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authorJohannes Ranke <jranke@uni-bremen.de>2019-10-31 01:55:01 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-10-31 01:59:05 +0100
commit7091d3738e7e55acb20edb88772b228f6f5b6c98 (patch)
treeb6e31700074605c702662e5238162c57de330453 /docs
parent5e4ea59a41e00b05ea6664c08c7922e892e8ab77 (diff)
Add likelihood ratio test and other methods, fixes
The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added.
Diffstat (limited to 'docs')
-rw-r--r--docs/news/index.html4
-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
-rw-r--r--docs/sitemap.xml12
10 files changed, 1239 insertions, 49 deletions
diff --git a/docs/news/index.html b/docs/news/index.html
index 1322f75d..52bc3458 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -134,6 +134,10 @@
<a href="#mkin-0-9-49-6-unreleased" class="anchor"></a>mkin 0.9.49.6 (unreleased)<small> Unreleased </small>
</h1>
<ul>
+<li><p>Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package</p></li>
+<li><p>Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate</p></li>
+<li><p>Add a ‘residuals’ method for mkinfit objects that supports scaling based on the error model</p></li>
+<li><p>Fix a bug in ‘mkinfit’ that prevented summaries of objects fitted with fixed parameters to be generated</p></li>
<li><p>Add ‘parms’ and ‘confint’ methods for mkinfit objects. Confidence intervals based on the quadratic approximation as in the summary, and based on the profile likelihood</p></li>
<li><p>Move long-running tests to tests/testthat/slow with a separate test log. They currently take around 7 minutes on my system</p></li>
<li><p>‘mkinfit’: Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals</p></li>
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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+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
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+
+<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>
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+<![endif]-->
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+ <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>
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+ <span class="navbar-brand">
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+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ </span>
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+
+ <div id="navbar" class="navbar-collapse collapse">
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+ </li>
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+ </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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+
+<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 -->
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+ <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
new file mode 100644
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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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+
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+ <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>
+
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 9e3363ba..3767bdda 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -73,6 +73,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/lrtest.mkinfit.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html</loc>
</url>
<url>
@@ -139,6 +142,12 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/reexports.html</loc>
+ </url>
+ <url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc>
</url>
<url>
@@ -157,6 +166,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/update.mkinfit.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/articles/FOCUS_D.html</loc>
</url>
<url>

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