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authorJohannes Ranke <jranke@uni-bremen.de>2019-02-26 20:28:15 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-02-26 20:33:32 +0100
commit396e40d2c45d81a8e74c41a2f632665021e980a1 (patch)
treec7ab9b5356361b1939e9b00183a7f31071782f64 /docs/reference
parent64e636d11311be57978ef394c48c9b43fe219059 (diff)
NAFTA SOP Attachment vignette
Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0
Diffstat (limited to 'docs/reference')
-rw-r--r--docs/reference/AIC.mmkin.html4
-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/NAFTA_SOP_2015.html13
-rw-r--r--docs/reference/NAFTA_SOP_Attachment-1.pngbin0 -> 42277 bytes
-rw-r--r--docs/reference/NAFTA_SOP_Attachment.html217
-rw-r--r--docs/reference/index.html4
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html44
-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/nafta.html19
-rw-r--r--docs/reference/plot.nafta.html12
-rw-r--r--docs/reference/print.nafta.html8
-rw-r--r--docs/reference/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html24
16 files changed, 310 insertions, 75 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html
index 69552d5f..2a4a6de4 100644
--- a/docs/reference/AIC.mmkin.html
+++ b/docs/reference/AIC.mmkin.html
@@ -160,8 +160,8 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>),
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>,
- <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>))
- <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[<span class='fl'>1</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#&gt; [1] 55.32452</div><div class='input'>
+ <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</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>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge:</span>
+#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[<span class='fl'>1</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#&gt; [1] 55.32452</div><div class='input'>
<span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span>
<span class='co'># of parameters, the higher (worse) the AIC</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#&gt; df AIC
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 873d75bd..f10805a0 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; 0.195 0.000 0.195
+#&gt; 0.071 0.000 0.071
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -469,8 +469,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555925ca08&gt;
-#&gt; &lt;environment: 0x55555b668200&gt;
+#&gt; &lt;bytecode: 0x55555bb55ad0&gt;
+#&gt; &lt;environment: 0x55555c4dcf70&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -492,8 +492,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555a590818&gt;
-#&gt; &lt;environment: 0x55555b668200&gt;
+#&gt; &lt;bytecode: 0x55555c537298&gt;
+#&gt; &lt;environment: 0x55555c4dcf70&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -560,7 +560,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Tue Feb 26 09:27:10 2019"
+#&gt; [1] "Tue Feb 26 20:23:09 2019"
#&gt;
#&gt; $version
#&gt; [1] "0.9.48.1"
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html
index 4a2c71a9..f4d89222 100644
--- a/docs/reference/NAFTA_SOP_2015.html
+++ b/docs/reference/NAFTA_SOP_2015.html
@@ -152,7 +152,8 @@
<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'>NAFTA_SOP_Appendix_D</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</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative 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; Sums of squares:
+ <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'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Calculation of the Jacobian failed for the cost function of the untransformed model.</span>
+#&gt; <span class='warning'>No t-test results will be available</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</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative 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; Sums of squares:
#&gt; SFO IORE DFOP
#&gt; 1378.6832 615.7730 517.8836
#&gt;
@@ -168,8 +169,8 @@
#&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; k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08
+#&gt; N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00
#&gt;
#&gt; $DFOP
#&gt; Estimate Pr(&gt;t) Lower Upper
@@ -181,9 +182,9 @@
#&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; SFO 407 1350 407
+#&gt; IORE 541 5190000 1560000
+#&gt; DFOP 429 2380 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_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre>
diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png
new file mode 100644
index 00000000..d781cdb0
--- /dev/null
+++ b/docs/reference/NAFTA_SOP_Attachment-1.png
Binary files differ
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
new file mode 100644
index 00000000..63b47855
--- /dev/null
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -0,0 +1,217 @@
+<!-- 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 Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • mkin</title>
+
+<!-- jquery -->
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+
+<!-- sticky kit -->
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+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
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+<meta property="og:title" content="Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment" />
+
+<meta property="og:description" content="Data taken from from Attachment 1 of the SOP." />
+<meta name="twitter:card" content="summary" />
+
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+<!-- mathjax -->
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+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span>
+ </span>
+ </div>
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+ <div id="navbar" class="navbar-collapse collapse">
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+ <a href="../articles/mkin.html">Introduction to mkin</a>
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+ <li>
+ <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>
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+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Example datasets from Attachment 1 to the NAFTA SOP published 2015</h1>
+
+ <div class="hidden name"><code>NAFTA_SOP_Attachment.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Data taken from from Attachment 1 of the SOP.</p>
+
+ </div>
+
+ <pre class="usage"><span class='no'>NAFTA_SOP_Attachment</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>Additionally, a list (NAFTA_SOP_Attachment) containing 16 datasets suitable
+ for the evaluation with <code><a href='nafta.html'>nafta</a></code></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_att_p5a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</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 half-life obtained from the IORE 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_att_p5a</span>)</div><div class='output co'>#&gt; Sums of squares:
+#&gt; SFO IORE DFOP
+#&gt; 465.21753 56.27506 32.06401
+#&gt;
+#&gt; Critical sum of squares for checking the SFO model:
+#&gt; [1] 64.4304
+#&gt;
+#&gt; Parameters:
+#&gt; $SFO
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 95.84012168 1.095639e-21 92.120517864 99.55972549
+#&gt; k_parent_sink 0.01024015 1.710227e-12 0.008996874 0.01165524
+#&gt;
+#&gt; $IORE
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02
+#&gt; k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05
+#&gt; N_parent 2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00
+#&gt;
+#&gt; $DFOP
+#&gt; Estimate Pr(&gt;t) Lower Upper
+#&gt; parent_0 9.994630e+01 4.330861e-27 NA NA
+#&gt; k1 2.674255e-02 3.171390e-05 NA NA
+#&gt; k2 2.161318e-12 5.000000e-01 NA NA
+#&gt; g 6.465276e-01 2.129114e-05 NA NA
+#&gt;
+#&gt;
+#&gt; DTx values:
+#&gt; DT50 DT90 DT50_rep
+#&gt; SFO 67.7 2.25e+02 6.77e+01
+#&gt; IORE 58.2 1.07e+03 3.22e+02
+#&gt; DFOP 55.5 5.84e+11 3.21e+11
+#&gt;
+#&gt; Representative half-life:
+#&gt; [1] 321.5119</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-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> 1.3.0.9000.</p>
+</div>
+ </footer>
+ </div>
+
+
+
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+</html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a251dc33..4e57fd3d 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -338,7 +338,9 @@
<td>
<p><code><a href="plot.nafta.html">plot(<i>&lt;nafta&gt;</i>)</a></code> </p>
</td>
- <td><p>Plot the results of the three models used in the NAFTA scheme</p></td>
+ <td><p>Plot the results of the three models used in the NAFTA scheme. The plots
+ are ordered with increasing complexity of the model in this function
+ (SFO, then IORE, then DFOP).</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 1845a31c..2e5f0ac2 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: Tue Feb 26 09:27:31 2019
-#&gt; Date of summary: Tue Feb 26 09:27:31 2019
+#&gt; Date of fit: Tue Feb 26 20:23:32 2019
+#&gt; Date of summary: Tue Feb 26 20:23:32 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 3.812 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.765 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: Tue Feb 26 09:27:33 2019
-#&gt; Date of summary: Tue Feb 26 09:27:33 2019
+#&gt; Date of fit: Tue Feb 26 20:23:34 2019
+#&gt; Date of summary: Tue Feb 26 20:23:34 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 1.597 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 53f46988..84c0fc49 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: Tue Feb 26 09:27:36 2019
-#&gt; Date of summary: Tue Feb 26 09:27:36 2019
+#&gt; Date of fit: Tue Feb 26 20:23:36 2019
+#&gt; Date of summary: Tue Feb 26 20:23:36 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 0.163 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.161 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; 1.008 0.000 1.008 </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; 1.081 0.000 1.081 </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; 0.812 0.000 0.813 </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; 0.812 0.000 0.812 </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: Tue Feb 26 09:27:48 2019
-#&gt; Date of summary: Tue Feb 26 09:27:48 2019
+#&gt; Date of fit: Tue Feb 26 20:23:48 2019
+#&gt; Date of summary: Tue Feb 26 20:23:48 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 0.845 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.852 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: Tue Feb 26 09:27:50 2019
-#&gt; Date of summary: Tue Feb 26 09:27:50 2019
+#&gt; Date of fit: Tue Feb 26 20:23:51 2019
+#&gt; Date of summary: Tue Feb 26 20:23:51 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 2.523 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.6 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: Tue Feb 26 09:27:51 2019
-#&gt; Date of summary: Tue Feb 26 09:27:51 2019
+#&gt; Date of fit: Tue Feb 26 20:23:52 2019
+#&gt; Date of summary: Tue Feb 26 20:23:52 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 0.705 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.704 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: Tue Feb 26 09:27:52 2019
-#&gt; Date of summary: Tue Feb 26 09:27:52 2019
+#&gt; Date of fit: Tue Feb 26 20:23:53 2019
+#&gt; Date of summary: Tue Feb 26 20:23:53 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 0.8 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.796 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: Tue Feb 26 09:27:54 2019
-#&gt; Date of summary: Tue Feb 26 09:27:54 2019
+#&gt; Date of fit: Tue Feb 26 20:23:54 2019
+#&gt; Date of summary: Tue Feb 26 20:23:54 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -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: Tue Feb 26 09:27:57 2019
-#&gt; Date of summary: Tue Feb 26 09:27:57 2019
+#&gt; Date of fit: Tue Feb 26 20:23:58 2019
+#&gt; Date of summary: Tue Feb 26 20:23:58 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 3.246 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.182 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index bcf39e7f..a6dd68c5 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 file4a116f6acbf1.c 2&gt; file4a116f6acbf1.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file240f6aec3e43.c 2&gt; file240f6aec3e43.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 a38de769..bab6deb8 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; 0.004 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>(
+#&gt; 0.003 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; 0.040 0.000 0.039 </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 6613f35c..0078baed 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; 0.052 0.024 7.037 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 22.463 0.000 22.476 </div><div class='input'>
+#&gt; 0.059 0.021 6.916 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 22.506 0.000 22.518 </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.html b/docs/reference/nafta.html
index b1d45272..9b879786 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -133,7 +133,7 @@
</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>
+ <pre class="usage">nafta(ds, title = NA, quiet = FALSE, &#8230;)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -153,6 +153,10 @@
<th>quiet</th>
<td><p>Should the evaluation text be shown?</p></td>
</tr>
+ <tr>
+ <th>&#8230;</th>
+ <td><p>Further arguments passed to <code><a href='mmkin.html'>mmkin</a></code>.</p></td>
+ </tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -175,7 +179,8 @@
<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'>NAFTA_SOP_Appendix_D</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</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative 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; Sums of squares:
+ <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'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Calculation of the Jacobian failed for the cost function of the untransformed model.</span>
+#&gt; <span class='warning'>No t-test results will be available</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</span></div><div class='output co'>#&gt; <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#&gt; <span class='message'>The representative 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; Sums of squares:
#&gt; SFO IORE DFOP
#&gt; 1378.6832 615.7730 517.8836
#&gt;
@@ -191,8 +196,8 @@
#&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; k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08
+#&gt; N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00
#&gt;
#&gt; $DFOP
#&gt; Estimate Pr(&gt;t) Lower Upper
@@ -204,9 +209,9 @@
#&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; SFO 407 1350 407
+#&gt; IORE 541 5190000 1560000
+#&gt; DFOP 429 2380 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>
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html
index 76da1ffa..7949d36c 100644
--- a/docs/reference/plot.nafta.html
+++ b/docs/reference/plot.nafta.html
@@ -6,7 +6,9 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Plot the results of the three models used in the NAFTA scheme — plot.nafta • mkin</title>
+<title>Plot the results of the three models used in the NAFTA scheme. The plots
+ are ordered with increasing complexity of the model in this function
+ (SFO, then IORE, then DFOP). — plot.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>
@@ -30,7 +32,9 @@
-<meta property="og:title" content="Plot the results of the three models used in the NAFTA scheme — plot.nafta" />
+<meta property="og:title" content="Plot the results of the three models used in the NAFTA scheme. The plots
+ are ordered with increasing complexity of the model in this function
+ (SFO, then IORE, then DFOP). — plot.nafta" />
<meta property="og:description" content="Calls plot.mmkin." />
<meta name="twitter:card" content="summary" />
@@ -118,7 +122,9 @@
<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>
+ <h1>Plot the results of the three models used in the NAFTA scheme. The plots
+ are ordered with increasing complexity of the model in this function
+ (SFO, then IORE, then DFOP).</h1>
<div class="hidden name"><code>plot.nafta.Rd</code></div>
</div>
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index ac276857..44f1f6e5 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -32,7 +32,9 @@
<meta property="og:title" content="Print nafta objects — print.nafta" />
-<meta property="og:description" content="Print nafta objects." />
+<meta property="og:description" content="Print nafta objects. The results for the three models
+ are printed in the order of increasing model complexity,
+ i.e. SFO, then IORE, and finally DFOP." />
<meta name="twitter:card" content="summary" />
@@ -125,7 +127,9 @@
<div class="ref-description">
- <p>Print nafta objects.</p>
+ <p>Print nafta objects. The results for the three models
+ are printed in the order of increasing model complexity,
+ i.e. SFO, then IORE, and finally DFOP.</p>
</div>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index ca0b1c4c..6ec72f80 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: Tue Feb 26 09:28:49 2019
-#&gt; Date of summary: Tue Feb 26 09:28:49 2019
+#&gt; Date of fit: Tue Feb 26 20:24:50 2019
+#&gt; Date of summary: Tue Feb 26 20:24:50 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 0.085 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.084 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index bcfbe975..6e65f609 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: Tue Feb 26 09:28:57 2019
-#&gt; Date of summary: Tue Feb 26 09:28:57 2019
+#&gt; Date of fit: Tue Feb 26 20:24:58 2019
+#&gt; Date of summary: Tue Feb 26 20:24:58 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 0.7 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.707 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: Tue Feb 26 09:28:59 2019
-#&gt; Date of summary: Tue Feb 26 09:28:59 2019
+#&gt; Date of fit: Tue Feb 26 20:25:00 2019
+#&gt; Date of summary: Tue Feb 26 20:25:00 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 1.59 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.584 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: Tue Feb 26 09:29:00 2019
-#&gt; Date of summary: Tue Feb 26 09:29:00 2019
+#&gt; Date of fit: Tue Feb 26 20:25:01 2019
+#&gt; Date of summary: Tue Feb 26 20:25:01 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 0.844 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.867 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: Tue Feb 26 09:29:01 2019
-#&gt; Date of summary: Tue Feb 26 09:29:01 2019
+#&gt; Date of fit: Tue Feb 26 20:25:02 2019
+#&gt; Date of summary: Tue Feb 26 20:25:02 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 0.467 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.472 s
#&gt;
#&gt; Weighting: none
#&gt;

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