aboutsummaryrefslogtreecommitdiff
path: root/docs
diff options
context:
space:
mode:
Diffstat (limited to 'docs')
-rw-r--r--docs/articles/FOCUS_D.html10
-rw-r--r--docs/articles/FOCUS_L.html44
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/FOCUS_Z.html2
-rw-r--r--docs/articles/web_only/compiled_models.html12
-rw-r--r--docs/news/index.html8
-rw-r--r--docs/reference/Extract.mmkin.html12
-rw-r--r--docs/reference/index.html6
-rw-r--r--docs/reference/logLik.mkinfit.html202
-rw-r--r--docs/reference/mccall81_245T.html12
-rw-r--r--docs/reference/mkinfit.html50
-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/summary.mkinfit.html6
-rw-r--r--docs/reference/transform_odeparms.html24
17 files changed, 308 insertions, 96 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index b44462aa..b03e7612 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-18</h4>
+ <h4 class="date">2018-11-23</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -160,10 +160,10 @@
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
<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">summary</span>(fit)</a></code></pre></div>
-<pre><code>## mkin version used for fitting: 0.9.47.5
+<pre><code>## mkin version used for fitting: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 17:17:43 2018
-## Date of summary: Fri Sep 14 17:17:44 2018
+## Date of fit: Fri Nov 23 19:58:46 2018
+## Date of summary: Fri Nov 23 19:58:47 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -171,7 +171,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.645 s
+## Fitted with method Port using 153 model solutions performed in 0.736 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index ea49ae10..37b4306f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-18</h4>
+ <h4 class="date">2018-11-23</h4>
<div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -110,15 +110,15 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:12 2018
-## Date of summary: Tue Sep 18 15:18:12 2018
+## Date of fit: Fri Nov 23 19:58:49 2018
+## Date of summary: Fri Nov 23 19:58:49 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.084 s
+## Fitted with method Port using 37 model solutions performed in 0.095 s
##
## Weighting: none
##
@@ -201,15 +201,15 @@
<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">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:14 2018
-## Date of summary: Tue Sep 18 15:18:14 2018
+## Date of fit: Fri Nov 23 19:58:51 2018
+## Date of summary: Fri Nov 23 19:58:51 2018
##
## 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 1.321 s
+## Fitted with method Port using 611 model solutions performed in 1.464 s
##
## Weighting: none
##
@@ -296,15 +296,15 @@
<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">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:14 2018
-## Date of summary: Tue Sep 18 15:18:14 2018
+## Date of fit: Fri Nov 23 19:58:51 2018
+## Date of summary: Fri Nov 23 19:58:51 2018
##
## 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 0.169 s
+## Fitted with method Port using 81 model solutions performed in 0.191 s
##
## Weighting: none
##
@@ -367,8 +367,8 @@
<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">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:15 2018
-## Date of summary: Tue Sep 18 15:18:15 2018
+## Date of fit: Fri Nov 23 19:58:52 2018
+## Date of summary: Fri Nov 23 19:58:52 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.739 s
+## Fitted with method Port using 336 model solutions performed in 0.824 s
##
## Weighting: none
##
@@ -459,8 +459,8 @@
<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">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:16 2018
-## Date of summary: Tue Sep 18 15:18:16 2018
+## Date of fit: Fri Nov 23 19:58:53 2018
+## Date of summary: Fri Nov 23 19:58:54 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.301 s
+## Fitted with method Port using 137 model solutions performed in 0.344 s
##
## Weighting: none
##
@@ -560,15 +560,15 @@
<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">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:17 2018
-## Date of summary: Tue Sep 18 15:18:17 2018
+## Date of fit: Fri Nov 23 19:58:54 2018
+## Date of summary: Fri Nov 23 19:58:54 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.108 s
##
## Weighting: none
##
@@ -620,15 +620,15 @@
<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">summary</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: 0.9.47.6
## R version used for fitting: 3.5.1
-## Date of fit: Tue Sep 18 15:18:17 2018
-## Date of summary: Tue Sep 18 15:18:17 2018
+## Date of fit: Fri Nov 23 19:58:54 2018
+## Date of summary: Fri Nov 23 19:58:54 2018
##
## 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 0.139 s
+## Fitted with method Port using 66 model solutions performed in 0.159 s
##
## Weighting: none
##
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index e483043b..4ead1062 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -84,7 +84,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-18</h4>
+ <h4 class="date">2018-11-23</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index d9249f9d..8c053c10 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -84,7 +84,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-18</h4>
+ <h4 class="date">2018-11-23</h4>
<div class="hidden name"><code>twa.Rmd</code></div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index a3e743d1..5215e039 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-18</h4>
+ <h4 class="date">2018-11-23</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 684f28cb..85efff61 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -84,7 +84,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-18</h4>
+ <h4 class="date">2018-11-23</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -125,9 +125,9 @@
<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 2.005 1.000 2.003 0
-## 1 deSolve, not compiled 3 15.480 7.721 15.474 0
-## 2 Eigenvalue based 3 2.460 1.227 2.459 0
+## 3 deSolve, compiled 3 2.284 1.000 2.282 0
+## 1 deSolve, not compiled 3 17.732 7.764 17.724 0
+## 2 Eigenvalue based 3 2.812 1.231 2.809 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -156,8 +156,8 @@
<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 3.524 1.00 3.523 0.000
-## 1 deSolve, not compiled 3 33.021 9.37 33.001 0.004
+## 2 deSolve, compiled 3 4.029 1.000 4.026 0
+## 1 deSolve, not compiled 3 37.760 9.372 37.744 0
## 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 a316612a..f3e57dd0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -117,14 +117,16 @@
</div>
- <div id="mkin-0-9-47-6-2018-09-18" class="section level1">
+ <div id="mkin-0-9-47-6-2018-09-21" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-47-6-2018-09-18" class="anchor"></a>mkin 0.9.47.6 (2018-09-18)<small> Unreleased </small>
+<a href="#mkin-0-9-47-6-2018-09-21" class="anchor"></a>mkin 0.9.47.6 (2018-09-21)<small> Unreleased </small>
</h1>
<ul>
<li><p>‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset</p></li>
<li><p>‘max_twa_parent’: Support maximum time weighted average concentration calculations for the hockey stick (HS) model</p></li>
<li><p>‘mkinpredict’: Make the function generic and create a method for mkinfit objects</p></li>
+<li><p>‘mkinfit’: Improve the correctness of the fitted two component error model by fitting the mean absolute deviance at each observation against the observed values, weighting with the current two-component error model</p></li>
+<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>
</ul>
</div>
<div id="mkin-0-9-47-5-2018-09-14" class="section level1">
@@ -668,7 +670,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#mkin-0-9-47-6-2018-09-18">0.9.47.6</a></li>
+ <li><a href="#mkin-0-9-47-6-2018-09-21">0.9.47.6</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 0447e2d9..a74a3067 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.175 0.000 0.175
+#&gt; 0.184 0.000 0.184
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bd99510&gt;
-#&gt; &lt;environment: 0x55555bc57c88&gt;
+#&gt; &lt;bytecode: 0x55555be47f20&gt;
+#&gt; &lt;environment: 0x55555bc31c70&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555cb90200&gt;
-#&gt; &lt;environment: 0x55555bc57c88&gt;
+#&gt; &lt;bytecode: 0x55555cd8de90&gt;
+#&gt; &lt;environment: 0x55555bc31c70&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,7 +558,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Tue Sep 18 15:16:36 2018"
+#&gt; [1] "Fri Nov 23 19:56:59 2018"
#&gt;
#&gt; $version
#&gt; [1] "0.9.47.6"
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a7806970..c1d31aff 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -193,6 +193,12 @@
<p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
</td>
<td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
new file mode 100644
index 00000000..1dda313f
--- /dev/null
+++ b/docs/reference/logLik.mkinfit.html
@@ -0,0 +1,202 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <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>Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+<meta property="og:title" content="Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit" />
+
+<meta property="og:description" content="This function simply calculates the product of the likelihood densities
+ calc" />
+<meta name="twitter:card" content="summary" />
+
+
+
+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[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">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <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>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Calculated the log-likelihood of a fitted mkinfit object</h1>
+
+ <div class="hidden name"><code>logLik.mkinfit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>This function simply calculates the product of the likelihood densities
+ calc</p>
+
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'>logLik</span>(<span class='no'>object</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>object</th>
+ <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>&#8230;</th>
+ <td><p>For compatibility with the generic method</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An object of class <code>logLik</code> with the number of
+ estimated parameters (degradation model parameters plus variance
+ model parameters) as attribute.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='no'>sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><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='no'>d_t</span> <span class='kw'>&lt;-</span> <span class='no'>FOCUS_2006_D</span>
+ <span class='no'>d_t</span>[<span class='fl'>23</span>:<span class='fl'>24</span>, <span class='st'>"value"</span>] <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='fl'>NA</span>) <span class='co'># can't cope with zero values at the moment</span>
+ <span class='no'>f_nw</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'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='no'>f_obs</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'>d_t</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='no'>f_tc</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'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>AIC</span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#&gt; df AIC
+#&gt; f_nw 5 204.4619
+#&gt; f_obs 6 205.8727
+#&gt; f_tc 6 143.8773</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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+ </body>
+</html>
+
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index be77df76..9f937a12 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -158,8 +158,8 @@
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:16:48 2018
-#&gt; Date of summary: Tue Sep 18 15:16:48 2018
+#&gt; Date of fit: Fri Nov 23 19:57:18 2018
+#&gt; Date of summary: Fri Nov 23 19:57:18 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -169,7 +169,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.602 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.661 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -247,8 +247,8 @@
<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'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:16:50 2018
-#&gt; Date of summary: Tue Sep 18 15:16:50 2018
+#&gt; Date of fit: Fri Nov 23 19:57:19 2018
+#&gt; Date of summary: Fri Nov 23 19:57:19 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -258,7 +258,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.513 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.549 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 3c8442b6..9bbe3900 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -326,7 +326,7 @@
<th>weight</th>
<td><p>only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none",
"std", "mean", see details of <code>modCost</code>, or "tc" for the
- two component error model. The option "manual" is available for
+ two component error model. The option "manual" is available for
the case that <code>err</code>!=<code>NULL</code>, but it is not necessary to specify it.</p></td>
</tr>
<tr>
@@ -406,6 +406,8 @@
<div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
<code><a href='mkinparplot.html'>mkinparplot</a></code>.</p>
+<p>Comparisons of models fitted to the same data can be made using <code>AIC</code>
+ by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p>
<p>Fitting of several models to several datasets in a single call to
<code><a href='mmkin.html'>mmkin</a></code>.</p></div>
@@ -434,15 +436,15 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:16:52 2018
-#&gt; Date of summary: Tue Sep 18 15:16:52 2018
+#&gt; Date of fit: Fri Nov 23 19:57:22 2018
+#&gt; Date of summary: Fri Nov 23 19:57:22 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.158 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.155 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -511,7 +513,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.011 0.000 1.012 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.995 0.000 0.995 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -586,7 +588,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.755 0.000 0.755 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.789 0.000 0.790 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -624,8 +626,8 @@
<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'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:04 2018
-#&gt; Date of summary: Tue Sep 18 15:17:04 2018
+#&gt; Date of fit: Fri Nov 23 19:57:34 2018
+#&gt; Date of summary: Fri Nov 23 19:57:34 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -633,7 +635,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.823 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.825 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -741,8 +743,8 @@
#&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'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:06 2018
-#&gt; Date of summary: Tue Sep 18 15:17:06 2018
+#&gt; Date of fit: Fri Nov 23 19:57:36 2018
+#&gt; Date of summary: Fri Nov 23 19:57:36 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -750,7 +752,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.374 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.528 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -863,8 +865,8 @@
#&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'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:07 2018
-#&gt; Date of summary: Tue Sep 18 15:17:07 2018
+#&gt; Date of fit: Fri Nov 23 19:57:37 2018
+#&gt; Date of summary: Fri Nov 23 19:57:37 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -872,7 +874,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.636 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.687 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -981,8 +983,8 @@
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:08 2018
-#&gt; Date of summary: Tue Sep 18 15:17:08 2018
+#&gt; Date of fit: Fri Nov 23 19:57:38 2018
+#&gt; Date of summary: Fri Nov 23 19:57:38 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -990,7 +992,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.717 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.781 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1101,8 +1103,8 @@
<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'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:09 2018
-#&gt; Date of summary: Tue Sep 18 15:17:09 2018
+#&gt; Date of fit: Fri Nov 23 19:57:39 2018
+#&gt; Date of summary: Fri Nov 23 19:57:39 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1110,7 +1112,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.181 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.201 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1219,8 +1221,8 @@
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:13 2018
-#&gt; Date of summary: Tue Sep 18 15:17:13 2018
+#&gt; Date of fit: Fri Nov 23 19:57:43 2018
+#&gt; Date of summary: Fri Nov 23 19:57:43 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1228,7 +1230,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 3.077 s
+#&gt; Fitted with method Port using 692 model solutions performed in 3.087 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index af364403..3148efd8 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -229,7 +229,7 @@ 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 file20267955fc75.c 2&gt; file20267955fc75.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file140043d42642.c 2&gt; file140043d42642.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 91e9289d..baa67000 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -323,17 +323,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.003 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.034 0.000 0.034 </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 ad011b75..8bc7b18c 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -189,8 +189,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</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; 0.054 0.027 6.836 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 20.444 0.000 20.459 </div><div class='input'>
+#&gt; 0.029 0.039 6.854 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 22.091 0.000 22.106 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340480 0.2659520 0.7505686 0.2494314
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index f8e09b45..9428f187 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:17:59 2018
-#&gt; Date of summary: Tue Sep 18 15:17:59 2018
+#&gt; Date of fit: Fri Nov 23 19:58:33 2018
+#&gt; Date of summary: Fri Nov 23 19:58:33 2018
#&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 0.071 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index f2602792..aa82269a 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ 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'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:18:06 2018
-#&gt; Date of summary: Tue Sep 18 15:18:06 2018
+#&gt; Date of fit: Fri Nov 23 19:58:40 2018
+#&gt; Date of summary: Fri Nov 23 19:58:40 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ 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 0.662 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.688 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -276,8 +276,8 @@ 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'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:18:08 2018
-#&gt; Date of summary: Tue Sep 18 15:18:08 2018
+#&gt; Date of fit: Fri Nov 23 19:58:42 2018
+#&gt; Date of summary: Fri Nov 23 19:58:42 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ 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 1.342 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.608 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -364,8 +364,8 @@ 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'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:18:09 2018
-#&gt; Date of summary: Tue Sep 18 15:18:09 2018
+#&gt; Date of fit: Fri Nov 23 19:58:43 2018
+#&gt; Date of summary: Fri Nov 23 19:58:43 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ 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 0.737 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.821 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -448,8 +448,8 @@ 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'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Tue Sep 18 15:18:10 2018
-#&gt; Date of summary: Tue Sep 18 15:18:10 2018
+#&gt; Date of fit: Fri Nov 23 19:58:44 2018
+#&gt; Date of summary: Fri Nov 23 19:58:44 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ 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 0.414 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.46 s
#&gt;
#&gt; Weighting: none
#&gt;

Contact - Imprint