23.232323 28.979721692
+#&gt; 29 parent 24.242424 27.561208025
+#&gt; 30 parent 25.252525 26.212128463
+#&gt; 31 parent 26.262626 24.929084310
+#&gt; 32 parent 27.272727 23.708843233
+#&gt; 33 parent 28.282828 22.548331117
+#&gt; 34 parent 29.292929 21.444624318
+#&gt; 35 parent 30.000000 20.704334210
+#&gt; 36 parent 30.303030 20.394942302
+#&gt; 37 parent 31.313131 19.396640638
+#&gt; 38 parent 32.323232 18.447204335
+#&gt; 39 parent 33.333333 17.544241506
+#&gt; 40 parent 34.343434 16.685477346
+#&gt; 41 parent 35.353535 15.868748397
+#&gt; 42 parent 36.363636 15.091997098
+#&gt; 43 parent 37.373737 14.353266603
+#&gt; 44 parent 38.383838 13.650695852
+#&gt; 45 parent 39.393939 12.982514879
+#&gt; 46 parent 40.404040 12.347040357
+#&gt; 47 parent 41.414141 11.742671354
+#&gt; 48 parent 42.424242 11.167885303
+#&gt; 49 parent 43.434343 10.621234162
+#&gt; 50 parent 44.444444 10.101340770
+#&gt; 51 parent 45.454545 9.606895375
+#&gt; 52 parent 46.464646 9.136652336
+#&gt; 53 parent 47.474747 8.689426985
+#&gt; 54 parent 48.484848 8.264092640
+#&gt; 55 parent 49.494949 7.859577770
+#&gt; 56 parent 50.505051 7.474863293
+#&gt; 57 parent 51.515152 7.108980009
+#&gt; 58 parent 52.525253 6.761006160
+#&gt; 59 parent 53.535354 6.430065106
+#&gt; 60 parent 54.545455 6.115323117
+#&gt; 61 parent 55.555556 5.815987274
+#&gt; 62 parent 56.565657 5.531303470
+#&gt; 63 parent 57.575758 5.260554508
+#&gt; 64 parent 58.585859 5.003058299
+#&gt; 65 parent 59.595960 4.758166141
+#&gt; 66 parent 60.606061 4.525261085
+#&gt; 67 parent 61.616162 4.303756381
+#&gt; 68 parent 62.000000 4.222456793
+#&gt; 69 parent 62.626263 4.093093997
+#&gt; 70 parent 63.636364 3.892743220
+#&gt; 71 parent 64.646465 3.702199310
+#&gt; 72 parent 65.656566 3.520982238
+#&gt; 73 parent 66.666667 3.348635468
+#&gt; 74 parent 67.676768 3.184724813
+#&gt; 75 parent 68.686869 3.028837337
+#&gt; 76 parent 69.696970 2.880580317
+#&gt; 77 parent 70.707071 2.739580256
+#&gt; 78 parent 71.717172 2.605481934
+#&gt; 79 parent 72.727273 2.477947523
+#&gt; 80 parent 73.737374 2.356655730
+#&gt; 81 parent 74.747475 2.241300986
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+#&gt; 482 A2 52.525253 3.457532417
+#&gt; 483 A2 53.535354 3.496656681
+#&gt; 484 A2 54.545455 3.533873012
+#&gt; 485 A2 55.555556 3.569203883
+#&gt; 486 A2 56.565657 3.602673379
+#&gt; 487 A2 57.575758 3.634307034
+#&gt; 488 A2 58.585859 3.664131686
+#&gt; 489 A2 59.595960 3.692175334
+#&gt; 490 A2 60.606061 3.718467012
+#&gt; 491 A2 61.616162 3.743036663
+#&gt; 492 A2 62.000000 3.751927986
+#&gt; 493 A2 62.626263 3.765915028
+#&gt; 494 A2 63.636364 3.787133539
+#&gt; 495 A2 64.646465 3.806724217
+#&gt; 496 A2 65.656566 3.824719582
+#&gt; 497 A2 66.666667 3.841152565
+#&gt; 498 A2 67.676768 3.856056426
+#&gt; 499 A2 68.686869 3.869464684
+#&gt; 500 A2 69.696970 3.881411040
+#&gt; 501 A2 70.707071 3.891929316
+#&gt; 502 A2 71.717172 3.901053396
+#&gt; 503 A2 72.727273 3.908817168
+#&gt; 504 A2 73.737374 3.915254472
+#&gt; 505 A2 74.747475 3.920399054
+#&gt; 506 A2 75.757576 3.924284521
+#&gt; 507 A2 76.767677 3.926944303
+#&gt; 508 A2 77.777778 3.928411610
+#&gt; 509 A2 78.787879 3.928719404
+#&gt; 510 A2 79.797980 3.927900364
+#&gt; 511 A2 80.808081 3.925986861
+#&gt; 512 A2 81.818182 3.923010926
+#&gt; 513 A2 82.828283 3.919004234
+#&gt; 514 A2 83.838384 3.913998077
+#&gt; 515 A2 84.848485 3.908023347
+#&gt; 516 A2 85.858586 3.901110518
+#&gt; 517 A2 86.868687 3.893289633
+#&gt; 518 A2 87.878788 3.884590288
+#&gt; 519 A2 88.888889 3.875041619
+#&gt; 520 A2 89.898990 3.864672297
+#&gt; 521 A2 90.909091 3.853510511
+#&gt; 522 A2 91.919192 3.841583970
+#&gt; 523 A2 92.929293 3.828919886
+#&gt; 524 A2 93.939394 3.815544978
+#&gt; 525 A2 94.949495 3.801485462
+#&gt; 526 A2 95.959596 3.786767051
+#&gt; 527 A2 96.969697 3.771414951
+#&gt; 528 A2 97.979798 3.755453860
+#&gt; 529 A2 98.989899 3.738907968
+#&gt; 530 A2 100.000000 3.721800959
+#&gt;
+#&gt; $cost
+#&gt; function (P)
+#&gt; {
+#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
+#&gt; if (trace_parms)
+#&gt; cat(P, &quot;\n&quot;)
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; transparms.fixed)
+#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
+#&gt; transform_fractions = transform_fractions)
+#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; if (mC$model &lt; cost.old) {
+#&gt; if (!quiet)
+#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
+#&gt; &quot;\n&quot;)
+#&gt; if (plot) {
+#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
+#&gt; length.out = 100)
+#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
+#&gt; solution_type = solution_type, use_compiled = use_compiled,
+#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
+#&gt; ...)
+#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
+#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
+#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
+#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
+#&gt; lty_obs &lt;- rep(1, length(obs_vars))
+#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
+#&gt; for (obs_var in obs_vars) {
+#&gt; points(subset(observed, name == obs_var, c(time,
+#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
+#&gt; }
+#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
+#&gt; lty = lty_obs)
+#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
+#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
+#&gt; }
+#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
+#&gt; }
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x36a83b0&gt;
+#&gt;
+#&gt; $cost_notrans
+#&gt; function (P)
+#&gt; {
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; parms.fixed)
+#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x36a83b0&gt;
+#&gt;
+#&gt; $hessian_notrans
+#&gt; parent_0 k_parent k_A1 k_B1
+#&gt; parent_0 7.365081 -1854.5113 -7.186039e+02 -1.307858e+02
+#&gt; k_parent -1854.511330 2686790.7676 -6.235542e+04 -1.429363e+04
+#&gt; k_A1 -718.603865 -62355.4211 3.128242e+06 0.000000e+00
+#&gt; k_B1 -130.785796 -14293.6348 0.000000e+00 4.545506e+05
+#&gt; k_C1 -76.404274 -38575.9391 1.190516e-02 -9.422820e-04
+#&gt; k_A2 -17.933942 -4390.5079 -5.838973e+04 0.000000e+00
+#&gt; f_parent_to_A1 75.150866 43257.2599 -1.733841e+05 0.000000e+00
+#&gt; f_parent_to_B1 29.265575 17940.1132 0.000000e+00 -6.150198e+04
+#&gt; f_parent_to_C1 20.661354 19692.5582 -6.146186e-05 -1.990817e-03
+#&gt; f_A1_to_A2 1.593279 597.0744 5.849840e+03 0.000000e+00
+#&gt; k_C1 k_A2 f_parent_to_A1 f_parent_to_B1
+#&gt; parent_0 -7.640427e+01 -1.793394e+01 7.515087e+01 2.926558e+01
+#&gt; k_parent -3.857594e+04 -4.390508e+03 4.325726e+04 1.794011e+04
+#&gt; k_A1 1.190516e-02 -5.838973e+04 -1.733841e+05 0.000000e+00
+#&gt; k_B1 -9.422820e-04 0.000000e+00 0.000000e+00 -6.150198e+04
+#&gt; k_C1 8.855106e+04 4.105787e-04 -1.354551e-03 5.852620e-04
+#&gt; k_A2 4.105787e-04 4.649850e+04 -4.327086e+03 0.000000e+00
+#&gt; f_parent_to_A1 -1.354551e-03 -4.327086e+03 1.813234e+04 0.000000e+00
+#&gt; f_parent_to_B1 5.852620e-04 0.000000e+00 0.000000e+00 1.376213e+04
+#&gt; f_parent_to_C1 -1.658031e+04 2.903794e-04 1.946385e-03 1.325258e-03
+#&gt; f_A1_to_A2 -4.367402e-05 -3.679910e+03 3.844249e+02 0.000000e+00
+#&gt; f_parent_to_C1 f_A1_to_A2
+#&gt; parent_0 2.066135e+01 1.593279e+00
+#&gt; k_parent 1.969256e+04 5.970744e+02
+#&gt; k_A1 -6.146186e-05 5.849840e+03
+#&gt; k_B1 -1.990817e-03 0.000000e+00
+#&gt; k_C1 -1.658031e+04 -4.367402e-05
+#&gt; k_A2 2.903794e-04 -3.679910e+03
+#&gt; f_parent_to_A1 1.946385e-03 3.844249e+02
+#&gt; f_parent_to_B1 1.325258e-03 0.000000e+00
+#&gt; f_parent_to_C1 4.483759e+03 -3.796730e-05
+#&gt; f_A1_to_A2 -3.796730e-05 3.269288e+02
+#&gt;
+#&gt; $start
+#&gt; value type
+#&gt; parent_0 93.2000000 state
+#&gt; k_parent 0.1000000 deparm
+#&gt; k_A1 0.1001000 deparm
+#&gt; k_B1 0.1002000 deparm
+#&gt; k_C1 0.1003000 deparm
+#&gt; k_A2 0.1004000 deparm
+#&gt; f_parent_to_A1 0.3333333 deparm
+#&gt; f_parent_to_B1 0.3333333 deparm
+#&gt; f_parent_to_C1 0.3333333 deparm
+#&gt; f_A1_to_A2 0.5000000 deparm
+#&gt;
+#&gt; $start_transformed
+#&gt; value lower upper
+#&gt; parent_0 93.200000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_A1 -2.301586 -Inf Inf
+#&gt; log_k_B1 -2.300587 -Inf Inf
+#&gt; log_k_C1 -2.299590 -Inf Inf
+#&gt; log_k_A2 -2.298593 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt; f_parent_ilr_2 0.000000 -Inf Inf
+#&gt; f_A1_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; $fixed
+#&gt; value type
+#&gt; A1_0 0 state
+#&gt; B1_0 0 state
+#&gt; C1_0 0 state
+#&gt; A2_0 0 state
+#&gt;
+#&gt; $data
+#&gt; time variable observed predicted residual
+#&gt; 1 0 parent 93.20 91.918159794 1.2818402
+#&gt; 2 1 parent 89.40 87.462788491 1.9372115
+#&gt; 3 3 parent 79.70 79.189448055 0.5105519
+#&gt; 4 7 parent 61.10 64.916531757 -3.8165318
+#&gt; 5 14 parent 48.20 45.846828365 2.3531716
+#&gt; 6 30 parent 15.90 20.704334210 -4.8043342
+#&gt; 7 62 parent 6.50 4.222456793 2.2775432
+#&gt; 8 100 parent 6.00 0.639147580 5.3608524
+#&gt; 9 0 A1 NA 0.000000000 NA
+#&gt; 10 1 A1 NA 1.685461006 NA
+#&gt; 11 3 A1 0.55 4.746752202 -4.1967522
+#&gt; 12 7 A1 6.87 9.773298725 -2.9032987
+#&gt; 13 14 A1 17.08 15.767512526 1.3124875
+#&gt; 14 30 A1 21.68 21.077890710 0.6021093
+#&gt; 15 62 A1 15.77 18.279232408 -2.5092324
+#&gt; 16 100 A1 13.63 11.743860400 1.8861396
+#&gt; 17 0 B1 NA 0.000000000 NA
+#&gt; 18 1 B1 NA 0.862762059 NA
+#&gt; 19 3 B1 NA 2.418226457 NA
+#&gt; 20 7 B1 0.55 4.930176837 -4.3801768
+#&gt; 21 14 B1 2.31 7.810248132 -5.5002481
+#&gt; 22 30 B1 15.76 9.968281596 5.7917184
+#&gt; 23 62 B1 6.36 7.745265792 -1.3852658
+#&gt; 24 100 B1 3.74 4.271330056 -0.5313301
+#&gt; 25 0 C1 NA 0.000000000 NA
+#&gt; 26 1 C1 0.55 1.829645786 -1.2796458
+#&gt; 27 3 C1 3.20 4.910531064 -1.7105311
+#&gt; 28 7 C1 5.46 9.171671206 -3.7116712
+#&gt; 29 14 C1 12.55 12.431704739 0.1182953
+#&gt; 30 30 C1 10.45 10.972842888 -0.5228429
+#&gt; 31 62 C1 4.74 3.882970158 0.8570298
+#&gt; 32 100 C1 4.33 0.782344364 3.5476556
+#&gt; 33 0 A2 NA 0.000000000 NA
+#&gt; 34 1 A2 0.55 0.005272357 0.5447276
+#&gt; 35 3 A2 1.41 0.044759575 1.3652404
+#&gt; 36 7 A2 0.55 0.216973934 0.3330261
+#&gt; 37 14 A2 1.29 0.709794102 0.5802059
+#&gt; 38 30 A2 1.95 2.078585030 -0.1285850
+#&gt; 39 62 A2 3.54 3.751927986 -0.2119280
+#&gt; 40 100 A2 3.86 3.721800959 0.1381990
+#&gt;
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt;
+#&gt; $weight.ini
+#&gt; [1] &quot;none&quot;
+#&gt;
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt;
+#&gt; $bparms.optim
+#&gt; parent_0 k_parent k_A1 k_B1 k_C1
+#&gt; 91.91815979 0.04968519 0.01393165 0.01859846 0.06171564
+#&gt; k_A2 f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 f_A1_to_A2
+#&gt; 0.02431549 0.38096192 0.19546676 0.42357132 0.44796066
+#&gt;
+#&gt; $bparms.fixed
+#&gt; A1_0 B1_0 C1_0 A2_0
+#&gt; 0 0 0 0
+#&gt;
+#&gt; $bparms.ode
+#&gt; k_parent f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 k_A1
+#&gt; 0.04968519 0.38096192 0.19546676 0.42357132 0.01393165
+#&gt; f_A1_to_A2 k_B1 k_C1 k_A2
+#&gt; 0.44796066 0.01859846 0.06171564 0.02431549
+#&gt;
+#&gt; $bparms.state
+#&gt; parent A1 B1 C1 A2
+#&gt; 91.91816 0.00000 0.00000 0.00000 0.00000
+#&gt;
+#&gt; $date
+#&gt; [1] &quot;Fri Nov 18 15:20:45 2016&quot;
+#&gt;
+#&gt; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 8dc57fb7..b334b3aa 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -142,15 +142,15 @@
<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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Nov 17 22:57:05 2016
-#&gt; Date of summary: Thu Nov 17 22:57:05 2016
+#&gt; Date of fit: Fri Nov 18 15:20:45 2016
+#&gt; Date of summary: Fri Nov 18 15:20:45 2016
#&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 0.085 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index c6f29582..97407402 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -121,28 +121,856 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># m_synth_SFO_lin &lt;- mkinmod(parent = list(type = "SFO", to = "M1"),</span>
-<span class='co'># M1 = list(type = "SFO", to = "M2"),</span>
-<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># </span>
-<span class='co'># m_synth_SFO_par &lt;- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),</span>
-<span class='co'># sink = FALSE),</span>
-<span class='co'># M1 = list(type = "SFO"),</span>
-<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># m_synth_DFOP_lin &lt;- mkinmod(parent = list(type = "DFOP", to = "M1"),</span>
-<span class='co'># M1 = list(type = "SFO", to = "M2"),</span>
-<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># m_synth_DFOP_par &lt;- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),</span>
-<span class='co'># sink = FALSE),</span>
-<span class='co'># M1 = list(type = "SFO"),</span>
-<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+ <pre class="examples"><div class='input'>
+<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
+ <span class='kw'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>m_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
+ <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>),
+ <span class='kw'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>m_synth_DFOP_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>"DFOP"</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>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
+ <span class='kw'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
+ <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>),
+ <span class='kw'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 31054.59
+#&gt; Model cost at call 3 : 31054.59
+#&gt; Model cost at call 8 : 15089.57
+#&gt; Model cost at call 9 : 11464.3
+#&gt; Model cost at call 11 : 11464.1
+#&gt; Model cost at call 16 : 5723.32
+#&gt; Model cost at call 17 : 5723.318
+#&gt; Model cost at call 19 : 5723.304
+#&gt; Model cost at call 21 : 5723.304
+#&gt; Model cost at call 24 : 3968.126
+#&gt; Model cost at call 25 : 3968.124
+#&gt; Model cost at call 28 : 3968.119
+#&gt; Model cost at call 31 : 3416.421
+#&gt; Model cost at call 32 : 3416.42
+#&gt; Model cost at call 36 : 3416.418
+#&gt; Model cost at call 38 : 866.5564
+#&gt; Model cost at call 42 : 866.5557
+#&gt; Model cost at call 45 : 670.4833
+#&gt; Model cost at call 47 : 670.476
+#&gt; Model cost at call 53 : 312.9905
+#&gt; Model cost at call 57 : 312.9904
+#&gt; Model cost at call 58 : 312.9904
+#&gt; Model cost at call 61 : 287.8916
+#&gt; Model cost at call 63 : 287.8916
+#&gt; Model cost at call 66 : 287.8916
+#&gt; Model cost at call 69 : 284.5441
+#&gt; Model cost at call 71 : 284.5441
+#&gt; Model cost at call 73 : 284.5441
+#&gt; Model cost at call 76 : 283.4533
+#&gt; Model cost at call 78 : 283.4533
+#&gt; Model cost at call 83 : 282.1356
+#&gt; Model cost at call 85 : 282.1356
+#&gt; Model cost at call 88 : 282.1356
+#&gt; Model cost at call 90 : 280.7846
+#&gt; Model cost at call 92 : 280.7846
+#&gt; Model cost at call 95 : 280.7846
+#&gt; Model cost at call 97 : 278.4856
+#&gt; Model cost at call 98 : 274.5025
+#&gt; Model cost at call 99 : 269.2866
+#&gt; Model cost at call 101 : 269.2866
+#&gt; Model cost at call 102 : 269.2866
+#&gt; Model cost at call 103 : 269.2866
+#&gt; Model cost at call 106 : 254.1284
+#&gt; Model cost at call 108 : 254.1283
+#&gt; Model cost at call 109 : 254.1283
+#&gt; Model cost at call 112 : 254.128
+#&gt; Model cost at call 114 : 233.1376
+#&gt; Model cost at call 116 : 233.1376
+#&gt; Model cost at call 118 : 233.1375
+#&gt; Model cost at call 121 : 227.5879
+#&gt; Model cost at call 124 : 227.5879
+#&gt; Model cost at call 125 : 227.5878
+#&gt; Model cost at call 129 : 217.0041
+#&gt; Model cost at call 133 : 217.0041
+#&gt; Model cost at call 135 : 217.0041
+#&gt; Model cost at call 136 : 215.1367
+#&gt; Model cost at call 138 : 215.1367
+#&gt; Model cost at call 143 : 213.3794
+#&gt; Model cost at call 145 : 213.3794
+#&gt; Model cost at call 150 : 211.0201
+#&gt; Model cost at call 152 : 211.0201
+#&gt; Model cost at call 154 : 211.0201
+#&gt; Model cost at call 155 : 211.0201
+#&gt; Model cost at call 157 : 210.6426
+#&gt; Model cost at call 159 : 210.6426
+#&gt; Model cost at call 160 : 210.6425
+#&gt; Model cost at call 164 : 207.6331
+#&gt; Model cost at call 167 : 207.6331
+#&gt; Model cost at call 171 : 206.2366
+#&gt; Model cost at call 173 : 206.2366
+#&gt; Model cost at call 174 : 206.2366
+#&gt; Model cost at call 178 : 204.8117
+#&gt; Model cost at call 180 : 204.8117
+#&gt; Model cost at call 185 : 204.7988
+#&gt; Model cost at call 187 : 204.7988
+#&gt; Model cost at call 190 : 204.7988
+#&gt; Model cost at call 192 : 203.5122
+#&gt; Model cost at call 194 : 203.5122
+#&gt; Model cost at call 197 : 203.5122
+#&gt; Model cost at call 198 : 203.5122
+#&gt; Model cost at call 199 : 203.354
+#&gt; Model cost at call 201 : 203.354
+#&gt; Model cost at call 204 : 203.354
+#&gt; Model cost at call 206 : 202.6825
+#&gt; Model cost at call 208 : 202.6825
+#&gt; Model cost at call 209 : 202.6825
+#&gt; Model cost at call 212 : 202.6825
+#&gt; Model cost at call 213 : 202.4582
+#&gt; Model cost at call 215 : 202.4582
+#&gt; Model cost at call 220 : 202.3261
+#&gt; Model cost at call 222 : 202.3261
+#&gt; Model cost at call 227 : 202.2306
+#&gt; Model cost at call 229 : 202.2306
+#&gt; Model cost at call 231 : 202.2306
+#&gt; Model cost at call 234 : 202.115
+#&gt; Model cost at call 236 : 202.115
+#&gt; Model cost at call 238 : 202.115
+#&gt; Model cost at call 241 : 202.0397
+#&gt; Model cost at call 243 : 202.0397
+#&gt; Model cost at call 248 : 201.8989
+#&gt; Model cost at call 249 : 201.8551
+#&gt; Model cost at call 252 : 201.8551
+#&gt; Model cost at call 257 : 201.676
+#&gt; Model cost at call 259 : 201.676
+#&gt; Model cost at call 264 : 201.6285
+#&gt; Model cost at call 266 : 201.6285
+#&gt; Model cost at call 270 : 201.6284
+#&gt; Model cost at call 271 : 201.5876
+#&gt; Model cost at call 272 : 201.5876
+#&gt; Model cost at call 278 : 201.5317
+#&gt; Model cost at call 279 : 201.5317
+#&gt; Model cost at call 286 : 201.5207
+#&gt; Model cost at call 287 : 201.5207
+#&gt; Model cost at call 289 : 201.5207
+#&gt; Model cost at call 293 : 201.5207
+#&gt; Model cost at call 294 : 201.5207
+#&gt; Model cost at call 296 : 201.5174
+#&gt; Model cost at call 301 : 201.5174
+#&gt; Model cost at call 304 : 201.5169
+#&gt; Model cost at call 305 : 201.5169
+#&gt; Model cost at call 306 : 201.5169
+#&gt; Model cost at call 309 : 201.5169
+#&gt; Model cost at call 312 : 201.5169
+#&gt; Model cost at call 314 : 201.5169
+#&gt; Model cost at call 322 : 201.5169
+#&gt; Model cost at call 325 : 201.5169
+#&gt; Model cost at call 340 : 201.5169
+#&gt; Optimisation by method Port successfully terminated.</div><div class='output co'>#&gt; $par
+#&gt; parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1
+#&gt; 102.0624835 -0.3020316 -1.2067882 -3.9007519 0.8491684
+#&gt; f_M1_ilr_1
+#&gt; 0.6780411
+#&gt;
+#&gt; $ssr
+#&gt; [1] 201.5169
+#&gt;
+#&gt; $convergence
+#&gt; [1] 0
+#&gt;
+#&gt; $iterations
+#&gt; [1] 43
+#&gt;
+#&gt; $evaluations
+#&gt; function gradient
+#&gt; 56 281
+#&gt;
+#&gt; $counts
+#&gt; [1] &quot;relative convergence (4)&quot;
+#&gt;
+#&gt; $hessian
+#&gt; parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1
+#&gt; parent_0 8.433594 -29.66715 -18.40708 -68.90161 115.9976
+#&gt; log_k_parent -29.667146 10561.33531 675.33998 55.94284 1666.8940
+#&gt; log_k_M1 -18.407082 675.33998 6274.11801 44.01714 -614.5674
+#&gt; log_k_M2 -68.901614 55.94284 44.01714 5021.66991 -2300.4467
+#&gt; f_parent_ilr_1 115.997604 1666.89403 -614.56735 -2300.44667 3872.8569
+#&gt; f_M1_ilr_1 92.819176 604.06870 1483.45826 -2755.79082 3098.9947
+#&gt; f_M1_ilr_1
+#&gt; parent_0 92.81918
+#&gt; log_k_parent 604.06870
+#&gt; log_k_M1 1483.45826
+#&gt; log_k_M2 -2755.79082
+#&gt; f_parent_ilr_1 3098.99466
+#&gt; f_M1_ilr_1 3712.39824
+#&gt;
+#&gt; $residuals
+#&gt; parent parent parent parent parent parent
+#&gt; 0.56248353 0.86248353 -5.17118695 1.22881305 0.70772795 3.50772795
+#&gt; parent parent parent parent parent parent
+#&gt; -0.52282962 0.27717038 -3.49673606 -3.19999990 -0.60000000 -3.50000000
+#&gt; M1 M1 M1 M1 M1 M1
+#&gt; -1.61088639 -2.61088639 5.07026619 -0.42973381 0.38714436 -2.31285564
+#&gt; M1 M1 M1 M1 M1 M1
+#&gt; -3.80468869 0.79531131 -0.49999789 -3.20000000 -1.50000000 -0.60000000
+#&gt; M2 M2 M2 M2 M2 M2
+#&gt; -0.34517017 0.62526794 2.22526794 -0.07941701 -1.17941701 -3.83353798
+#&gt; M2 M2 M2 M2 M2 M2
+#&gt; 1.26646202 0.87274743 2.47274743 -0.21837410 0.98162590 -0.47130583
+#&gt; M2 M2 M2
+#&gt; -0.67130583 -4.27893112 2.22106888
+#&gt;
+#&gt; $ms
+#&gt; [1] 5.1671
+#&gt;
+#&gt; $var_ms
+#&gt; parent M1 M2
+#&gt; 6.461983 5.750942 3.664121
+#&gt;
+#&gt; $var_ms_unscaled
+#&gt; parent M1 M2
+#&gt; 6.461983 5.750942 3.664121
+#&gt;
+#&gt; $var_ms_unweighted
+#&gt; parent M1 M2
+#&gt; 6.461983 5.750942 3.664121
+#&gt;
+#&gt; $rank
+#&gt; [1] 6
+#&gt;
+#&gt; $df.residual
+#&gt; [1] 33
+#&gt;
+#&gt; $solution_type
+#&gt; [1] &quot;deSolve&quot;
+#&gt;
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt;
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt;
+#&gt; $method.modFit
+#&gt; [1] &quot;Port&quot;
+#&gt;
+#&gt; $maxit.modFit
+#&gt; [1] &quot;auto&quot;
+#&gt;
+#&gt; $calls
+#&gt; [1] 351
+#&gt;
+#&gt; $time
+#&gt; user system elapsed
+#&gt; 2.116 0.000 2.113
+#&gt;
+#&gt; $mkinmod
+#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: max
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: SFO; $to: M1; $sink: TRUE
+#&gt; $M1
+#&gt; $type: SFO; $to: M2; $sink: TRUE
+#&gt; $M2
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt; Compiled model $cf available
+#&gt;
+#&gt; $observed
+#&gt; name time value override err
+#&gt; 1 parent 0 101.5 NA 1
+#&gt; 2 parent 0 101.2 NA 1
+#&gt; 3 parent 1 53.9 NA 1
+#&gt; 4 parent 1 47.5 NA 1
+#&gt; 5 parent 3 10.4 NA 1
+#&gt; 6 parent 3 7.6 NA 1
+#&gt; 7 parent 7 1.1 NA 1
+#&gt; 8 parent 7 0.3 NA 1
+#&gt; 9 parent 14 NA NA 1
+#&gt; 10 parent 14 3.5 NA 1
+#&gt; 11 parent 28 NA NA 1
+#&gt; 12 parent 28 3.2 NA 1
+#&gt; 13 parent 60 NA NA 1
+#&gt; 14 parent 60 NA NA 1
+#&gt; 15 parent 90 0.6 NA 1
+#&gt; 16 parent 90 NA NA 1
+#&gt; 17 parent 120 NA NA 1
+#&gt; 18 parent 120 3.5 NA 1
+#&gt; 19 M1 0 NA NA 1
+#&gt; 20 M1 0 NA NA 1
+#&gt; 21 M1 1 36.4 NA 1
+#&gt; 22 M1 1 37.4 NA 1
+#&gt; 23 M1 3 34.3 NA 1
+#&gt; 24 M1 3 39.8 NA 1
+#&gt; 25 M1 7 15.1 NA 1
+#&gt; 26 M1 7 17.8 NA 1
+#&gt; 27 M1 14 5.8 NA 1
+#&gt; 28 M1 14 1.2 NA 1
+#&gt; 29 M1 28 NA NA 1
+#&gt; 30 M1 28 NA NA 1
+#&gt; 31 M1 60 0.5 NA 1
+#&gt; 32 M1 60 NA NA 1
+#&gt; 33 M1 90 NA NA 1
+#&gt; 34 M1 90 3.2 NA 1
+#&gt; 35 M1 120 1.5 NA 1
+#&gt; 36 M1 120 0.6 NA 1
+#&gt; 37 M2 0 NA NA 1
+#&gt; 38 M2 0 NA NA 1
+#&gt; 39 M2 1 NA NA 1
+#&gt; 40 M2 1 4.8 NA 1
+#&gt; 41 M2 3 20.9 NA 1
+#&gt; 42 M2 3 19.3 NA 1
+#&gt; 43 M2 7 42.0 NA 1
+#&gt; 44 M2 7 43.1 NA 1
+#&gt; 45 M2 14 49.4 NA 1
+#&gt; 46 M2 14 44.3 NA 1
+#&gt; 47 M2 28 34.6 NA 1
+#&gt; 48 M2 28 33.0 NA 1
+#&gt; 49 M2 60 18.8 NA 1
+#&gt; 50 M2 60 17.6 NA 1
+#&gt; 51 M2 90 10.6 NA 1
+#&gt; 52 M2 90 10.8 NA 1
+#&gt; 53 M2 120 9.8 NA 1
+#&gt; 54 M2 120 3.3 NA 1
+#&gt;
+#&gt; $obs_vars
+#&gt; [1] &quot;parent&quot; &quot;M1&quot; &quot;M2&quot;
+#&gt;
+#&gt; $predicted
+#&gt; name time value
+#&gt; 1 parent 0.000000 1.020625e+02
+#&gt; 2 parent 1.000000 4.872881e+01
+#&gt; 3 parent 1.212121 4.165603e+01
+#&gt; 4 parent 2.424242 1.700159e+01
+#&gt; 5 parent 3.000000 1.110773e+01
+#&gt; 6 parent 3.636364 6.939072e+00
+#&gt; 7 parent 4.848485 2.832130e+00
+#&gt; 8 parent 6.060606 1.155912e+00
+#&gt; 9 parent 7.000000 5.771704e-01
+#&gt; 10 parent 7.272727 4.717769e-01
+#&gt; 11 parent 8.484848 1.925522e-01
+#&gt; 12 parent 9.696970 7.858872e-02
+#&gt; 13 parent 10.909091 3.207539e-02
+#&gt; 14 parent 12.121212 1.309133e-02
+#&gt; 15 parent 13.333333 5.343128e-03
+#&gt; 16 parent 14.000000 3.263939e-03
+#&gt; 17 parent 14.545455 2.180757e-03
+#&gt; 18 parent 15.757576 8.900590e-04
+#&gt; 19 parent 16.969697 3.632705e-04
+#&gt; 20 parent 18.181818 1.482660e-04
+#&gt; 21 parent 19.393939 6.051327e-05
+#&gt; 22 parent 20.606061 2.469808e-05
+#&gt; 23 parent 21.818182 1.008035e-05
+#&gt; 24 parent 23.030303 4.114467e-06
+#&gt; 25 parent 24.242424 1.679140e-06
+#&gt; 26 parent 25.454545 6.853728e-07
+#&gt; 27 parent 26.666667 2.797450e-07
+#&gt; 28 parent 27.878788 1.142138e-07
+#&gt; 29 parent 28.000000 1.044512e-07
+#&gt; 30 parent 29.090909 4.657425e-08
+#&gt; 31 parent 30.303030 1.900245e-08
+#&gt; 32 parent 31.515152 7.760238e-09
+#&gt; 33 parent 32.727273 3.164577e-09
+#&gt; 34 parent 33.939394 1.291779e-09
+#&gt; 35 parent 35.151515 5.261577e-10
+#&gt; 36 parent 36.363636 2.132915e-10
+#&gt; 37 parent 37.575758 8.767818e-11
+#&gt; 38 parent 38.787879 3.442792e-11
+#&gt; 39 parent 40.000000 1.827291e-11
+#&gt; 40 parent 41.212121 3.771071e-12
+#&gt; 41 parent 42.424242 6.084856e-12
+#&gt; 42 parent 43.636364 -3.377858e-12
+#&gt; 43 parent 44.848485 5.870338e-12
+#&gt; 44 parent 46.060606 -6.263257e-12
+#&gt; 45 parent 47.272727 8.743492e-12
+#&gt; 46 parent 48.484848 -9.381771e-12
+#&gt; 47 parent 49.696970 1.403389e-11
+#&gt; 48 parent 50.909091 -3.592528e-11
+#&gt; 49 parent 52.121212 -8.487459e-11
+#&gt; 50 parent 53.333333 -3.309153e-12
+#&gt; 51 parent 54.545455 -2.966799e-11
+#&gt; 52 parent 55.757576 -4.723329e-11
+#&gt; 53 parent 56.969697 7.635833e-11
+#&gt; 54 parent 58.181818 -1.887064e-11
+#&gt; 55 parent 59.393939 -1.548352e-10
+#&gt; 56 parent 60.000000 -1.053819e-10
+#&gt; 57 parent 60.606061 5.780435e-12
+#&gt; 58 parent 61.818182 9.056244e-11
+#&gt; 59 parent 63.030303 -8.889581e-11
+#&gt; 60 parent 64.242424 -6.653389e-11
+#&gt; 61 parent 65.454545 1.181114e-10
+#&gt; 62 parent 66.666667 -9.226329e-12
+#&gt; 63 parent 67.878788 -8.897326e-11
+#&gt; 64 parent 69.090909 1.984998e-10
+#&gt; 65 parent 70.303030 3.255550e-11
+#&gt; 66 parent 71.515152 -2.991002e-10
+#&gt; 67 parent 72.727273 2.254268e-10
+#&gt; 68 parent 73.939394 2.696039e-10
+#&gt; 69 parent 75.151515 1.226806e-10
+#&gt; 70 parent 76.363636 3.447399e-11
+#&gt; 71 parent 77.575758 2.048902e-11
+#&gt; 72 parent 78.787879 6.830755e-12
+#&gt; 73 parent 80.000000 8.242171e-13
+#&gt; 74 parent 81.212121 -5.357740e-12
+#&gt; 75 parent 82.424242 2.198907e-11
+#&gt; 76 parent 83.636364 3.739511e-11
+#&gt; 77 parent 84.848485 -6.616091e-12
+#&gt; 78 parent 86.060606 -2.562689e-12
+#&gt; 79 parent 87.272727 4.089395e-11
+#&gt; 80 parent 88.484848 -2.042159e-11
+#&gt; 81 parent 89.696970 -4.088127e-11
+#&gt; 82 parent 90.000000 -1.874889e-11
+#&gt; 83 parent 90.909091 4.225747e-11
+#&gt; 84 parent 92.121212 8.054402e-12
+#&gt; 85 parent 93.333333 3.917595e-12
+#&gt; 86 parent 94.545455 6.591454e-12
+#&gt; 87 parent 95.757576 2.790958e-11
+#&gt; 88 parent 96.969697 2.720721e-12
+#&gt; 89 parent 98.181818 -1.304470e-12
+#&gt; 90 parent 99.393939 1.345055e-11
+#&gt; 91 parent 100.606061 -9.662077e-12
+#&gt; 92 parent 101.818182 -2.086798e-11
+#&gt; 93 parent 103.030303 9.332507e-12
+#&gt; 94 parent 104.242424 -6.752606e-12
+#&gt; 95 parent 105.454545 -3.326620e-11
+#&gt; 96 parent 106.666667 2.500680e-11
+#&gt; 97 parent 107.878788 2.184148e-11
+#&gt; 98 parent 109.090909 -5.985657e-11
+#&gt; 99 parent 110.303030 -8.750836e-14
+#&gt; 100 parent 111.515152 1.820588e-12
+#&gt; 101 parent 112.727273 -1.261472e-11
+#&gt; 102 parent 113.939394 1.455439e-11
+#&gt; 103 parent 115.151515 1.945812e-12
+#&gt; 104 parent 116.363636 9.598249e-13
+#&gt; 105 parent 117.575758 1.724679e-12
+#&gt; 106 parent 118.787879 -1.334504e-12
+#&gt; 107 parent 120.000000 -2.804801e-11
+#&gt; 108 M1 0.000000 0.000000e+00
+#&gt; 109 M1 1.000000 3.478911e+01
+#&gt; 110 M1 1.212121 3.791354e+01
+#&gt; 111 M1 2.424242 4.185645e+01
+#&gt; 112 M1 3.000000 3.937027e+01
+#&gt; 113 M1 3.636364 3.544167e+01
+#&gt; 114 M1 4.848485 2.723995e+01
+#&gt; 115 M1 6.060606 2.000711e+01
+#&gt; 116 M1 7.000000 1.548714e+01
+#&gt; 117 M1 7.272727 1.435144e+01
+#&gt; 118 M1 8.484848 1.016177e+01
+#&gt; 119 M1 9.696970 7.142649e+00
+#&gt; 120 M1 10.909091 4.999441e+00
+#&gt; 121 M1 12.121212 3.490801e+00
+#&gt; 122 M1 13.333333 2.433954e+00
+#&gt; 123 M1 14.000000 1.995311e+00
+#&gt; 124 M1 14.545455 1.695664e+00
+#&gt; 125 M1 15.757576 1.180746e+00
+#&gt; 126 M1 16.969697 8.219589e-01
+#&gt; 127 M1 18.181818 5.720991e-01
+#&gt; 128 M1 19.393939 3.981531e-01
+#&gt; 129 M1 20.606061 2.770793e-01
+#&gt; 130 M1 21.818182 1.928162e-01
+#&gt; 131 M1 23.030303 1.341758e-01
+#&gt; 132 M1 24.242424 9.336844e-02
+#&gt; 133 M1 25.454545 6.497152e-02
+#&gt; 134 M1 26.666667 4.521101e-02
+#&gt; 135 M1 27.878788 3.146041e-02
+#&gt; 136 M1 28.000000 3.034005e-02
+#&gt; 137 M1 29.090909 2.189192e-02
+#&gt; 138 M1 30.303030 1.523362e-02
+#&gt; 139 M1 31.515152 1.060040e-02
+#&gt; 140 M1 32.727273 7.376345e-03
+#&gt; 141 M1 33.939394 5.132870e-03
+#&gt; 142 M1 35.151515 3.571730e-03
+#&gt; 143 M1 36.363636 2.485406e-03
+#&gt; 144 M1 37.575758 1.729482e-03
+#&gt; 145 M1 38.787879 1.203467e-03
+#&gt; 146 M1 40.000000 8.374380e-04
+#&gt; 147 M1 41.212121 5.827347e-04
+#&gt; 148 M1 42.424242 4.054989e-04
+#&gt; 149 M1 43.636364 2.821681e-04
+#&gt; 150 M1 44.848485 1.963481e-04
+#&gt; 151 M1 46.060606 1.366297e-04
+#&gt; 152 M1 47.272727 9.507439e-05
+#&gt; 153 M1 48.484848 6.615797e-05
+#&gt; 154 M1 49.696970 4.603629e-05
+#&gt; 155 M1 50.909091 3.203434e-05
+#&gt; 156 M1 52.121212 2.229196e-05
+#&gt; 157 M1 53.333333 1.551223e-05
+#&gt; 158 M1 54.545455 1.079420e-05
+#&gt; 159 M1 55.757576 7.511255e-06
+#&gt; 160 M1 56.969697 5.226640e-06
+#&gt; 161 M1 58.181818 3.636450e-06
+#&gt; 162 M1 59.393939 2.530191e-06
+#&gt; 163 M1 60.000000 2.110651e-06
+#&gt; 164 M1 60.606061 1.760625e-06
+#&gt; 165 M1 61.818182 1.225095e-06
+#&gt; 166 M1 63.030303 8.527010e-07
+#&gt; 167 M1 64.242424 5.934161e-07
+#&gt; 168 M1 65.454545 4.127474e-07
+#&gt; 169 M1 66.666667 2.874114e-07
+#&gt; 170 M1 67.878788 2.001921e-07
+#&gt; 171 M1 69.090909 1.389331e-07
+#&gt; 172 M1 70.303030 9.678549e-08
+#&gt; 173 M1 71.515152 6.777214e-08
+#&gt; 174 M1 72.727273 4.658761e-08
+#&gt; 175 M1 73.939394 3.226837e-08
+#&gt; 176 M1 75.151515 2.253752e-08
+#&gt; 177 M1 76.363636 1.574843e-08
+#&gt; 178 M1 77.575758 1.096303e-08
+#&gt; 179 M1 78.787879 7.638209e-09
+#&gt; 180 M1 80.000000 5.319996e-09
+#&gt; 181 M1 81.212121 3.709993e-09
+#&gt; 182 M1 82.424242 2.548810e-09
+#&gt; 183 M1 83.636364 1.744629e-09
+#&gt; 184 M1 84.848485 1.256081e-09
+#&gt; 185 M1 86.060606 8.714672e-10
+#&gt; 186 M1 87.272727 5.511830e-10
+#&gt; 187 M1 88.484848 4.466725e-10
+#&gt; 188 M1 89.696970 3.452654e-10
+#&gt; 189 M1 90.000000 2.913252e-10
+#&gt; 190 M1 90.909091 1.489262e-10
+#&gt; 191 M1 92.121212 1.311985e-10
+#&gt; 192 M1 93.333333 9.347248e-11
+#&gt; 193 M1 94.545455 6.004640e-11
+#&gt; 194 M1 95.757576 1.166926e-11
+#&gt; 195 M1 96.969697 2.968203e-11
+#&gt; 196 M1 98.181818 2.478228e-11
+#&gt; 197 M1 99.393939 -1.291838e-12
+#&gt; 198 M1 100.606061 2.366481e-11
+#&gt; 199 M1 101.818182 3.472871e-11
+#&gt; 200 M1 103.030303 -6.633877e-12
+#&gt; 201 M1 104.242424 1.248743e-11
+#&gt; 202 M1 105.454545 4.557313e-11
+#&gt; 203 M1 106.666667 -3.046261e-11
+#&gt; 204 M1 107.878788 -2.693037e-11
+#&gt; 205 M1 109.090909 7.816593e-11
+#&gt; 206 M1 110.303030 7.276098e-13
+#&gt; 207 M1 111.515152 -1.922924e-12
+#&gt; 208 M1 112.727273 1.658481e-11
+#&gt; 209 M1 113.939394 -1.858452e-11
+#&gt; 210 M1 115.151515 -2.368198e-12
+#&gt; 211 M1 116.363636 -1.138989e-12
+#&gt; 212 M1 117.575758 -2.157011e-12
+#&gt; 213 M1 118.787879 1.771568e-12
+#&gt; 214 M1 120.000000 3.624738e-11
+#&gt; 215 M2 0.000000 0.000000e+00
+#&gt; 216 M2 1.000000 4.454830e+00
+#&gt; 217 M2 1.212121 6.103803e+00
+#&gt; 218 M2 2.424242 1.667567e+01
+#&gt; 219 M2 3.000000 2.152527e+01
+#&gt; 220 M2 3.636364 2.637280e+01
+#&gt; 221 M2 4.848485 3.384106e+01
+#&gt; 222 M2 6.060606 3.910279e+01
+#&gt; 223 M2 7.000000 4.192058e+01
+#&gt; 224 M2 7.272727 4.256708e+01
+#&gt; 225 M2 8.484848 4.467909e+01
+#&gt; 226 M2 9.696970 4.581396e+01
+#&gt; 227 M2 10.909091 4.625927e+01
+#&gt; 228 M2 12.121212 4.622588e+01
+#&gt; 229 M2 13.333333 4.586473e+01
+#&gt; 230 M2 14.000000 4.556646e+01
+#&gt; 231 M2 14.545455 4.528249e+01
+#&gt; 232 M2 15.757576 4.455394e+01
+#&gt; 233 M2 16.969697 4.373119e+01
+#&gt; 234 M2 18.181818 4.285048e+01
+#&gt; 235 M2 19.393939 4.193685e+01
+#&gt; 236 M2 20.606061 4.100759e+01
+#&gt; 237 M2 21.818182 4.007456e+01
+#&gt; 238 M2 23.030303 3.914584e+01
+#&gt; 239 M2 24.242424 3.822688e+01
+#&gt; 240 M2 25.454545 3.732133e+01
+#&gt; 241 M2 26.666667 3.643154e+01
+#&gt; 242 M2 27.878788 3.555901e+01
+#&gt; 243 M2 28.000000 3.547275e+01
+#&gt; 244 M2 29.090909 3.470463e+01
+#&gt; 245 M2 30.303030 3.386887e+01
+#&gt; 246 M2 31.515152 3.305190e+01
+#&gt; 247 M2 32.727273 3.225371e+01
+#&gt; 248 M2 33.939394 3.147416e+01
+#&gt; 249 M2 35.151515 3.071300e+01
+#&gt; 250 M2 36.363636 2.996993e+01
+#&gt; 251 M2 37.575758 2.924463e+01
+#&gt; 252 M2 38.787879 2.853672e+01
+#&gt; 253 M2 40.000000 2.784585e+01
+#&gt; 254 M2 41.212121 2.717163e+01
+#&gt; 255 M2 42.424242 2.651368e+01
+#&gt; 256 M2 43.636364 2.587163e+01
+#&gt; 257 M2 44.848485 2.524511e+01
+#&gt; 258 M2 46.060606 2.463374e+01
+#&gt; 259 M2 47.272727 2.403716e+01
+#&gt; 260 M2 48.484848 2.345502e+01
+#&gt; 261 M2 49.696970 2.288698e+01
+#&gt; 262 M2 50.909091 2.233268e+01
+#&gt; 263 M2 52.121212 2.179181e+01
+#&gt; 264 M2 53.333333 2.126404e+01
+#&gt; 265 M2 54.545455 2.074905e+01
+#&gt; 266 M2 55.757576 2.024653e+01
+#&gt; 267 M2 56.969697 1.975618e+01
+#&gt; 268 M2 58.181818 1.927770e+01
+#&gt; 269 M2 59.393939 1.881081e+01
+#&gt; 270 M2 60.000000 1.858163e+01
+#&gt; 271 M2 60.606061 1.835523e+01
+#&gt; 272 M2 61.818182 1.791068e+01
+#&gt; 273 M2 63.030303 1.747690e+01
+#&gt; 274 M2 64.242424 1.705363e+01
+#&gt; 275 M2 65.454545 1.664061e+01
+#&gt; 276 M2 66.666667 1.623759e+01
+#&gt; 277 M2 67.878788 1.584433e+01
+#&gt; 278 M2 69.090909 1.546059e+01
+#&gt; 279 M2 70.303030 1.508615e+01
+#&gt; 280 M2 71.515152 1.472078e+01
+#&gt; 281 M2 72.727273 1.436425e+01
+#&gt; 282 M2 73.939394 1.401636e+01
+#&gt; 283 M2 75.151515 1.367690e+01
+#&gt; 284 M2 76.363636 1.334566e+01
+#&gt; 285 M2 77.575758 1.302244e+01
+#&gt; 286 M2 78.787879 1.270705e+01
+#&gt; 287 M2 80.000000 1.239929e+01
+#&gt; 288 M2 81.212121 1.209899e+01
+#&gt; 289 M2 82.424242 1.180597e+01
+#&gt; 290 M2 83.636364 1.152004e+01
+#&gt; 291 M2 84.848485 1.124103e+01
+#&gt; 292 M2 86.060606 1.096878e+01
+#&gt; 293 M2 87.272727 1.070313e+01
+#&gt; 294 M2 88.484848 1.044391e+01
+#&gt; 295 M2 89.696970 1.019097e+01
+#&gt; 296 M2 90.000000 1.012869e+01
+#&gt; 297 M2 90.909091 9.944151e+00
+#&gt; 298 M2 92.121212 9.703312e+00
+#&gt; 299 M2 93.333333 9.468307e+00
+#&gt; 300 M2 94.545455 9.238993e+00
+#&gt; 301 M2 95.757576 9.015233e+00
+#&gt; 302 M2 96.969697 8.796892e+00
+#&gt; 303 M2 98.181818 8.583839e+00
+#&gt; 304 M2 99.393939 8.375946e+00
+#&gt; 305 M2 100.606061 8.173088e+00
+#&gt; 306 M2 101.818182 7.975143e+00
+#&gt; 307 M2 103.030303 7.781992e+00
+#&gt; 308 M2 104.242424 7.593520e+00
+#&gt; 309 M2 105.454545 7.409611e+00
+#&gt; 310 M2 106.666667 7.230157e+00
+#&gt; 311 M2 107.878788 7.055049e+00
+#&gt; 312 M2 109.090909 6.884182e+00
+#&gt; 313 M2 110.303030 6.717454e+00
+#&gt; 314 M2 111.515152 6.554763e+00
+#&gt; 315 M2 112.727273 6.396012e+00
+#&gt; 316 M2 113.939394 6.241107e+00
+#&gt; 317 M2 115.151515 6.089953e+00
+#&gt; 318 M2 116.363636 5.942460e+00
+#&gt; 319 M2 117.575758 5.798538e+00
+#&gt; 320 M2 118.787879 5.658103e+00
+#&gt; 321 M2 120.000000 5.521069e+00
+#&gt;
+#&gt; $cost
+#&gt; function (P)
+#&gt; {
+#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
+#&gt; if (trace_parms)
+#&gt; cat(P, &quot;\n&quot;)
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; transparms.fixed)
+#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
+#&gt; transform_fractions = transform_fractions)
+#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; if (mC$model &lt; cost.old) {
+#&gt; if (!quiet)
+#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
+#&gt; &quot;\n&quot;)
+#&gt; if (plot) {
+#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
+#&gt; length.out = 100)
+#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
+#&gt; solution_type = solution_type, use_compiled = use_compiled,
+#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
+#&gt; ...)
+#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
+#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
+#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
+#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
+#&gt; lty_obs &lt;- rep(1, length(obs_vars))
+#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
+#&gt; for (obs_var in obs_vars) {
+#&gt; points(subset(observed, name == obs_var, c(time,
+#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
+#&gt; }
+#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
+#&gt; lty = lty_obs)
+#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
+#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
+#&gt; }
+#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
+#&gt; }
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x3ff8420&gt;
+#&gt;
+#&gt; $cost_notrans
+#&gt; function (P)
+#&gt; {
+#&gt; if (length(state.ini.optim) &gt; 0) {
+#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt; }
+#&gt; else {
+#&gt; odeini &lt;- state.ini.fixed
+#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt; }
+#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
+#&gt; parms.fixed)
+#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
+#&gt; use_compiled = use_compiled, method.ode = method.ode,
+#&gt; atol = atol, rtol = rtol, ...)
+#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
+#&gt; scaleVar = scaleVar)
+#&gt; return(mC)
+#&gt; }
+#&gt; &lt;environment: 0x3ff8420&gt;
+#&gt;
+#&gt; $hessian_notrans
+#&gt; parent_0 k_parent k_M1 k_M2 f_parent_to_M1
+#&gt; parent_0 8.433594 -40.12785 -61.53042 -3406.469 461.2995
+#&gt; k_parent -40.127847 19322.43697 3053.54654 3740.691 8966.4055
+#&gt; k_M1 -61.530424 3053.54654 70106.05907 7274.316 -8169.6841
+#&gt; k_M2 -3406.468786 3740.69112 7274.31610 12274341.595 -452294.7998
+#&gt; f_parent_to_M1 461.299501 8966.40549 -8169.68407 -452294.800 61249.1755
+#&gt; f_M1_to_M2 327.648696 2884.22668 17504.38651 -480941.198 43503.6440
+#&gt; f_M1_to_M2
+#&gt; parent_0 327.6487
+#&gt; k_parent 2884.2267
+#&gt; k_M1 17504.3865
+#&gt; k_M2 -480941.1983
+#&gt; f_parent_to_M1 43503.6440
+#&gt; f_M1_to_M2 46258.9775
+#&gt;
+#&gt; $start
+#&gt; value type
+#&gt; parent_0 101.3500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_M1 0.1001 deparm
+#&gt; k_M2 0.1002 deparm
+#&gt; f_parent_to_M1 0.5000 deparm
+#&gt; f_M1_to_M2 0.5000 deparm
+#&gt;
+#&gt; $start_transformed
+#&gt; value lower upper
+#&gt; parent_0 101.350000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_M1 -2.301586 -Inf Inf
+#&gt; log_k_M2 -2.300587 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt; f_M1_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; $fixed
+#&gt; value type
+#&gt; M1_0 0 state
+#&gt; M2_0 0 state
+#&gt;
+#&gt; $data
+#&gt; time variable observed predicted residual
+#&gt; 1 0 parent 101.5 1.020625e+02 -0.56248353
+#&gt; 2 0 parent 101.2 1.020625e+02 -0.86248353
+#&gt; 3 1 parent 53.9 4.872881e+01 5.17118695
+#&gt; 4 1 parent 47.5 4.872881e+01 -1.22881305
+#&gt; 5 3 parent 10.4 1.110773e+01 -0.70772795
+#&gt; 6 3 parent 7.6 1.110773e+01 -3.50772795
+#&gt; 7 7 parent 1.1 5.771704e-01 0.52282962
+#&gt; 8 7 parent 0.3 5.771704e-01 -0.27717038
+#&gt; 9 14 parent NA 3.263939e-03 NA
+#&gt; 10 14 parent 3.5 3.263939e-03 3.49673606
+#&gt; 11 28 parent NA 1.044512e-07 NA
+#&gt; 12 28 parent 3.2 1.044512e-07 3.19999990
+#&gt; 13 60 parent NA -1.053819e-10 NA
+#&gt; 14 60 parent NA -1.053819e-10 NA
+#&gt; 15 90 parent 0.6 -1.874889e-11 0.60000000
+#&gt; 16 90 parent NA -1.874889e-11 NA
+#&gt; 17 120 parent NA -2.804801e-11 NA
+#&gt; 18 120 parent 3.5 -2.804801e-11 3.50000000
+#&gt; 19 0 M1 NA 0.000000e+00 NA
+#&gt; 20 0 M1 NA 0.000000e+00 NA
+#&gt; 21 1 M1 36.4 3.478911e+01 1.61088639
+#&gt; 22 1 M1 37.4 3.478911e+01 2.61088639
+#&gt; 23 3 M1 34.3 3.937027e+01 -5.07026619
+#&gt; 24 3 M1 39.8 3.937027e+01 0.42973381
+#&gt; 25 7 M1 15.1 1.548714e+01 -0.38714436
+#&gt; 26 7 M1 17.8 1.548714e+01 2.31285564
+#&gt; 27 14 M1 5.8 1.995311e+00 3.80468869
+#&gt; 28 14 M1 1.2 1.995311e+00 -0.79531131
+#&gt; 29 28 M1 NA 3.034005e-02 NA
+#&gt; 30 28 M1 NA 3.034005e-02 NA
+#&gt; 31 60 M1 0.5 2.110651e-06 0.49999789
+#&gt; 32 60 M1 NA 2.110651e-06 NA
+#&gt; 33 90 M1 NA 2.913252e-10 NA
+#&gt; 34 90 M1 3.2 2.913252e-10 3.20000000
+#&gt; 35 120 M1 1.5 3.624738e-11 1.50000000
+#&gt; 36 120 M1 0.6 3.624738e-11 0.60000000
+#&gt; 37 0 M2 NA 0.000000e+00 NA
+#&gt; 38 0 M2 NA 0.000000e+00 NA
+#&gt; 39 1 M2 NA 4.454830e+00 NA
+#&gt; 40 1 M2 4.8 4.454830e+00 0.34517017
+#&gt; 41 3 M2 20.9 2.152527e+01 -0.62526794
+#&gt; 42 3 M2 19.3 2.152527e+01 -2.22526794
+#&gt; 43 7 M2 42.0 4.192058e+01 0.07941701
+#&gt; 44 7 M2 43.1 4.192058e+01 1.17941701
+#&gt; 45 14 M2 49.4 4.556646e+01 3.83353798
+#&gt; 46 14 M2 44.3 4.556646e+01 -1.26646202
+#&gt; 47 28 M2 34.6 3.547275e+01 -0.87274743
+#&gt; 48 28 M2 33.0 3.547275e+01 -2.47274743
+#&gt; 49 60 M2 18.8 1.858163e+01 0.21837410
+#&gt; 50 60 M2 17.6 1.858163e+01 -0.98162590
+#&gt; 51 90 M2 10.6 1.012869e+01 0.47130583
+#&gt; 52 90 M2 10.8 1.012869e+01 0.67130583
+#&gt; 53 120 M2 9.8 5.521069e+00 4.27893112
+#&gt; 54 120 M2 3.3 5.521069e+00 -2.22106888
+#&gt;
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt;
+#&gt; $weight.ini
+#&gt; [1] &quot;none&quot;
+#&gt;
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt;
+#&gt; $bparms.optim
+#&gt; parent_0 k_parent k_M1 k_M2 f_parent_to_M1
+#&gt; 102.0624835 0.7393147 0.2991566 0.0202267 0.7686858
+#&gt; f_M1_to_M2
+#&gt; 0.7229005
+#&gt;
+#&gt; $bparms.fixed
+#&gt; M1_0 M2_0
+#&gt; 0 0
+#&gt;
+#&gt; $bparms.ode
+#&gt; k_parent f_parent_to_M1 k_M1 f_M1_to_M2 k_M2
+#&gt; 0.7393147 0.7686858 0.2991566 0.7229005 0.0202267
+#&gt;
+#&gt; $bparms.state
+#&gt; parent M1 M2
+#&gt; 102.0625 0.0000 0.0000
+#&gt;
+#&gt; $date
+#&gt; [1] &quot;Fri Nov 18 15:20:48 2016&quot;
+#&gt;
+#&gt; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'>
+</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 00af0267..08fbf368 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -149,8 +149,8 @@
<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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Nov 17 22:57:06 2016
-#&gt; Date of summary: Thu Nov 17 22:57:06 2016
+#&gt; Date of fit: Fri Nov 18 15:20:49 2016
+#&gt; Date of summary: Fri Nov 18 15:20:49 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +158,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.684 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.681 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -222,10 +222,220 @@
#&gt; DT50 DT90
#&gt; parent 7.023 23.33
#&gt; m1 131.761 437.70</div><div class='input'>
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># fit.2 &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span>
-<span class='co'># summary(fit.2, data=FALSE)</span>
-<span class='co'>## ---------------------------------------------</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</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18915.53
+#&gt; Model cost at call 2 : 18915.53
+#&gt; Model cost at call 7 : 10205.88
+#&gt; Model cost at call 10 : 10205.05
+#&gt; Model cost at call 13 : 8136.609
+#&gt; Model cost at call 18 : 2504.352
+#&gt; Model cost at call 20 : 2504.35
+#&gt; Model cost at call 22 : 2504.285
+#&gt; Model cost at call 25 : 1747.542
+#&gt; Model cost at call 27 : 1745.941
+#&gt; Model cost at call 29 : 1745.431
+#&gt; Model cost at call 30 : 1341.034
+#&gt; Model cost at call 34 : 1341.034
+#&gt; Model cost at call 35 : 1032.65
+#&gt; Model cost at call 39 : 1032.649
+#&gt; Model cost at call 40 : 919.9522
+#&gt; Model cost at call 42 : 919.952
+#&gt; Model cost at call 44 : 919.9518
+#&gt; Model cost at call 45 : 903.8272
+#&gt; Model cost at call 47 : 903.827
+#&gt; Model cost at call 49 : 903.8268
+#&gt; Model cost at call 50 : 780.8699
+#&gt; Model cost at call 52 : 780.8698
+#&gt; Model cost at call 54 : 780.8697
+#&gt; Model cost at call 55 : 734.3043
+#&gt; Model cost at call 57 : 734.3036
+#&gt; Model cost at call 60 : 717.8438
+#&gt; Model cost at call 67 : 676.3908
+#&gt; Model cost at call 68 : 676.3907
+#&gt; Model cost at call 69 : 676.3906
+#&gt; Model cost at call 71 : 676.3885
+#&gt; Model cost at call 72 : 642.2738
+#&gt; Model cost at call 73 : 642.2738
+#&gt; Model cost at call 76 : 642.2738
+#&gt; Model cost at call 77 : 604.7128
+#&gt; Model cost at call 78 : 604.7126
+#&gt; Model cost at call 82 : 560.1285
+#&gt; Model cost at call 83 : 560.1285
+#&gt; Model cost at call 86 : 560.1285
+#&gt; Model cost at call 87 : 521.6932
+#&gt; Model cost at call 88 : 521.6932
+#&gt; Model cost at call 91 : 521.6931
+#&gt; Model cost at call 92 : 453.6483
+#&gt; Model cost at call 93 : 453.6483
+#&gt; Model cost at call 96 : 453.6483
+#&gt; Model cost at call 98 : 422.5498
+#&gt; Model cost at call 102 : 422.5497
+#&gt; Model cost at call 106 : 413.6426
+#&gt; Model cost at call 108 : 413.6416
+#&gt; Model cost at call 111 : 407.4639
+#&gt; Model cost at call 113 : 407.4639
+#&gt; Model cost at call 115 : 407.4639
+#&gt; Model cost at call 116 : 403.6974
+#&gt; Model cost at call 118 : 403.6973
+#&gt; Model cost at call 120 : 403.6973
+#&gt; Model cost at call 121 : 396.004
+#&gt; Model cost at call 123 : 396.004
+#&gt; Model cost at call 126 : 391.2533
+#&gt; Model cost at call 128 : 391.2533
+#&gt; Model cost at call 130 : 391.2533
+#&gt; Model cost at call 131 : 388.4056
+#&gt; Model cost at call 133 : 388.4056
+#&gt; Model cost at call 135 : 388.4055
+#&gt; Model cost at call 137 : 384.0739
+#&gt; Model cost at call 139 : 384.0734
+#&gt; Model cost at call 143 : 383.6352
+#&gt; Model cost at call 145 : 383.635
+#&gt; Model cost at call 148 : 381.1342
+#&gt; Model cost at call 152 : 381.1342
+#&gt; Model cost at call 153 : 380.1443
+#&gt; Model cost at call 157 : 380.1443
+#&gt; Model cost at call 158 : 378.5615
+#&gt; Model cost at call 162 : 378.5614
+#&gt; Model cost at call 164 : 378.4583
+#&gt; Model cost at call 168 : 378.4583
+#&gt; Model cost at call 169 : 377.7047
+#&gt; Model cost at call 173 : 377.7047
+#&gt; Model cost at call 175 : 377.7042
+#&gt; Model cost at call 178 : 377.7042
+#&gt; Model cost at call 179 : 377.7042
+#&gt; Model cost at call 180 : 377.1553
+#&gt; Model cost at call 182 : 377.1553
+#&gt; Model cost at call 183 : 377.1553
+#&gt; Model cost at call 185 : 377.0866
+#&gt; Model cost at call 187 : 377.0866
+#&gt; Model cost at call 190 : 377.0288
+#&gt; Model cost at call 194 : 377.0288
+#&gt; Model cost at call 196 : 376.9814
+#&gt; Model cost at call 200 : 376.9814
+#&gt; Model cost at call 201 : 376.9488
+#&gt; Model cost at call 203 : 376.9488
+#&gt; Model cost at call 205 : 376.9488
+#&gt; Model cost at call 206 : 376.9184
+#&gt; Model cost at call 208 : 376.9184
+#&gt; Model cost at call 211 : 376.9095
+#&gt; Model cost at call 213 : 376.9095
+#&gt; Model cost at call 215 : 376.9095
+#&gt; Model cost at call 216 : 376.901
+#&gt; Model cost at call 218 : 376.901
+#&gt; Model cost at call 221 : 376.8936
+#&gt; Model cost at call 225 : 376.8936
+#&gt; Model cost at call 226 : 376.8848
+#&gt; Model cost at call 227 : 376.8608
+#&gt; Model cost at call 228 : 376.7665
+#&gt; Model cost at call 229 : 376.4162
+#&gt; Model cost at call 230 : 375.4439
+#&gt; Model cost at call 235 : 375.4439
+#&gt; Model cost at call 237 : 375.2281
+#&gt; Model cost at call 241 : 375.2281
+#&gt; Model cost at call 242 : 374.3381
+#&gt; Model cost at call 244 : 374.3381
+#&gt; Model cost at call 251 : 374.2632
+#&gt; Model cost at call 253 : 374.2632
+#&gt; Model cost at call 256 : 374.2391
+#&gt; Model cost at call 257 : 374.2247
+#&gt; Model cost at call 259 : 374.2247
+#&gt; Model cost at call 261 : 374.2247
+#&gt; Model cost at call 263 : 374.2024
+#&gt; Model cost at call 266 : 374.2024
+#&gt; Model cost at call 270 : 374.1952
+#&gt; Model cost at call 274 : 374.1952
+#&gt; Model cost at call 275 : 374.186
+#&gt; Model cost at call 279 : 374.186
+#&gt; Model cost at call 280 : 374.1724
+#&gt; Model cost at call 281 : 374.156
+#&gt; Model cost at call 282 : 374.0763
+#&gt; Model cost at call 283 : 373.7692
+#&gt; Model cost at call 284 : 372.729
+#&gt; Model cost at call 285 : 371.4251
+#&gt; Model cost at call 287 : 371.4251
+#&gt; Model cost at call 290 : 371.2142
+#&gt; Model cost at call 291 : 371.2142
+#&gt; Model cost at call 292 : 371.2142
+#&gt; Model cost at call 295 : 371.2134
+#&gt; Model cost at call 298 : 371.2134
+#&gt; Model cost at call 300 : 371.2134
+#&gt; Model cost at call 309 : 371.2134
+#&gt; Model cost at call 320 : 371.2134
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><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: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:20:51 2016
+#&gt; Date of summary: Fri Nov 18 15:20:51 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 327 model solutions performed in 1.34 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent_sink 0.1000 deparm
+#&gt; k_parent_m1 0.1001 deparm
+#&gt; k_m1_sink 0.1002 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.7500 -Inf Inf
+#&gt; k_parent_sink 0.1000 0 Inf
+#&gt; k_parent_m1 0.1001 0 Inf
+#&gt; k_m1_sink 0.1002 0 Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.600000 1.6140000 96.330000 1.029e+02
+#&gt; k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02
+#&gt; k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02
+#&gt; k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
+#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
+#&gt; k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
+#&gt; k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
+#&gt; k_m1_sink -0.17006 -0.6253 0.47164 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02
+#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02
+#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.827 3 6
+#&gt; m1 4.490 1 9
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_sink 0.4855
+#&gt; parent_m1 0.5145
+#&gt; m1_sink 1.0000
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70</div><div class='input'>
<span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span>
<span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>)
@@ -234,29 +444,286 @@
<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
#&gt; 100.7500 0.1000 0.1001 0.1002 </div><div class='input'>
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># # The case of formation fractions</span>
-<span class='co'># SFO_SFO.ff &lt;- mkinmod(</span>
-<span class='co'># parent = list(type = "SFO", to = "m1", sink = TRUE),</span>
-<span class='co'># m1 = list(type = "SFO"),</span>
-<span class='co'># use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># fit.ff &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span>
-<span class='co'># summary(fit.ff, data = FALSE)</span>
-<span class='co'># initials &lt;- c("f_parent_to_m1" = 0.5)</span>
-<span class='co'># transformed &lt;- transform_odeparms(initials, SFO_SFO.ff)</span>
-<span class='co'># backtransform_odeparms(transformed, SFO_SFO.ff)</span>
-<span class='co'># </span>
-<span class='co'># # And without sink</span>
-<span class='co'># SFO_SFO.ff.2 &lt;- mkinmod(</span>
-<span class='co'># parent = list(type = "SFO", to = "m1", sink = FALSE),</span>
-<span class='co'># m1 = list(type = "SFO"),</span>
-<span class='co'># use_of_ff = "max")</span>
-<span class='co'># </span>
-<span class='co'># </span>
-<span class='co'># fit.ff.2 &lt;- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span>
-<span class='co'># summary(fit.ff.2, data = FALSE)</span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+
+<span class='co'># The case of formation fractions</span>
+<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15156.12
+#&gt; Model cost at call 2 : 15156.12
+#&gt; Model cost at call 6 : 8243.644
+#&gt; Model cost at call 12 : 6290.714
+#&gt; Model cost at call 13 : 6290.684
+#&gt; Model cost at call 15 : 6290.453
+#&gt; Model cost at call 18 : 1700.75
+#&gt; Model cost at call 20 : 1700.612
+#&gt; Model cost at call 24 : 1190.923
+#&gt; Model cost at call 26 : 1190.922
+#&gt; Model cost at call 29 : 1017.417
+#&gt; Model cost at call 31 : 1017.417
+#&gt; Model cost at call 33 : 1017.416
+#&gt; Model cost at call 34 : 644.0471
+#&gt; Model cost at call 36 : 644.0469
+#&gt; Model cost at call 38 : 644.0468
+#&gt; Model cost at call 39 : 590.5024
+#&gt; Model cost at call 41 : 590.5021
+#&gt; Model cost at call 43 : 590.5015
+#&gt; Model cost at call 44 : 543.2187
+#&gt; Model cost at call 45 : 543.2183
+#&gt; Model cost at call 46 : 543.2182
+#&gt; Model cost at call 50 : 391.348
+#&gt; Model cost at call 51 : 391.3479
+#&gt; Model cost at call 56 : 386.4789
+#&gt; Model cost at call 58 : 386.4789
+#&gt; Model cost at call 60 : 386.4779
+#&gt; Model cost at call 61 : 384.0686
+#&gt; Model cost at call 63 : 384.0686
+#&gt; Model cost at call 66 : 382.7812
+#&gt; Model cost at call 68 : 382.7812
+#&gt; Model cost at call 70 : 382.7812
+#&gt; Model cost at call 71 : 378.9272
+#&gt; Model cost at call 73 : 378.9272
+#&gt; Model cost at call 75 : 378.9272
+#&gt; Model cost at call 76 : 377.4846
+#&gt; Model cost at call 78 : 377.4846
+#&gt; Model cost at call 81 : 375.9738
+#&gt; Model cost at call 83 : 375.9738
+#&gt; Model cost at call 86 : 375.3387
+#&gt; Model cost at call 88 : 375.3387
+#&gt; Model cost at call 91 : 374.5774
+#&gt; Model cost at call 93 : 374.5774
+#&gt; Model cost at call 95 : 374.5774
+#&gt; Model cost at call 96 : 373.5447
+#&gt; Model cost at call 100 : 373.5446
+#&gt; Model cost at call 102 : 373.2643
+#&gt; Model cost at call 104 : 373.2643
+#&gt; Model cost at call 107 : 372.6799
+#&gt; Model cost at call 111 : 372.6798
+#&gt; Model cost at call 114 : 372.6325
+#&gt; Model cost at call 116 : 372.6325
+#&gt; Model cost at call 119 : 372.6159
+#&gt; Model cost at call 121 : 372.6159
+#&gt; Model cost at call 123 : 372.6159
+#&gt; Model cost at call 124 : 372.5845
+#&gt; Model cost at call 126 : 372.5845
+#&gt; Model cost at call 129 : 372.5375
+#&gt; Model cost at call 130 : 372.4771
+#&gt; Model cost at call 131 : 372.2008
+#&gt; Model cost at call 132 : 371.4923
+#&gt; Model cost at call 134 : 371.4923
+#&gt; Model cost at call 137 : 371.3022
+#&gt; Model cost at call 139 : 371.3022
+#&gt; Model cost at call 143 : 371.2271
+#&gt; Model cost at call 144 : 371.2271
+#&gt; Model cost at call 148 : 371.2202
+#&gt; Model cost at call 149 : 371.215
+#&gt; Model cost at call 152 : 371.215
+#&gt; Model cost at call 154 : 371.2136
+#&gt; Model cost at call 155 : 371.2136
+#&gt; Model cost at call 156 : 371.2136
+#&gt; Model cost at call 160 : 371.2134
+#&gt; Model cost at call 164 : 371.2134
+#&gt; Model cost at call 167 : 371.2134
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:20:52 2016
+#&gt; Date of summary: Fri Nov 18 15:20:52 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 185 model solutions performed in 0.764 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
+#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
+#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
+#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
+#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
+#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
+#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent 0.098700 23.880 5.701e-24 0.090660 1.074e-01
+#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
+#&gt; f_parent_to_m1 0.514500 22.490 4.374e-23 0.468100 5.606e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.459 2 7
+#&gt; m1 4.690 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5145
+#&gt; parent_sink 0.4855
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+<span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>)
+<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#&gt; f_parent_to_m1
+#&gt; 0.5 </div><div class='input'>
+<span class='co'># And without sink</span>
+<span class='no'>SFO_SFO.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 12435.14
+#&gt; Model cost at call 2 : 12435.14
+#&gt; Model cost at call 5 : 8276.306
+#&gt; Model cost at call 6 : 8276.294
+#&gt; Model cost at call 7 : 8275.676
+#&gt; Model cost at call 9 : 5256.953
+#&gt; Model cost at call 11 : 5256.951
+#&gt; Model cost at call 12 : 5256.943
+#&gt; Model cost at call 14 : 4469.745
+#&gt; Model cost at call 18 : 4462.927
+#&gt; Model cost at call 21 : 4462.925
+#&gt; Model cost at call 22 : 4376.059
+#&gt; Model cost at call 24 : 4376.058
+#&gt; Model cost at call 27 : 4366.956
+#&gt; Model cost at call 29 : 4366.956
+#&gt; Model cost at call 31 : 4365.275
+#&gt; Model cost at call 33 : 4365.275
+#&gt; Model cost at call 35 : 4351.877
+#&gt; Model cost at call 37 : 4351.877
+#&gt; Model cost at call 39 : 4338.109
+#&gt; Model cost at call 41 : 4338.109
+#&gt; Model cost at call 43 : 4297.053
+#&gt; Model cost at call 44 : 4218.591
+#&gt; Model cost at call 45 : 3940.397
+#&gt; Model cost at call 46 : 3690.395
+#&gt; Model cost at call 48 : 3690.395
+#&gt; Model cost at call 49 : 3690.385
+#&gt; Model cost at call 50 : 3038.366
+#&gt; Model cost at call 53 : 3038.365
+#&gt; Model cost at call 54 : 2637.866
+#&gt; Model cost at call 57 : 2637.865
+#&gt; Model cost at call 59 : 2588.01
+#&gt; Model cost at call 60 : 2588.009
+#&gt; Model cost at call 63 : 2576.742
+#&gt; Model cost at call 66 : 2576.742
+#&gt; Model cost at call 67 : 2574
+#&gt; Model cost at call 68 : 2574
+#&gt; Model cost at call 69 : 2574
+#&gt; Model cost at call 71 : 2569.76
+#&gt; Model cost at call 73 : 2569.76
+#&gt; Model cost at call 74 : 2569.76
+#&gt; Model cost at call 75 : 2569.403
+#&gt; Model cost at call 76 : 2569.403
+#&gt; Model cost at call 79 : 2569.4
+#&gt; Model cost at call 80 : 2569.4
+#&gt; Model cost at call 81 : 2569.4
+#&gt; Model cost at call 83 : 2569.4
+#&gt; Model cost at call 86 : 2569.4
+#&gt; Model cost at call 90 : 2569.4
+#&gt; Model cost at call 99 : 2569.4
+#&gt; Model cost at call 100 : 2569.4
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:20:52 2016
+#&gt; Date of summary: Fri Nov 18 15:20:52 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 104 model solutions performed in 0.44 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 84.790 2.96500 78.78 90.800
+#&gt; log_k_parent -2.756 0.08088 -2.92 -2.593
+#&gt; log_k_m1 -4.214 0.11150 -4.44 -3.988
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1
+#&gt; parent_0 1.0000 0.11059 0.46156
+#&gt; log_k_parent 0.1106 1.00000 0.06274
+#&gt; log_k_m1 0.4616 0.06274 1.00000
+#&gt;
+#&gt; Residual standard error: 8.333 on 37 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000
+#&gt; k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483
+#&gt; k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 19.66 3 16
+#&gt; parent 17.56 2 7
+#&gt; m1 18.71 1 9
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 10.91 36.25
+#&gt; m1 46.89 155.75</div><div class='input'>
+</div></pre>
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