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-rw-r--r--docs/reference/confint.mkinfit.html5
-rw-r--r--docs/reference/index.html66
-rw-r--r--docs/reference/logLik.mkinfit.html18
-rw-r--r--docs/reference/lrtest.mkinfit.html231
-rw-r--r--docs/reference/mkinfit.html32
-rw-r--r--docs/reference/reexports.html180
-rw-r--r--docs/reference/residuals.mkinfit.html196
-rw-r--r--docs/reference/update.mkinfit.html544
8 files changed, 1223 insertions, 49 deletions
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
index 27fdb304..6fb806fc 100644
--- a/docs/reference/confint.mkinfit.html
+++ b/docs/reference/confint.mkinfit.html
@@ -236,13 +236,14 @@ machines, cores &gt; 1 is not supported.</p></td>
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>f_d_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</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; User System verstrichen
-#&gt; 50.787 0.000 50.815 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span>
+#&gt; 50.987 0.008 51.023 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span>
<span class='co'># system.time(ci_profile &lt;- confint(f_d_1, cores = 5))</span>
<span class='co'># system.time(ci_profile &lt;- confint(f_d_1,</span>
<span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))</span>
<span class='co'># If we exclude parent_0 (the confidence of which is often of minor interest), we get a nice</span>
<span class='co'># performance improvement from about 30 seconds to about 12 seconds</span>
-<span class='co'># system.time(ci_profile_no_parent_0 &lt;- confint(f_d_1, c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 4))</span>
+<span class='co'># system.time(ci_profile_no_parent_0 &lt;- confint(f_d_1, </span>
+<span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 4))</span>
<span class='no'>ci_profile</span></div><div class='output co'>#&gt; 2.5% 97.5%
#&gt; parent_0 96.456003650 1.027703e+02
#&gt; k_parent_sink 0.040762501 5.549764e-02
diff --git a/docs/reference/index.html b/docs/reference/index.html
index fa424060..8987db96 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -185,45 +185,39 @@ more datasets</p></td>
</tr><tr>
<td>
- <p><code><a href="parms.html">parms()</a></code> </p>
- </td>
- <td><p>Extract model parameters from mkinfit models</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="confint.mkinfit.html">confint(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+ <p><code><a href="summary.mkinfit.html">summary(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="summary.mkinfit.html">print(<i>&lt;summary.mkinfit&gt;</i>)</a></code> </p>
</td>
- <td><p>Confidence intervals for parameters of mkinfit objects</p></td>
+ <td><p>Summary method for class "mkinfit"</p></td>
</tr><tr>
<td>
- <p><code><a href="summary.mkinfit.html">summary(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="summary.mkinfit.html">print(<i>&lt;summary.mkinfit&gt;</i>)</a></code> </p>
+ <p><code><a href="parms.html">parms()</a></code> </p>
</td>
- <td><p>Summary method for class "mkinfit"</p></td>
+ <td><p>Extract model parameters from mkinfit models</p></td>
</tr><tr>
<td>
- <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+ <p><code><a href="confint.mkinfit.html">confint(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
</td>
- <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
+ <td><p>Confidence intervals for parameters of mkinfit objects</p></td>
</tr><tr>
<td>
- <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p>
+ <p><code><a href="update.mkinfit.html">update(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
</td>
- <td><p>Function to plot residuals stored in an mkin object</p></td>
+ <td><p>Update an mkinfit model with different arguments</p></td>
</tr><tr>
<td>
- <p><code><a href="mkinparplot.html">mkinparplot()</a></code> </p>
+ <p><code><a href="lrtest.mkinfit.html">lrtest(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
</td>
- <td><p>Function to plot the confidence intervals obtained using mkinfit</p></td>
+ <td><p>Likelihood ratio test for mkinfit models</p></td>
</tr><tr>
<td>
- <p><code><a href="mkinerrplot.html">mkinerrplot()</a></code> </p>
+ <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
</td>
- <td><p>Function to plot squared residuals and the error model for an mkin object</p></td>
+ <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
</tr><tr>
<td>
@@ -234,9 +228,9 @@ with mkinfit</p></td>
</tr><tr>
<td>
- <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
+ <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
</td>
- <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
+ <td><p>Export a list of datasets format to a CAKE study file</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -380,7 +374,7 @@ of an mmkin object</p></td>
</tbody><tbody>
<tr>
<th colspan="2">
- <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
+ <h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2>
<p class="section-desc"></p>
</th>
</tr>
@@ -442,9 +436,33 @@ kinetic models fitted with mkinfit</p></td>
</tr><tr>
<td>
- <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
+ <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
</td>
- <td><p>Export a list of datasets format to a CAKE study file</p></td>
+ <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="residuals.mkinfit.html">residuals(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Extract residuals from an mkinfit model</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p>
+ </td>
+ <td><p>Function to plot residuals stored in an mkin object</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="mkinparplot.html">mkinparplot()</a></code> </p>
+ </td>
+ <td><p>Function to plot the confidence intervals obtained using mkinfit</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="mkinerrplot.html">mkinerrplot()</a></code> </p>
+ </td>
+ <td><p>Function to plot squared residuals and the error model for an mkin object</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -536,7 +554,7 @@ kinetic models fitted with mkinfit</p></td>
<li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
<li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
<li><a href="#section-nafta-guidance">NAFTA guidance</a></li>
- <li><a href="#section-helper-functions">Helper functions</a></li>
+ <li><a href="#section-helper-functions-mainly-used-internally">Helper functions mainly used internally</a></li>
<li><a href="#section-analytical-solutions">Analytical solutions</a></li>
<li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li>
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index c79146a9..9a54496e 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -36,10 +36,11 @@
<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
-calculated using dnorm, i.e. assuming normal distribution,
-with of the mean predicted by the degradation model, and the standard
-deviation predicted by the error model." />
+<meta property="og:description" content="This function returns the product of the likelihood densities of each
+observed value, as calculated as part of the fitting procedure using
+dnorm, i.e. assuming normal distribution, and with the means
+predicted by the degradation model, and the standard deviations predicted by
+the error model." />
<meta name="twitter:card" content="summary" />
@@ -136,10 +137,11 @@ deviation predicted by the error model." />
</div>
<div class="ref-description">
- <p>This function simply calculates the product of the likelihood densities
-calculated using <code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution,
-with of the mean predicted by the degradation model, and the standard
-deviation predicted by the error model.</p>
+ <p>This function returns the product of the likelihood densities of each
+observed value, as calculated as part of the fitting procedure using
+<code><a href='https://rdrr.io/r/stats/Normal.html'>dnorm</a></code>, i.e. assuming normal distribution, and with the means
+predicted by the degradation model, and the standard deviations predicted by
+the error model.</p>
</div>
<pre class="usage"><span class='co'># S3 method for mkinfit</span>
diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html
new file mode 100644
index 00000000..dd47d91d
--- /dev/null
+++ b/docs/reference/lrtest.mkinfit.html
@@ -0,0 +1,231 @@
+<!-- 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">
+
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+
+
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+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../pkgdown.js"></script>
+
+
+
+
+<meta property="og:title" content="Likelihood ratio test for mkinfit models — lrtest.mkinfit" />
+<meta property="og:description" content="Compare two mkinfit models based on their likelihood. If two fitted
+mkinfit objects are given as arguments, it is checked if they have been
+fitted to the same data. It is the responsibility of the user to make sure
+that the models are nested, i.e. one of them has less degrees of freedom
+and can be expressed by fixing the parameters of the other." />
+<meta name="twitter:card" content="summary" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
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+<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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+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
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+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
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+ <a href="../reference/index.html">Functions and data</a>
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+ Articles
+
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+ <a href="../articles/mkin.html">Introduction to mkin</a>
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+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Likelihood ratio test for mkinfit models</h1>
+
+ <div class="hidden name"><code>lrtest.mkinfit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Compare two mkinfit models based on their likelihood. If two fitted
+mkinfit objects are given as arguments, it is checked if they have been
+fitted to the same data. It is the responsibility of the user to make sure
+that the models are nested, i.e. one of them has less degrees of freedom
+and can be expressed by fixing the parameters of the other.</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>object</span>, <span class='kw'>object_2</span> <span class='kw'>=</span> <span class='kw'>NULL</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 <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
+ </tr>
+ <tr>
+ <th>object_2</th>
+ <td><p>Optionally, another mkinfit object fitted to the same data.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Argument to <code><a href='mkinfit.html'>mkinfit</a></code>, passed to
+<code><a href='update.mkinfit.html'>update.mkinfit</a></code> for creating the alternative fitted object.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Alternatively, an argument to mkinfit can be given which is then passed
+to <code><a href='update.mkinfit.html'>update.mkinfit</a></code> to obtain the alternative model.</p>
+<p>The comparison is then made by the <code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code>
+method from the lmtest package. The model with the higher number of fitted
+parameters (alternative hypothesis) is listed first, then the model with the
+lower number of fitted parameters (null hypothesis).</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
+<span class='no'>test_data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)
+<span class='no'>sfo_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>dfop_fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='no'>test_data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='no'>sfo_fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt;
+#&gt; Model 1: DFOP with error model const
+#&gt; Model 2: SFO with error model const
+#&gt; #Df LogLik Df Chisq Pr(&gt;Chisq)
+#&gt; 1 5 -42.453
+#&gt; 2 3 -63.954 -2 43.002 4.594e-10 ***
+#&gt; ---
+#&gt; Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>sfo_fit</span>, <span class='no'>dfop_fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt;
+#&gt; Model 1: DFOP with error model const
+#&gt; Model 2: SFO with error model const
+#&gt; #Df LogLik Df Chisq Pr(&gt;Chisq)
+#&gt; 1 5 -42.453
+#&gt; 2 3 -63.954 -2 43.002 4.594e-10 ***
+#&gt; ---
+#&gt; Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(mkinmod = "DFOP", observed = test_data, quiet = TRUE, error_model = "tc", parms.ini = c(k1 = 0.359673923258109, k2 = 0.0219997339436148, g = 0.692423284341522), state.ini = c(parent = 103.83323992643)): Objekt 'test_data' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>dfop_fit</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0</span>))</div><div class='output co'>#&gt; <span class='error'>Error in mkinfit(mkinmod = "DFOP", observed = test_data, quiet = TRUE, fixed_parms = ..1, parms.ini = c(k1 = 0.359673923258109, k2 = 0.0219997339436148, g = 0.692423284341522), state.ini = c(parent = 103.83323992643)): Objekt 'test_data' nicht gefunden</span></div><div class='input'># }
+</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="#details">Details</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> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 6c98bc38..c72d1cd0 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -218,7 +218,9 @@ must be given.</p></td>
<tr>
<th>fixed_parms</th>
<td><p>The names of parameters that should not be optimised but
-rather kept at the values specified in <code>parms.ini</code>.</p></td>
+rather kept at the values specified in <code>parms.ini</code>. Alternatively,
+a named numeric vector of parameters to be fixed, regardless of the values
+in parms.ini.</p></td>
</tr>
<tr>
<th>fixed_initials</th>
@@ -400,15 +402,15 @@ estimators.</p>
<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://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Fri Oct 25 02:08:07 2019
-#&gt; Date of summary: Fri Oct 25 02:08:07 2019
+#&gt; Date of fit: Thu Oct 31 01:48:29 2019
+#&gt; Date of summary: Thu Oct 31 01:48:29 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 using 222 model solutions performed in 0.453 s
+#&gt; Fitted using 222 model solutions performed in 0.455 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -480,7 +482,7 @@ estimators.</p>
<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://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>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; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.447 0.000 1.448 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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; 1.464 0.000 1.465 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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
#&gt;
@@ -553,7 +555,7 @@ estimators.</p>
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
#&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.032 0.000 1.032 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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; 1.047 0.000 1.047 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -589,8 +591,8 @@ estimators.</p>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Fri Oct 25 02:08:22 2019
-#&gt; Date of summary: Fri Oct 25 02:08:22 2019
+#&gt; Date of fit: Thu Oct 31 01:48:44 2019
+#&gt; Date of summary: Thu Oct 31 01:48:44 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -598,7 +600,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 421 model solutions performed in 1.062 s
+#&gt; Fitted using 421 model solutions performed in 1.136 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -706,8 +708,8 @@ estimators.</p>
#&gt; 120 m1 25.15 28.78984 -3.640e+00
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</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: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Fri Oct 25 02:08:25 2019
-#&gt; Date of summary: Fri Oct 25 02:08:25 2019
+#&gt; Date of fit: Thu Oct 31 01:48:47 2019
+#&gt; Date of summary: Thu Oct 31 01:48:47 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -715,7 +717,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 978 model solutions performed in 2.523 s
+#&gt; Fitted using 978 model solutions performed in 2.512 s
#&gt;
#&gt; Error model: Variance unique to each observed variable
#&gt;
@@ -838,8 +840,8 @@ estimators.</p>
#&gt; 120 m1 25.15 28.80429 -3.654e+00
#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.6
#&gt; R version used for fitting: 3.6.1
-#&gt; Date of fit: Fri Oct 25 02:08:34 2019
-#&gt; Date of summary: Fri Oct 25 02:08:34 2019
+#&gt; Date of fit: Thu Oct 31 01:48:56 2019
+#&gt; Date of summary: Thu Oct 31 01:48:56 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -847,7 +849,7 @@ estimators.</p>
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2289 model solutions performed in 9.136 s
+#&gt; Fitted using 2289 model solutions performed in 9.124 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
new file mode 100644
index 00000000..90cbec1a
--- /dev/null
+++ b/docs/reference/reexports.html
@@ -0,0 +1,180 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
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+
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+ <h1>Objects exported from other packages</h1>
+
+ <div class="hidden name"><code>reexports.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>These objects are imported from other packages. Follow the links
+below to see their documentation.</p>
+<dl class='dl-horizontal'>
+ <dt>lmtest</dt><dd><p><code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></code></p></dd>
+
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diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html
new file mode 100644
index 00000000..7dd25012
--- /dev/null
+++ b/docs/reference/residuals.mkinfit.html
@@ -0,0 +1,196 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+
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+ <div class="page-header">
+ <h1>Extract residuals from an mkinfit model</h1>
+
+ <div class="hidden name"><code>residuals.mkinfit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Extract residuals from an mkinfit model</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span>(<span class='no'>object</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
+ </tr>
+ <tr>
+ <th>standardized</th>
+ <td><p>Should the residuals be standardized by dividing by the
+standard deviation obtained from the fitted error model?</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Not used</p></td>
+ </tr>
+ </table>
+
+
+ <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='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</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://rdrr.io/r/stats/residuals.html'>residuals</a></span>(<span class='no'>f</span>)</div><div class='output co'>#&gt; [1] 0.09726306 -0.13912135 -0.15351176 0.73388319 -0.08657030 -0.93204730
+#&gt; [7] -0.03269102 1.45347805 -0.88423710</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span>(<span class='no'>f</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; [1] 0.13969820 -0.19981894 -0.22048777 1.05407086 -0.12434027 -1.33869248
+#&gt; [7] -0.04695387 2.08761953 -1.27002305</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="#examples">Examples</a></li>
+ </ul>
+
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diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html
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+<meta property="og:title" content="Update an mkinfit model with different arguments — update.mkinfit" />
+<meta property="og:description" content="This function will return an updated mkinfit object. The fitted degradation
+model parameters from the old fit are used as starting values for the
+updated fit. Values specified as 'parms.ini' and/or 'state.ini' will
+override these starting values." />
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+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
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+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
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+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
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+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
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+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Update an mkinfit model with different arguments</h1>
+
+ <div class="hidden name"><code>update.mkinfit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>This function will return an updated mkinfit object. The fitted degradation
+model parameters from the old fit are used as starting values for the
+updated fit. Values specified as 'parms.ini' and/or 'state.ini' will
+override these starting values.</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</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 mkinfit object to be updated</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Arguments to <code><a href='mkinfit.html'>mkinfit</a></code> that should replace
+the arguments from the original call. Arguments set to NULL will
+remove arguments given in the original call</p></td>
+ </tr>
+ <tr>
+ <th>evaluate</th>
+ <td><p>Should the call be evaluated or returned as a call</p></td>
+ </tr>
+ </table>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#&gt; $par
+#&gt; parent_0 log_k1 log_k2 g_ilr sigma_low rsd_high
+#&gt; 100.85489822 8.84468217 -2.29693632 -14.95263998 0.00375222 0.06763435
+#&gt;
+#&gt; $objective
+#&gt; [1] 19.40656
+#&gt;
+#&gt; $convergence
+#&gt; [1] 0
+#&gt;
+#&gt; $iterations
+#&gt; [1] 120
+#&gt;
+#&gt; $evaluations
+#&gt; function gradient
+#&gt; 144 847
+#&gt;
+#&gt; $message
+#&gt; [1] "relative convergence (4)"
+#&gt;
+#&gt; $logLik
+#&gt; [1] -19.40656
+#&gt;
+#&gt; $d_3_message
+#&gt; threestep
+#&gt; "Three-step fitting yielded a higher likelihood than direct fitting"
+#&gt;
+#&gt; $hessian
+#&gt; parent_0 log_k1 log_k2 g_ilr sigma_low
+#&gt; parent_0 3.662473e-01 -2.914408e-16 -7.241561e+01 -3.021629e-08 1.923504e+01
+#&gt; log_k1 -2.914408e-16 0.000000e+00 -2.215935e-13 -7.291307e-25 3.416474e-15
+#&gt; log_k2 -7.241561e+01 -2.215935e-13 3.127457e+04 6.766544e-06 -1.495826e+04
+#&gt; g_ilr -3.021629e-08 -7.291307e-25 6.766544e-06 3.122099e-09 -1.797429e-06
+#&gt; sigma_low 1.923504e+01 3.416474e-15 -1.495826e+04 -1.797429e-06 7.759299e+04
+#&gt; rsd_high 3.902119e+00 -1.801019e-16 -1.685343e+02 -3.750713e-07 3.984179e+03
+#&gt; rsd_high
+#&gt; parent_0 3.902119e+00
+#&gt; log_k1 -1.801019e-16
+#&gt; log_k2 -1.685343e+02
+#&gt; g_ilr -3.750713e-07
+#&gt; sigma_low 3.984179e+03
+#&gt; rsd_high 7.188991e+03
+#&gt;
+#&gt; $hessian_notrans
+#&gt; parent_0 k1 k2 g sigma_low
+#&gt; parent_0 3.662473e-01 -3.714445e-19 -7.201669e+02 -3.261485e+01 1.923504e+01
+#&gt; k1 -3.714445e-19 0.000000e+00 -4.258512e-15 7.218123e-21 4.355854e-18
+#&gt; k2 -7.201669e+02 -4.258512e-15 3.092510e+06 7.263235e+04 -1.456870e+05
+#&gt; g -3.261485e+01 7.218123e-21 7.263235e+04 3.291750e+03 -1.939948e+03
+#&gt; sigma_low 1.923504e+01 4.355854e-18 -1.456870e+05 -1.939948e+03 7.759299e+04
+#&gt; rsd_high 3.902119e+00 -2.259812e-19 -1.779680e+03 -4.048658e+02 3.984179e+03
+#&gt; rsd_high
+#&gt; parent_0 3.902119e+00
+#&gt; k1 -2.259812e-19
+#&gt; k2 -1.779680e+03
+#&gt; g -4.048658e+02
+#&gt; sigma_low 3.984179e+03
+#&gt; rsd_high 7.188991e+03
+#&gt;
+#&gt; $call
+#&gt; mkinfit(mkinmod = "DFOP", observed = subset(FOCUS_2006_D, value !=
+#&gt; 0), parms.ini = c(k1 = 0.699298911979803, k2 = 0.0899931270871125,
+#&gt; g = 0.0923391681138686), state.ini = c(parent = 101.948852047129),
+#&gt; quiet = TRUE, error_model = "tc")
+#&gt;
+#&gt; $error_model_algorithm
+#&gt; [1] "d_3"
+#&gt;
+#&gt; $solution_type
+#&gt; [1] "analytical"
+#&gt;
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt;
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt;
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt;
+#&gt; $control
+#&gt; $control$eval.max
+#&gt; [1] 300
+#&gt;
+#&gt; $control$iter.max
+#&gt; [1] 200
+#&gt;
+#&gt;
+#&gt; $calls
+#&gt; [1] 3105
+#&gt;
+#&gt; $time
+#&gt; User System verstrichen
+#&gt; 10.314 0.000 10.320
+#&gt;
+#&gt; $mkinmod
+#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: min
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: DFOP; $sink: TRUE
+#&gt; Differential equations:
+#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#&gt; * parent
+#&gt;
+#&gt; $observed
+#&gt; name time value
+#&gt; 1 parent 0 99.46
+#&gt; 2 parent 0 102.04
+#&gt; 3 parent 1 93.50
+#&gt; 4 parent 1 92.50
+#&gt; 5 parent 3 63.23
+#&gt; 6 parent 3 68.99
+#&gt; 7 parent 7 52.32
+#&gt; 8 parent 7 55.13
+#&gt; 9 parent 14 27.27
+#&gt; 10 parent 14 26.64
+#&gt; 11 parent 21 11.50
+#&gt; 12 parent 21 11.64
+#&gt; 13 parent 35 2.85
+#&gt; 14 parent 35 2.91
+#&gt; 15 parent 50 0.69
+#&gt; 16 parent 50 0.63
+#&gt; 17 parent 75 0.05
+#&gt; 18 parent 75 0.06
+#&gt;
+#&gt; $obs_vars
+#&gt; [1] "parent"
+#&gt;
+#&gt; $predicted
+#&gt; name time value
+#&gt; 1 parent 0.0000000 100.85489822
+#&gt; 2 parent 0.7575758 93.45650191
+#&gt; 3 parent 1.0000000 91.20560523
+#&gt; 4 parent 1.5151515 86.60082860
+#&gt; 5 parent 2.2727273 80.24806580
+#&gt; 6 parent 3.0000000 74.58828105
+#&gt; 7 parent 3.0303030 74.36132158
+#&gt; 8 parent 3.7878788 68.90641029
+#&gt; 9 parent 4.5454545 63.85165403
+#&gt; 10 parent 5.3030303 59.16769870
+#&gt; 11 parent 6.0606061 54.82734352
+#&gt; 12 parent 6.8181818 50.80538306
+#&gt; 13 parent 7.0000000 49.88485755
+#&gt; 14 parent 7.5757576 47.07846089
+#&gt; 15 parent 8.3333333 43.62493394
+#&gt; 16 parent 9.0909091 40.42474681
+#&gt; 17 parent 9.8484848 37.45931528
+#&gt; 18 parent 10.6060606 34.71141842
+#&gt; 19 parent 11.3636364 32.16509858
+#&gt; 20 parent 12.1212121 29.80556871
+#&gt; 21 parent 12.8787879 27.61912649
+#&gt; 22 parent 13.6363636 25.59307475
+#&gt; 23 parent 14.0000000 24.67405211
+#&gt; 24 parent 14.3939394 23.71564776
+#&gt; 25 parent 15.1515152 21.97594287
+#&gt; 26 parent 15.9090909 20.36385722
+#&gt; 27 parent 16.6666667 18.87002909
+#&gt; 28 parent 17.4242424 17.48578345
+#&gt; 29 parent 18.1818182 16.20308170
+#&gt; 30 parent 18.9393939 15.01447489
+#&gt; 31 parent 19.6969697 13.91306051
+#&gt; 32 parent 20.4545455 12.89244241
+#&gt; 33 parent 21.0000000 12.20428157
+#&gt; 34 parent 21.2121212 11.94669362
+#&gt; 35 parent 21.9696970 11.07032198
+#&gt; 36 parent 22.7272727 10.25823818
+#&gt; 37 parent 23.4848485 9.50572628
+#&gt; 38 parent 24.2424242 8.80841627
+#&gt; 39 parent 25.0000000 8.16225872
+#&gt; 40 parent 25.7575758 7.56350125
+#&gt; 41 parent 26.5151515 7.00866672
+#&gt; 42 parent 27.2727273 6.49453311
+#&gt; 43 parent 28.0303030 6.01811471
+#&gt; 44 parent 28.7878788 5.57664485
+#&gt; 45 parent 29.5454545 5.16755983
+#&gt; 46 parent 30.3030303 4.78848399
+#&gt; 47 parent 31.0606061 4.43721595
+#&gt; 48 parent 31.8181818 4.11171583
+#&gt; 49 parent 32.5757576 3.81009336
+#&gt; 50 parent 33.3333333 3.53059697
+#&gt; 51 parent 34.0909091 3.27160354
+#&gt; 52 parent 34.8484848 3.03160906
+#&gt; 53 parent 35.0000000 2.98576554
+#&gt; 54 parent 35.6060606 2.80921981
+#&gt; 55 parent 36.3636364 2.60314433
+#&gt; 56 parent 37.1212121 2.41218590
+#&gt; 57 parent 37.8787879 2.23523557
+#&gt; 58 parent 38.6363636 2.07126576
+#&gt; 59 parent 39.3939394 1.91932426
+#&gt; 60 parent 40.1515152 1.77852870
+#&gt; 61 parent 40.9090909 1.64806147
+#&gt; 62 parent 41.6666667 1.52716489
+#&gt; 63 parent 42.4242424 1.41513691
+#&gt; 64 parent 43.1818182 1.31132694
+#&gt; 65 parent 43.9393939 1.21513214
+#&gt; 66 parent 44.6969697 1.12599389
+#&gt; 67 parent 45.4545455 1.04339454
+#&gt; 68 parent 46.2121212 0.96685442
+#&gt; 69 parent 46.9696970 0.89592904
+#&gt; 70 parent 47.7272727 0.83020652
+#&gt; 71 parent 48.4848485 0.76930520
+#&gt; 72 parent 49.2424242 0.71287140
+#&gt; 73 parent 50.0000000 0.66057741
+#&gt; 74 parent 50.7575758 0.61211954
+#&gt; 75 parent 51.5151515 0.56721639
+#&gt; 76 parent 52.2727273 0.52560719
+#&gt; 77 parent 53.0303030 0.48705031
+#&gt; 78 parent 53.7878788 0.45132184
+#&gt; 79 parent 54.5454545 0.41821430
+#&gt; 80 parent 55.3030303 0.38753542
+#&gt; 81 parent 56.0606061 0.35910705
+#&gt; 82 parent 56.8181818 0.33276409
+#&gt; 83 parent 57.5757576 0.30835357
+#&gt; 84 parent 58.3333333 0.28573373
+#&gt; 85 parent 59.0909091 0.26477320
+#&gt; 86 parent 59.8484848 0.24535028
+#&gt; 87 parent 60.6060606 0.22735216
+#&gt; 88 parent 61.3636364 0.21067432
+#&gt; 89 parent 62.1212121 0.19521992
+#&gt; 90 parent 62.8787879 0.18089921
+#&gt; 91 parent 63.6363636 0.16762901
+#&gt; 92 parent 64.3939394 0.15533228
+#&gt; 93 parent 65.1515152 0.14393759
+#&gt; 94 parent 65.9090909 0.13337879
+#&gt; 95 parent 66.6666667 0.12359454
+#&gt; 96 parent 67.4242424 0.11452804
+#&gt; 97 parent 68.1818182 0.10612662
+#&gt; 98 parent 68.9393939 0.09834151
+#&gt; 99 parent 69.6969697 0.09112749
+#&gt; 100 parent 70.4545455 0.08444266
+#&gt; 101 parent 71.2121212 0.07824822
+#&gt; 102 parent 71.9696970 0.07250818
+#&gt; 103 parent 72.7272727 0.06718920
+#&gt; 104 parent 73.4848485 0.06226042
+#&gt; 105 parent 74.2424242 0.05769319
+#&gt; 106 parent 75.0000000 0.05346100
+#&gt;
+#&gt; $rss
+#&gt; function (P)
+#&gt; cost_function(P, OLS = TRUE, update_data = FALSE)
+#&gt; &lt;bytecode: 0x555557c557c8&gt;
+#&gt; &lt;environment: 0x55555bb0e330&gt;
+#&gt;
+#&gt; $ll
+#&gt; function (P, fixed_degparms = FALSE, fixed_errparms = FALSE)
+#&gt; {
+#&gt; -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms,
+#&gt; fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE)
+#&gt; }
+#&gt; &lt;bytecode: 0x555557c55bf0&gt;
+#&gt; &lt;environment: 0x55555bb0e330&gt;
+#&gt;
+#&gt; $start
+#&gt; value type
+#&gt; parent_0 101.94885205 state
+#&gt; k1 0.69929891 deparm
+#&gt; k2 0.08999313 deparm
+#&gt; g 0.09233917 deparm
+#&gt; sigma_low 0.10000000 error
+#&gt; rsd_high 0.10000000 error
+#&gt;
+#&gt; $start_transformed
+#&gt; value lower upper
+#&gt; parent_0 101.948852 -Inf Inf
+#&gt; log_k1 -0.357677 -Inf Inf
+#&gt; log_k2 -2.408022 -Inf Inf
+#&gt; g_ilr -1.616024 -Inf Inf
+#&gt; sigma_low 0.100000 0 Inf
+#&gt; rsd_high 0.100000 0 Inf
+#&gt;
+#&gt; $fixed
+#&gt; [1] value type
+#&gt; &lt;0 Zeilen&gt; (oder row.names mit Länge 0)
+#&gt;
+#&gt; $data
+#&gt; time variable observed predicted residual
+#&gt; 1 0 parent 99.46 100.8548982 -1.39489822
+#&gt; 2 0 parent 102.04 100.8548982 1.18510178
+#&gt; 3 1 parent 93.50 91.2056052 2.29439477
+#&gt; 4 1 parent 92.50 91.2056052 1.29439477
+#&gt; 5 3 parent 63.23 74.5882810 -11.35828105
+#&gt; 6 3 parent 68.99 74.5882810 -5.59828105
+#&gt; 7 7 parent 52.32 49.8848576 2.43514245
+#&gt; 8 7 parent 55.13 49.8848576 5.24514245
+#&gt; 9 14 parent 27.27 24.6740521 2.59594789
+#&gt; 10 14 parent 26.64 24.6740521 1.96594789
+#&gt; 11 21 parent 11.50 12.2042816 -0.70428157
+#&gt; 12 21 parent 11.64 12.2042816 -0.56428157
+#&gt; 13 35 parent 2.85 2.9857655 -0.13576554
+#&gt; 14 35 parent 2.91 2.9857655 -0.07576554
+#&gt; 15 50 parent 0.69 0.6605774 0.02942259
+#&gt; 16 50 parent 0.63 0.6605774 -0.03057741
+#&gt; 17 75 parent 0.05 0.0534610 -0.00346100
+#&gt; 18 75 parent 0.06 0.0534610 0.00653900
+#&gt;
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt;
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt;
+#&gt; $err_mod
+#&gt; [1] "tc"
+#&gt;
+#&gt; $bparms.optim
+#&gt; parent_0 k1 k2 g
+#&gt; 1.008549e+02 6.937399e+03 1.005665e-01 6.551046e-10
+#&gt;
+#&gt; $bparms.fixed
+#&gt; numeric(0)
+#&gt;
+#&gt; $bparms.ode
+#&gt; k1 k2 g
+#&gt; 6.937399e+03 1.005665e-01 6.551046e-10
+#&gt;
+#&gt; $bparms.state
+#&gt; parent
+#&gt; 100.8549
+#&gt;
+#&gt; $errparms
+#&gt; sigma_low rsd_high
+#&gt; 0.00375222 0.06763435
+#&gt;
+#&gt; $df.residual
+#&gt; [1] 12
+#&gt;
+#&gt; $date
+#&gt; [1] "Thu Oct 31 01:49:09 2019"
+#&gt;
+#&gt; $version
+#&gt; [1] "0.9.49.6"
+#&gt;
+#&gt; $Rversion
+#&gt; [1] "3.6.1"
+#&gt;
+#&gt; attr(,"class")
+#&gt; [1] "mkinfit" "modFit" </div><div class='input'># }
+</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="#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> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+

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