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-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/web_only/compiled_models.html12
-rw-r--r--docs/news/index.html7
-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/NAFTA_2015_datasets-1.pngbin0 -> 41450 bytes
-rw-r--r--docs/reference/NAFTA_2015_datasets.html213
-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.html6
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/nafta-1.pngbin0 -> 41450 bytes
-rw-r--r--docs/reference/nafta.html239
-rw-r--r--docs/reference/plot.nafta.html190
-rw-r--r--docs/reference/print.nafta.html178
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html24
18 files changed, 910 insertions, 89 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 38e59d9d..ad8413dc 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -163,8 +163,8 @@
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:20 2019
-## Date of summary: Fri Feb 22 09:51:21 2019
+## Date of fit: Fri Feb 22 20:48:30 2019
+## Date of summary: Fri Feb 22 20:48:31 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.693 s
+## Fitted with method Port using 153 model solutions performed in 0.731 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 13131315..17c7bf59 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,15 +111,15 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:22 2019
-## Date of summary: Fri Feb 22 09:51:22 2019
+## Date of fit: Fri Feb 22 20:48:32 2019
+## Date of summary: Fri Feb 22 20:48:32 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.095 s
+## Fitted with method Port using 37 model solutions performed in 0.105 s
##
## Weighting: none
##
@@ -202,15 +202,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:24 2019
-## Date of summary: Fri Feb 22 09:51:24 2019
+## Date of fit: Fri Feb 22 20:48:34 2019
+## Date of summary: Fri Feb 22 20:48:34 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.515 s
+## Fitted with method Port using 611 model solutions performed in 1.604 s
##
## Weighting: none
##
@@ -297,15 +297,15 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:25 2019
-## Date of summary: Fri Feb 22 09:51:25 2019
+## Date of fit: Fri Feb 22 20:48:35 2019
+## Date of summary: Fri Feb 22 20:48:35 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.198 s
+## Fitted with method Port using 81 model solutions performed in 0.216 s
##
## Weighting: none
##
@@ -368,8 +368,8 @@
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:26 2019
-## Date of summary: Fri Feb 22 09:51:26 2019
+## Date of fit: Fri Feb 22 20:48:36 2019
+## Date of summary: Fri Feb 22 20:48:36 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.847 s
+## Fitted with method Port using 336 model solutions performed in 0.864 s
##
## Weighting: none
##
@@ -460,8 +460,8 @@
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:27 2019
-## Date of summary: Fri Feb 22 09:51:27 2019
+## Date of fit: Fri Feb 22 20:48:37 2019
+## Date of summary: Fri Feb 22 20:48:38 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.347 s
+## Fitted with method Port using 137 model solutions performed in 0.362 s
##
## Weighting: none
##
@@ -561,15 +561,15 @@
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:27 2019
-## Date of summary: Fri Feb 22 09:51:28 2019
+## Date of fit: Fri Feb 22 20:48:38 2019
+## Date of summary: Fri Feb 22 20:48:38 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.112 s
+## Fitted with method Port using 46 model solutions performed in 0.123 s
##
## Weighting: none
##
@@ -621,15 +621,15 @@
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.48.1
## R version used for fitting: 3.5.2
-## Date of fit: Fri Feb 22 09:51:28 2019
-## Date of summary: Fri Feb 22 09:51:28 2019
+## Date of fit: Fri Feb 22 20:48:38 2019
+## Date of summary: Fri Feb 22 20:48:38 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.165 s
+## Fitted with method Port using 66 model solutions performed in 0.184 s
##
## Weighting: none
##
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index e9f8fa99..fbf2de33 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.336 1.000 2.335 0
-## 1 deSolve, not compiled 3 17.610 7.539 17.602 0
-## 2 Eigenvalue based 3 2.899 1.241 2.897 0
+## 3 deSolve, compiled 3 2.484 1.000 2.483 0
+## 1 deSolve, not compiled 3 17.963 7.231 17.951 0
+## 2 Eigenvalue based 3 3.146 1.267 3.144 0
## user.child sys.child
## 3 0 0
## 1 0 0
## 2 0 0</code></pre>
-<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p>
+<p>We see that using the compiled model is by a factor of around 7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor">
@@ -157,8 +157,8 @@
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.122 1.000 4.119 0
-## 1 deSolve, not compiled 3 37.359 9.063 37.343 0
+## 2 deSolve, compiled 3 4.232 1.000 4.226 0.004
+## 1 deSolve, not compiled 3 37.946 8.966 37.924 0.000
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/news/index.html b/docs/news/index.html
index 2e62819c..cd82d187 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -119,9 +119,9 @@
</div>
- <div id="mkin-0-9-48-1-2019-02-21" class="section level1">
+ <div id="mkin-0-9-48-1-2019-02-22" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-48-1-2019-02-21" class="anchor"></a>mkin 0.9.48.1 (2019-02-21)<small> Unreleased </small>
+<a href="#mkin-0-9-48-1-2019-02-22" class="anchor"></a>mkin 0.9.48.1 (2019-02-22)<small> Unreleased </small>
</h1>
<ul>
<li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li>
@@ -133,6 +133,7 @@
<li><p>‘tests/testthat/test_irls.R’: Test if the components of the error model used to generate the data can be reproduced with moderate accuracy</p></li>
<li><p>Add the function ‘CAKE_export’ to facilitate cross-checking of results</p></li>
<li><p>Implement the logistic model (only tested for parent fits)</p></li>
+<li><p>‘nafta’: Add evaluations according to the NAFTA guidance</p></li>
</ul>
</div>
<div id="mkin-0-9-47-5-2018-09-14" class="section level1">
@@ -676,7 +677,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-48-1-2019-02-21">0.9.48.1</a></li>
+ <li><a href="#mkin-0-9-48-1-2019-02-22">0.9.48.1</a></li>
<li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li>
<li><a href="#mkin-0-9-47-3">0.9.47.3</a></li>
<li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 20949a8f..e3285ed3 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.197 0.000 0.197
+#&gt; 0.201 0.000 0.200
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -469,8 +469,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555920cf58&gt;
-#&gt; &lt;environment: 0x5555560a01f8&gt;
+#&gt; &lt;bytecode: 0x555559103bf0&gt;
+#&gt; &lt;environment: 0x55555a51ba10&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -492,8 +492,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555a322750&gt;
-#&gt; &lt;environment: 0x5555560a01f8&gt;
+#&gt; &lt;bytecode: 0x55555a537b00&gt;
+#&gt; &lt;environment: 0x55555a51ba10&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -560,7 +560,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Fri Feb 22 09:49:27 2019"
+#&gt; [1] "Fri Feb 22 20:46:31 2019"
#&gt;
#&gt; $version
#&gt; [1] "0.9.48.1"
diff --git a/docs/reference/NAFTA_2015_datasets-1.png b/docs/reference/NAFTA_2015_datasets-1.png
new file mode 100644
index 00000000..c4f9f048
--- /dev/null
+++ b/docs/reference/NAFTA_2015_datasets-1.png
Binary files differ
diff --git a/docs/reference/NAFTA_2015_datasets.html b/docs/reference/NAFTA_2015_datasets.html
new file mode 100644
index 00000000..9ef56fb0
--- /dev/null
+++ b/docs/reference/NAFTA_2015_datasets.html
@@ -0,0 +1,213 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Example datasets from the NAFTA guidance published 2015 — NAFTA_2015_datasets • mkin</title>
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+
+<!-- pkgdown -->
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+<script src="../pkgdown.js"></script>
+
+
+
+<meta property="og:title" content="Example datasets from the NAFTA guidance published 2015 — NAFTA_2015_datasets" />
+
+<meta property="og:description" content="Data taken from US EPA (2015), p. 23." />
+<meta name="twitter:card" content="summary" />
+
+
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+<!-- mathjax -->
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+ <a href="../articles/mkin.html">Introduction to mkin</a>
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+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
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+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Example datasets from the NAFTA guidance published 2015</h1>
+
+ <div class="hidden name"><code>NAFTA_2015_datasets.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Data taken from US EPA (2015), p. 23.</p>
+
+ </div>
+
+ <pre class="usage"><span class='no'>NAFTA_2015_datasets</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>1 dataset with observations on the following variables.</p><dl class='dl-horizontal'>
+ <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd>
+ <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd>
+ <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</p></dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
+ in environmental media. NAFTA Technical Working Group on Pesticides
+ <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
+ accessed 2019-02-22</p>
+<p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
+ Calculate Representative Half-life Values and Characterizing Pesticide
+ Degradation
+ <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The reprentative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Parameters:
+#&gt; $SFO
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063
+#&gt; k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164
+#&gt;
+#&gt; $IORE
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02
+#&gt; k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08
+#&gt; N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00
+#&gt;
+#&gt; $DFOP
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02
+#&gt; k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01
+#&gt; k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03
+#&gt; g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01
+#&gt;
+#&gt;
+#&gt; DTx values:
+#&gt; DT50 DT90 DT50_rep
+#&gt; SFO 407 1352 407
+#&gt; IORE 541 5192066 1562968
+#&gt; DFOP 429 2383 841
+#&gt;
+#&gt; Representative half-life:
+#&gt; [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_2015_datasets-1.png' alt='' width='700' height='433' /></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="#format">Format</a></li>
+
+ <li><a href="#source">Source</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 46de4255..7b3418de 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:49:48 2019
-#&gt; Date of summary: Fri Feb 22 09:49:48 2019
+#&gt; Date of fit: Fri Feb 22 20:46:54 2019
+#&gt; Date of summary: Fri Feb 22 20:46:54 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 3.837 s
+#&gt; Fitted with method Port using 574 model solutions performed in 4.461 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:49:50 2019
-#&gt; Date of summary: Fri Feb 22 09:49:50 2019
+#&gt; Date of fit: Fri Feb 22 20:46:56 2019
+#&gt; Date of summary: Fri Feb 22 20:46:56 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 1.611 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.709 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index addb23e5..dfdddb25 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:49:53 2019
-#&gt; Date of summary: Fri Feb 22 09:49:53 2019
+#&gt; Date of fit: Fri Feb 22 20:46:59 2019
+#&gt; Date of summary: Fri Feb 22 20:46:59 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 0.159 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.185 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; 1.015 0.000 1.016 </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; 1.071 0.000 1.072 </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; 0.821 0.000 0.822 </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; 0.852 0.000 0.852 </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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:05 2019
-#&gt; Date of summary: Fri Feb 22 09:50:05 2019
+#&gt; Date of fit: Fri Feb 22 20:47:11 2019
+#&gt; Date of summary: Fri Feb 22 20:47:11 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 0.853 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.864 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:07 2019
-#&gt; Date of summary: Fri Feb 22 09:50:07 2019
+#&gt; Date of fit: Fri Feb 22 20:47:14 2019
+#&gt; Date of summary: Fri Feb 22 20:47:14 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 2.535 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.584 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:08 2019
-#&gt; Date of summary: Fri Feb 22 09:50:08 2019
+#&gt; Date of fit: Fri Feb 22 20:47:15 2019
+#&gt; Date of summary: Fri Feb 22 20:47:15 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 0.717 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.716 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:09 2019
-#&gt; Date of summary: Fri Feb 22 09:50:09 2019
+#&gt; Date of fit: Fri Feb 22 20:47:16 2019
+#&gt; Date of summary: Fri Feb 22 20:47:16 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 0.796 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.83 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:11 2019
-#&gt; Date of summary: Fri Feb 22 09:50:11 2019
+#&gt; Date of fit: Fri Feb 22 20:47:17 2019
+#&gt; Date of summary: Fri Feb 22 20:47:17 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 1.325 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.286 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:50:14 2019
-#&gt; Date of summary: Fri Feb 22 09:50:14 2019
+#&gt; Date of fit: Fri Feb 22 20:47:21 2019
+#&gt; Date of summary: Fri Feb 22 20:47:21 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 3.303 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.38 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index b2f290d1..64fba5e5 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 file4d9c2c394c1.c 2&gt; file4d9c2c394c1.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file622753352edd.c 2&gt; file622753352edd.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 6f789fa4..2b4c33aa 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -325,17 +325,17 @@
<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 0.003 </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
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.001 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.002 0.000 0.002 </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='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; 0.039 0.000 0.040 </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 73a25ef2..71ec89e8 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; 0.040 0.047 7.314 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.751 0.000 22.766 </div><div class='input'>
+#&gt; 0.052 0.044 7.383 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 23.652 0.004 23.672 </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/nafta-1.png b/docs/reference/nafta-1.png
new file mode 100644
index 00000000..c4f9f048
--- /dev/null
+++ b/docs/reference/nafta-1.png
Binary files differ
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
new file mode 100644
index 00000000..c74c3939
--- /dev/null
+++ b/docs/reference/nafta.html
@@ -0,0 +1,239 @@
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+ <h1>Evaluate parent kinetics using the NAFTA guidance</h1>
+
+ <div class="hidden name"><code>nafta.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>The function fits the SFO, IORE and DFOP models using
+ <code><a href='mmkin.html'>mmkin</a></code> and returns an object of class
+ <code>nafta</code> that has methods for printing and plotting.</p>
+
+ </div>
+
+ <pre class="usage"><span class='fu'>nafta</span>(<span class='no'>ds</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>ds</th>
+ <td><p>A dataframe that must contain one variable called "time" with the time
+ values specified by the <code>time</code> argument, one column called "name" with
+ the grouping of the observed values, and finally one column of observed
+ values called "value".</p></td>
+ </tr>
+ <tr>
+ <th>title</th>
+ <td><p>Optional title of the dataset</p></td>
+ </tr>
+ <tr>
+ <th>quiet</th>
+ <td><p>Should the evaluation text be shown?</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An list of class <code>nafta</code>. The list element named "mmkin" is the
+ <code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models.
+ The list element named "title" contains the title of the dataset used.
+ The list element "data" contains the dataset used in the fits.</p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
+ in environmental media. NAFTA Technical Working Group on Pesticides
+ <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
+ accessed 2019-02-22</p>
+<p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
+ Calculate Representative Half-life Values and Characterizing Pesticide
+ Degradation
+ <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'>&lt;-</span> <span class='fu'>nafta</span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#&gt; <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#&gt; <span class='message'>The representative half-life of the IORE model is longer than the one corresponding to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The reprentative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#&gt; Parameters:
+#&gt; $SFO
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063
+#&gt; k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164
+#&gt;
+#&gt; $IORE
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02
+#&gt; k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08
+#&gt; N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00
+#&gt;
+#&gt; $DFOP
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02
+#&gt; k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01
+#&gt; k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03
+#&gt; g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01
+#&gt;
+#&gt;
+#&gt; DTx values:
+#&gt; DT50 DT90 DT50_rep
+#&gt; SFO 407 1352 407
+#&gt; IORE 541 5192066 1562968
+#&gt; DFOP 429 2383 841
+#&gt;
+#&gt; Representative half-life:
+#&gt; [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></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="#value">Value</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+ <p>Johannes Ranke</p>
+ </div>
+</div>
+
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+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
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diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
new file mode 100644
index 00000000..ccc98b23
--- /dev/null
+++ b/docs/reference/plot.nafta.html
@@ -0,0 +1,190 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+ </li>
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+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Plot the results of the three models used in the NAFTA scheme</h1>
+
+ <div class="hidden name"><code>plot.nafta.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p>
+
+ </div>
+
+ <pre class="usage"># S3 method for nafta
+plot(x, legend = FALSE, main = "auto", &#8230;)</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>x</th>
+ <td><p>An object of class <code><a href='nafta.html'>nafta</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>legend</th>
+ <td><p>Should a legend be added?</p></td>
+ </tr>
+ <tr>
+ <th>main</th>
+ <td><p>Possibility to override the main title of the plot.</p></td>
+ </tr>
+ <tr>
+ <th>&#8230;</th>
+ <td><p>Further arguments passed to <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The function is called for its side effect.</p>
+
+
+ </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="#value">Value</a></li>
+ </ul>
+
+ <h2>Author</h2>
+ <p>Johannes Ranke</p>
+ </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>
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diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
new file mode 100644
index 00000000..dc9373f7
--- /dev/null
+++ b/docs/reference/print.nafta.html
@@ -0,0 +1,178 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+<title>Print nafta objects — print.nafta • mkin</title>
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+
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+<meta property="og:title" content="Print nafta objects — print.nafta" />
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+<meta property="og:description" content="Print nafta objects." />
+<meta name="twitter:card" content="summary" />
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+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span>
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+ <a href="../articles/mkin.html">Introduction to mkin</a>
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+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
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+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Print nafta objects</h1>
+
+ <div class="hidden name"><code>print.nafta.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Print nafta objects.</p>
+
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for nafta</span>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>An <code><a href='nafta.html'>nafta</a></code> object.</p></td>
+ </tr>
+ <tr>
+ <th>quiet</th>
+ <td><p>Should the evaluation text be shown?</p></td>
+ </tr>
+ <tr>
+ <th>&#8230;</th>
+ <td><p>Not used.</p></td>
+ </tr>
+ </table>
+
+
+ </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>
+ </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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 1543c328..39ef962c 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,15 +208,15 @@
<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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:51:06 2019
-#&gt; Date of summary: Fri Feb 22 09:51:06 2019
+#&gt; Date of fit: Fri Feb 22 20:48:16 2019
+#&gt; Date of summary: Fri Feb 22 20:48:16 2019
#&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 0.086 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.088 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 65a6b4ee..9d18fbb2 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:51:14 2019
-#&gt; Date of summary: Fri Feb 22 09:51:14 2019
+#&gt; Date of fit: Fri Feb 22 20:48:24 2019
+#&gt; Date of summary: Fri Feb 22 20:48:24 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 0.775 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.717 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:51:16 2019
-#&gt; Date of summary: Fri Feb 22 09:51:16 2019
+#&gt; Date of fit: Fri Feb 22 20:48:26 2019
+#&gt; Date of summary: Fri Feb 22 20:48:26 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 1.584 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.661 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:51:17 2019
-#&gt; Date of summary: Fri Feb 22 09:51:17 2019
+#&gt; Date of fit: Fri Feb 22 20:48:27 2019
+#&gt; Date of summary: Fri Feb 22 20:48:27 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 0.858 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.871 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: 0.9.48.1
#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Fri Feb 22 09:51:18 2019
-#&gt; Date of summary: Fri Feb 22 09:51:18 2019
+#&gt; Date of fit: Fri Feb 22 20:48:28 2019
+#&gt; Date of summary: Fri Feb 22 20:48:28 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 0.47 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.484 s
#&gt;
#&gt; Weighting: none
#&gt;

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