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-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/index.html6
-rw-r--r--docs/reference/logistic.solution-1.pngbin0 -> 63411 bytes
-rw-r--r--docs/reference/logistic.solution-2.pngbin0 -> 29229 bytes
-rw-r--r--docs/reference/logistic.solution.html295
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html46
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html4
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/summary.mkinfit.html4
-rw-r--r--docs/reference/transform_odeparms.html24
12 files changed, 355 insertions, 54 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 2a1d63b5..dd088a0f 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
#>
#> $time
#> User System verstrichen
-#> 0.197 0.000 0.198
+#> 0.196 0.000 0.196
#>
#> $mkinmod
#> <mkinmod> model generated with
@@ -469,8 +469,8 @@
#> }
#> return(mC)
#> }
-#> <bytecode: 0x55555916c520>
-#> <environment: 0x55555b68a808>
+#> <bytecode: 0x555559201470>
+#> <environment: 0x555555ce4640>
#>
#> $cost_notrans
#> function (P)
@@ -492,8 +492,8 @@
#> scaleVar = scaleVar)
#> return(mC)
#> }
-#> <bytecode: 0x55555a1242b0>
-#> <environment: 0x55555b68a808>
+#> <bytecode: 0x55555a3214d8>
+#> <environment: 0x555555ce4640>
#>
#> $hessian_notrans
#> parent_0 k_parent_sink
@@ -560,7 +560,7 @@
#> 99.17407
#>
#> $date
-#> [1] "Thu Jan 31 16:50:45 2019"
+#> [1] "Thu Feb 21 14:30:10 2019"
#>
#> $version
#> [1] "0.9.47.6"
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7dd32430..78eb0337 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -419,6 +419,12 @@
<p><code><a href="IORE.solution.html">IORE.solution()</a></code> </p>
</td>
<td><p>Indeterminate order rate equation kinetics</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
+ </td>
+ <td><p>Logistic kinetics</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png
new file mode 100644
index 00000000..0aaa520b
--- /dev/null
+++ b/docs/reference/logistic.solution-1.png
Binary files differ
diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png
new file mode 100644
index 00000000..d1831a46
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Binary files differ
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
new file mode 100644
index 00000000..b0ab72d7
--- /dev/null
+++ b/docs/reference/logistic.solution.html
@@ -0,0 +1,295 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+ an increasing rate constant, supposedly caused by microbial growth" />
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+ <h1>Logistic kinetics</h1>
+
+ <div class="hidden name"><code>logistic.solution.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Function describing exponential decline from a defined starting value, with
+ an increasing rate constant, supposedly caused by microbial growth</p>
+
+ </div>
+
+ <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>t</th>
+ <td><p>Time.</p></td>
+ </tr>
+ <tr>
+ <th>parent.0</th>
+ <td><p>Starting value for the response variable at time zero.</p></td>
+ </tr>
+ <tr>
+ <th>kmax</th>
+ <td><p>Maximum rate constant.</p></td>
+ </tr>
+ <tr>
+ <th>k0</th>
+ <td><p>Minumum rate constant effective at time zero.</p></td>
+ </tr>
+ <tr>
+ <th>r</th>
+ <td><p>Growth rate of the increase in the rate constant.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>The solution of the logistic model reduces to the
+ <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to
+ <code>kmax</code>.</p>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
+ <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>),
+ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
+ <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
+ <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
+ <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
+ <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
+ <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
+ <span class='st'>", r = "</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
+ <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-1.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='co'># Fit with synthetic data</span>
+ <span class='no'>logistic</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'>"logistic"</span>))
+
+ <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
+ <span class='no'>parms_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>kmax</span> <span class='kw'>=</span> <span class='fl'>0.08</span>, <span class='kw'>k0</span> <span class='kw'>=</span> <span class='fl'>0.0001</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.2</span>)
+ <span class='no'>parms_logistic_optim</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='no'>parms_logistic</span>)
+ <span class='no'>d_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>logistic</span>,
+ <span class='no'>parms_logistic</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+ <span class='no'>sampling_times</span>)
+ <span class='no'>d_2_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_logistic</span>,
+ <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
+ <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
+
+ <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 789.6044
+#&gt; Model cost at call 2 : 789.6043
+#&gt; Model cost at call 7 : 716.9934
+#&gt; Model cost at call 12 : 697.1186
+#&gt; Model cost at call 15 : 697.1185
+#&gt; Model cost at call 16 : 697.1184
+#&gt; Model cost at call 17 : 661.1574
+#&gt; Model cost at call 20 : 661.1573
+#&gt; Model cost at call 22 : 620.0542
+#&gt; Model cost at call 25 : 620.0541
+#&gt; Model cost at call 29 : 616.6874
+#&gt; Model cost at call 32 : 616.6874
+#&gt; Model cost at call 33 : 616.6874
+#&gt; Model cost at call 34 : 615.1671
+#&gt; Model cost at call 37 : 615.1671
+#&gt; Model cost at call 39 : 612.0795
+#&gt; Model cost at call 42 : 612.0795
+#&gt; Model cost at call 43 : 612.0795
+#&gt; Model cost at call 44 : 605.9119
+#&gt; Model cost at call 45 : 593.0433
+#&gt; Model cost at call 46 : 548.0815
+#&gt; Model cost at call 47 : 504.9062
+#&gt; Model cost at call 50 : 504.9061
+#&gt; Model cost at call 51 : 504.9061
+#&gt; Model cost at call 53 : 485.929
+#&gt; Model cost at call 55 : 485.929
+#&gt; Model cost at call 56 : 485.929
+#&gt; Model cost at call 58 : 485.241
+#&gt; Model cost at call 60 : 485.241
+#&gt; Model cost at call 61 : 485.2409
+#&gt; Model cost at call 62 : 485.2409
+#&gt; Model cost at call 63 : 484.0717
+#&gt; Model cost at call 69 : 483.9062
+#&gt; Model cost at call 74 : 483.5646
+#&gt; Model cost at call 79 : 483.4908
+#&gt; Model cost at call 84 : 483.4859
+#&gt; Model cost at call 85 : 483.4859
+#&gt; Model cost at call 89 : 483.4848
+#&gt; Model cost at call 90 : 483.4836
+#&gt; Model cost at call 92 : 483.4836
+#&gt; Model cost at call 94 : 483.4836
+#&gt; Model cost at call 97 : 483.4833
+#&gt; Model cost at call 100 : 483.4833
+#&gt; Model cost at call 105 : 483.4832
+#&gt; Model cost at call 108 : 483.4832
+#&gt; Model cost at call 114 : 483.4832
+#&gt; Model cost at call 128 : 483.4832
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; parent_0 1.057896e+02 2.3743105248 44.5559374 6.656664e-16 1.006602e+02
+#&gt; kmax 6.398190e-02 0.0193490291 3.3067243 2.836921e-03 3.329058e-02
+#&gt; k0 1.612775e-04 0.0009640761 0.1672871 4.348592e-01 3.972250e-10
+#&gt; r 2.263946e-01 0.2822811886 0.8020181 2.184792e-01 1.531165e-02
+#&gt; Upper
+#&gt; parent_0 110.9190170
+#&gt; kmax 0.1229682
+#&gt; k0 65.4803698
+#&gt; r 3.3474197</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#note">Note</a></li>
+
+ <li><a href="#value">Value</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+</div>
+ </footer>
+ </div>
+
+
+
+ </body>
+</html>
+
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 93d7f197..dcfc499f 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,8 +160,8 @@
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </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'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:05 2019
-#&gt; Date of summary: Thu Jan 31 16:51:05 2019
+#&gt; Date of fit: Thu Feb 21 14:30:31 2019
+#&gt; Date of summary: Thu Feb 21 14:30:31 2019
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.87 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.822 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -249,8 +249,8 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:07 2019
-#&gt; Date of summary: Thu Jan 31 16:51:07 2019
+#&gt; Date of fit: Thu Feb 21 14:30:32 2019
+#&gt; Date of summary: Thu Feb 21 14:30:32 2019
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.618 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.601 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 42845d68..d09b9232 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,15 +438,15 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:10 2019
-#&gt; Date of summary: Thu Jan 31 16:51:10 2019
+#&gt; Date of fit: Thu Feb 21 14:30:35 2019
+#&gt; Date of summary: Thu Feb 21 14:30:35 2019
#&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 0.162 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.16 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -515,7 +515,7 @@
<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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 verstrichen
-#&gt; 1.022 0.000 1.025 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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; 1.017 0.004 1.022 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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
@@ -590,7 +590,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.823 0.000 0.823 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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; 0.845 0.000 0.846 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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
@@ -628,8 +628,8 @@
<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:22 2019
-#&gt; Date of summary: Thu Jan 31 16:51:22 2019
+#&gt; Date of fit: Thu Feb 21 14:30:47 2019
+#&gt; Date of summary: Thu Feb 21 14:30:47 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.872 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.86 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -745,8 +745,8 @@
#&gt; 120 m1 33.31 28.78984 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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:24 2019
-#&gt; Date of summary: Thu Jan 31 16:51:24 2019
+#&gt; Date of fit: Thu Feb 21 14:30:50 2019
+#&gt; Date of summary: Thu Feb 21 14:30:50 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.558 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.529 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -867,8 +867,8 @@
#&gt; 120 m1 33.31 28.80898 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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:25 2019
-#&gt; Date of summary: Thu Jan 31 16:51:25 2019
+#&gt; Date of fit: Thu Feb 21 14:30:51 2019
+#&gt; Date of summary: Thu Feb 21 14:30:51 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.711 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.707 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -985,8 +985,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:26 2019
-#&gt; Date of summary: Thu Jan 31 16:51:26 2019
+#&gt; Date of fit: Thu Feb 21 14:30:52 2019
+#&gt; Date of summary: Thu Feb 21 14:30:52 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.807 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.792 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1105,8 +1105,8 @@
<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:28 2019
-#&gt; Date of summary: Thu Jan 31 16:51:28 2019
+#&gt; Date of fit: Thu Feb 21 14:30:53 2019
+#&gt; Date of summary: Thu Feb 21 14:30:53 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.257 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.243 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1223,8 +1223,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:51:31 2019
-#&gt; Date of summary: Thu Jan 31 16:51:31 2019
+#&gt; Date of fit: Thu Feb 21 14:30:57 2019
+#&gt; Date of summary: Thu Feb 21 14:30:57 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.3 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.27 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 84b335f7..0710e6de 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given
<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 file165a4bc987b7.c 2&gt; file165a4bc987b7.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file33652d0fd552.c 2&gt; file33652d0fd552.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index c34da511..8c5bf22b 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -325,7 +325,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
@@ -335,7 +335,7 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.042 0.000 0.042 </div><div class='input'>
+#&gt; 0.047 0.000 0.047 </div><div class='input'>
</div><div class='input'> <span class='co'># Predict from a fitted model</span>
<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 552.5739
#&gt; Model cost at call 3 : 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 3fa5c9a5..75da28c7 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -191,8 +191,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.045 0.036 7.264 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.905 0.000 22.919 </div><div class='input'>
+#&gt; 0.039 0.040 7.082 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 22.650 0.004 22.666 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340480 0.2659520 0.7505686 0.2494314
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 2815eccb..242d9f63 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,8 +208,8 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:52:23 2019
-#&gt; Date of summary: Thu Jan 31 16:52:23 2019
+#&gt; Date of fit: Thu Feb 21 14:31:48 2019
+#&gt; Date of summary: Thu Feb 21 14:31:48 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index d3c20ed8..939fa7b4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:52:31 2019
-#&gt; Date of summary: Thu Jan 31 16:52:31 2019
+#&gt; Date of fit: Thu Feb 21 14:31:57 2019
+#&gt; Date of summary: Thu Feb 21 14:31:57 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.703 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.849 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
</div><div class='input'><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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:52:33 2019
-#&gt; Date of summary: Thu Jan 31 16:52:33 2019
+#&gt; Date of fit: Thu Feb 21 14:31:59 2019
+#&gt; Date of summary: Thu Feb 21 14:31:59 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 350 model solutions performed in 1.597 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.649 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:52:34 2019
-#&gt; Date of summary: Thu Jan 31 16:52:34 2019
+#&gt; Date of fit: Thu Feb 21 14:32:00 2019
+#&gt; Date of summary: Thu Feb 21 14:32:00 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.898 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.976 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
<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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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 used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Thu Jan 31 16:52:35 2019
-#&gt; Date of summary: Thu Jan 31 16:52:35 2019
+#&gt; Date of fit: Thu Feb 21 14:32:01 2019
+#&gt; Date of summary: Thu Feb 21 14:32:01 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.482 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.512 s
#&gt;
#&gt; Weighting: none
#&gt;

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