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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-08 02:59:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-08 02:59:07 +0100
commit1c647363430e0db732c23feebe4293dc48978608 (patch)
treeff7e6933a851b449e533df083b741898d724ee67
parent279a1d83d7cbe39a953467762629eb1abb9addf4 (diff)
Update static docs
-rw-r--r--docs/dev/news/index.html1
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/endpoints.html14
-rw-r--r--docs/dev/reference/index.html6
-rw-r--r--docs/dev/reference/saem.html44
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html436
-rw-r--r--docs/dev/sitemap.xml3
7 files changed, 482 insertions, 24 deletions
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 3980ea88..4f811b9f 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -146,6 +146,7 @@
<a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small>
</h1>
<ul>
+<li><p>‘saem’ generic function to fit saemix models, with a method ‘saem.mmkin’ and a corresponding ‘summary.saem.mmkin’</p></li>
<li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li>
<li><p>‘update’ method for ‘mmkin’ objects</p></li>
<li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index aebac46b..120f4975 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-11-07T12:14Z
+last_built: 2020-11-08T01:44Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index 5a20a34c..db702c2e 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -165,8 +165,11 @@ advantage that the SFORB model can also be used for metabolites.</p>
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>fit</th>
- <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code> or
-<code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
+ <td><p>An object of class <a href='mkinfit.html'>mkinfit</a>, <a href='nlme.mmkin.html'>nlme.mmkin</a> or
+<a href='saem.html'>saem.mmkin</a>. Or another object that has list components
+mkinmod containing an <a href='mkinmod.html'>mkinmod</a> degradation model, and two numeric vectors,
+bparms.optim and bparms.fixed, that contain parameter values
+for that model.</p></td>
</tr>
</table>
@@ -176,9 +179,14 @@ advantage that the SFORB model can also be used for metabolites.</p>
and, if applicable, a vector of formation fractions named ff
and, if the SFORB model was in use, a vector of eigenvalues
of these SFORB models, equivalent to DFOP rate constants</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from
+HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
- <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p>
+ <p>The function is used internally by <a href='summary.mkinfit.html'>summary.mkinfit</a>,
+<a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a> and <a href='summary.saem.mmkin.html'>summary.saem.mmkin</a>.</p>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Johannes Ranke</p>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index f1884d2b..825c4d27 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -343,6 +343,12 @@ of an mmkin object</p></td>
</tr><tr>
<td>
+ <p><code><a href="summary.saem.mmkin.html">summary(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i>&lt;summary.saem.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Summary method for class "saem.mmkin"</p></td>
+ </tr><tr>
+
+ <td>
<p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
</td>
<td><p>Helper functions to create nlme models from mmkin row objects</p></td>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index f883eb11..06fcfaa7 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -41,8 +41,8 @@
<meta property="og:title" content="Fit nonlinear mixed models with SAEM — saem" />
<meta property="og:description" content="This function uses saemix::saemix() as a backend for fitting nonlinear mixed
-effects models created from mmkin row objects using the stochastic approximation
-to the expectation maximisation algorithm (SAEM)." />
+effects models created from mmkin row objects using the Stochastic Approximation
+Expectation Maximisation algorithm (SAEM)." />
<meta name="robots" content="noindex">
@@ -147,8 +147,8 @@ to the expectation maximisation algorithm (SAEM)." />
<div class="ref-description">
<p>This function uses <code><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix::saemix()</a></code> as a backend for fitting nonlinear mixed
-effects models created from <a href='mmkin.html'>mmkin</a> row objects using the stochastic approximation
-to the expectation maximisation algorithm (SAEM).</p>
+effects models created from <a href='mmkin.html'>mmkin</a> row objects using the Stochastic Approximation
+Expectation Maximisation algorithm (SAEM).</p>
</div>
<pre class="usage"><span class='fu'>saem</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>control</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -205,7 +205,8 @@ by the saemix function?</p></td>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a>.</p>
+ <p>An S3 object of class 'saem.mmkin', containing the fitted
+<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'.</p>
<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p>
<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -215,6 +216,9 @@ obtained by fitting the same model to a list of datasets using <a href='mkinfit.
<p>Starting values for the fixed effects (population mean parameters, argument
psi0 of <code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel()</a></code> are the mean values of the parameters found
using <a href='mmkin.html'>mmkin</a>.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
@@ -225,27 +229,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:14:50 2020"
+#&gt; [1] "Sun Nov 8 02:44:42 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:14:52 2020"</div><div class='input'>
+#&gt; [1] "Sun Nov 8 02:44:43 2020"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:14:53 2020"
+#&gt; [1] "Sun Nov 8 02:44:45 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:14:55 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Sun Nov 8 02:44:46 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:14:55 2020"
+#&gt; [1] "Sun Nov 8 02:44:47 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:14:57 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Sun Nov 8 02:44:49 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:14:57 2020"
+#&gt; [1] "Sun Nov 8 02:44:49 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:15:00 2020"</div><div class='input'>
+#&gt; [1] "Sun Nov 8 02:44:52 2020"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, we can use</span>
<span class='co'># functions from saemix</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -258,10 +262,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:15:02 2020"
+#&gt; [1] "Sun Nov 8 02:44:54 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:15:07 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Sun Nov 8 02:44:59 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
#&gt; 1 467.7644 465.0305
#&gt; 2 469.4862 466.3617</div><div class='input'>
@@ -271,20 +275,20 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># This takes about 4 minutes on my system</span>
<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:15:08 2020"
+#&gt; [1] "Sun Nov 8 02:45:00 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:19:07 2020"</div><div class='input'>
+#&gt; [1] "Sun Nov 8 02:49:01 2020"</div><div class='output co'>#&gt; <span class='error'>Error in exp(trans_k): non-numeric argument to mathematical function</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 317.7 169.9 258.9</span></div><div class='input'>
<span class='va'>f_mmkin_des</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
<span class='co'># Using a single core, the following takes about 6 minutes, using 10 cores</span>
<span class='co'># it is slower instead of faster</span>
<span class='va'>f_saem_des</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_des</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Nov 7 13:19:26 2020"
+#&gt; [1] "Sun Nov 8 02:49:20 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Nov 7 13:27:33 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saemix</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saemix_des</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saemix$so, f_saemix_des$so)): object 'f_saemix' not found</span></div><div class='input'><span class='co'># }</span>
+#&gt; [1] "Sun Nov 8 02:57:30 2020"</div><div class='output co'>#&gt; <span class='error'>Error in exp(trans_k): non-numeric argument to mathematical function</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 591.7 205.6 521.4</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_des</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem$so, f_saem_des$so)): object 'f_saem' not found</span></div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
new file mode 100644
index 00000000..01e8eb12
--- /dev/null
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -0,0 +1,436 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Summary method for class "saem.mmkin" — summary.saem.mmkin • mkin</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="Summary method for class "saem.mmkin" — summary.saem.mmkin" />
+<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters
+for fixed effects (population), random effects (deviations from the
+population mean) and residual error model, as well as the resulting
+endpoints such as formation fractions and DT50 values. Optionally
+(default is FALSE), the data are listed in full." />
+
+
+<meta name="robots" content="noindex">
+
+<!-- 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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+ <div class="page-header">
+ <h1>Summary method for class "saem.mmkin"</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.saem.mmkin.R'><code>R/summary.saem.mmkin.R</code></a></small>
+ <div class="hidden name"><code>summary.saem.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Lists model equations, initial parameter values, optimised parameters
+for fixed effects (population), random effects (deviations from the
+population mean) and residual error model, as well as the resulting
+endpoints such as formation fractions and DT50 values. Optionally
+(default is FALSE), the data are listed in full.</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
+
+<span class='co'># S3 method for summary.saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>an object of class <a href='saem.html'>saem.mmkin</a></p></td>
+ </tr>
+ <tr>
+ <th>data</th>
+ <td><p>logical, indicating whether the full data should be included in
+the summary.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>Should the summary be verbose?</p></td>
+ </tr>
+ <tr>
+ <th>distimes</th>
+ <td><p>logical, indicating whether DT50 and DT90 values should be
+included.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>optional arguments passed to methods like <code>print</code>.</p></td>
+ </tr>
+ <tr>
+ <th>x</th>
+ <td><p>an object of class summary.saem.mmkin</p></td>
+ </tr>
+ <tr>
+ <th>digits</th>
+ <td><p>Number of digits to use for printing</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The summary function returns a list based on the <a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a>
+obtained in the fit, with at least the following additional components</p>
+<dt>saemixversion, mkinversion, Rversion</dt><dd><p>The saemix, mkin and R versions used</p></dd>
+<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were
+produced</p></dd>
+<dt>diffs</dt><dd><p>The differential equations used in the degradation model</p></dd>
+<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
+<dt>data</dt><dd><p>The data</p></dd>
+<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>
+<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>
+<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
+model.</p></dd>
+<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
+The print method is called for its side effect, i.e. printing the summary.
+
+ <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+ <p>Johannes Ranke for the mkin specific parts
+saemix authors for the parts inherited from saemix.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Generate five datasets following SFO kinetics</span>
+<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
+<span class='va'>dt50_sfo_in_pop</span> <span class='op'>&lt;-</span> <span class='fl'>50</span>
+<span class='va'>k_in_pop</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in_pop</span>
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span>
+<span class='va'>k_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</span>
+<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+
+<span class='va'>pred_sfo</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span>
+ <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><span class='op'>)</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>,
+ <span class='va'>sampling_times</span><span class='op'>)</span>
+<span class='op'>}</span>
+
+<span class='va'>ds_sfo_mean</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span>
+
+<span class='va'>ds_sfo_syn</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span>
+ <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>,
+ sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>,
+ n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>
+<span class='op'>}</span><span class='op'>)</span>
+
+<span class='co'># \dontrun{</span>
+<span class='co'># Evaluate using mmkin and saem</span>
+<span class='va'>f_mmkin</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Sun Nov 8 02:58:03 2020"
+#&gt; ....
+#&gt; Minimisation finished
+#&gt; [1] "Sun Nov 8 02:58:07 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
+#&gt; mkin version used for pre-fitting: 0.9.50.4
+#&gt; R version used for fitting: 4.0.3
+#&gt; Date of fit: Sun Nov 8 02:58:07 2020
+#&gt; Date of summary: Sun Nov 8 02:58:07 2020
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt;
+#&gt; Data:
+#&gt; 90 observations of 1 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Model predictions using solution type analytical
+#&gt;
+#&gt; Fitted in 4.175 s using 300, 100 iterations
+#&gt;
+#&gt; Variance model: Two-component variance function
+#&gt;
+#&gt; Mean of starting values for individual parameters:
+#&gt; parent_0 log_k_parent
+#&gt; 97.849556 -4.455036
+#&gt;
+#&gt; Fixed degradation parameter values:
+#&gt; None
+#&gt;
+#&gt; Results:
+#&gt;
+#&gt; Likelihood computed by importance sampling
+#&gt; AIC BIC logLik
+#&gt; 555.6718 553.3284 -271.8359
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; est. lower upper
+#&gt; parent_0 97.840291 94.701895 100.978686
+#&gt; log_k_parent -4.464246 -5.001413 -3.927078
+#&gt;
+#&gt; Correlation:
+#&gt; prnt_0
+#&gt; log_k_parent 0.022
+#&gt;
+#&gt; Random effects:
+#&gt; est. lower upper
+#&gt; SD.parent_0 3.0805465 0.4960170 5.6650760
+#&gt; SD.log_k_parent 0.6109508 0.2301398 0.9917617
+#&gt;
+#&gt; Variance model:
+#&gt; est. lower upper
+#&gt; a.1 1.06249961 0.23012265 1.89487657
+#&gt; b.1 0.04649661 0.03060849 0.06238473
+#&gt;
+#&gt; Backtransformed parameters with asymmetric confidence intervals:
+#&gt; est. lower upper
+#&gt; parent_0 97.84029088 94.701895315 100.97868644
+#&gt; k_parent 0.01151338 0.006728434 0.01970115
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 60.2 200
+#&gt;
+#&gt; Data:
+#&gt; ds name time observed predicted residual standardized
+#&gt; ds 1 parent 0 103.6 97.303 6.297361 -1.12720
+#&gt; ds 1 parent 0 95.9 97.303 -1.402639 0.25107
+#&gt; ds 1 parent 1 95.4 96.599 -1.198705 0.21583
+#&gt; ds 1 parent 1 95.3 96.599 -1.298705 0.23383
+#&gt; ds 1 parent 3 91.6 95.206 -3.606076 0.65693
+#&gt; ds 1 parent 3 94.5 95.206 -0.706076 0.12863
+#&gt; ds 1 parent 7 88.1 92.481 -4.380761 0.81692
+#&gt; ds 1 parent 7 89.6 92.481 -2.880761 0.53720
+#&gt; ds 1 parent 14 90.3 87.898 2.402166 -0.46649
+#&gt; ds 1 parent 14 96.0 87.898 8.102166 -1.57340
+#&gt; ds 1 parent 28 80.2 79.402 0.797948 -0.16783
+#&gt; ds 1 parent 28 77.9 79.402 -1.502052 0.31593
+#&gt; ds 1 parent 60 59.3 62.940 -3.639829 0.91247
+#&gt; ds 1 parent 60 59.6 62.940 -3.339829 0.83726
+#&gt; ds 1 parent 90 59.4 50.620 8.779547 -2.56999
+#&gt; ds 1 parent 90 51.0 50.620 0.379547 -0.11110
+#&gt; ds 1 parent 120 38.8 40.712 -1.912380 0.64706
+#&gt; ds 1 parent 120 38.9 40.712 -1.812380 0.61323
+#&gt; ds 2 parent 0 103.2 97.185 6.015158 -1.07774
+#&gt; ds 2 parent 0 95.1 97.185 -2.084842 0.37354
+#&gt; ds 2 parent 1 88.3 95.609 -7.309466 1.32706
+#&gt; ds 2 parent 1 102.4 95.609 6.790534 -1.23285
+#&gt; ds 2 parent 3 88.4 92.535 -4.134911 0.77071
+#&gt; ds 2 parent 3 95.2 92.535 2.665089 -0.49675
+#&gt; ds 2 parent 7 83.5 86.679 -3.179231 0.62426
+#&gt; ds 2 parent 7 96.4 86.679 9.720769 -1.90873
+#&gt; ds 2 parent 14 77.3 77.309 -0.009268 0.00199
+#&gt; ds 2 parent 14 76.0 77.309 -1.309268 0.28113
+#&gt; ds 2 parent 28 61.7 61.499 0.201491 -0.05137
+#&gt; ds 2 parent 28 56.5 61.499 -4.998509 1.27449
+#&gt; ds 2 parent 60 35.1 36.454 -1.353571 0.49087
+#&gt; ds 2 parent 60 32.2 36.454 -4.253571 1.54256
+#&gt; ds 2 parent 90 21.2 22.326 -1.125996 0.53604
+#&gt; ds 2 parent 90 23.3 22.326 0.974004 -0.46368
+#&gt; ds 2 parent 120 14.1 13.674 0.426440 -0.25110
+#&gt; ds 2 parent 120 16.9 13.674 3.226440 -1.89983
+#&gt; ds 3 parent 0 92.4 93.838 -1.437848 0.26501
+#&gt; ds 3 parent 0 94.0 93.838 0.162152 -0.02989
+#&gt; ds 3 parent 1 95.7 91.709 3.991384 -0.74932
+#&gt; ds 3 parent 1 90.8 91.709 -0.908616 0.17058
+#&gt; ds 3 parent 3 86.7 87.594 -0.893997 0.17409
+#&gt; ds 3 parent 3 85.8 87.594 -1.793997 0.34934
+#&gt; ds 3 parent 7 77.1 79.910 -2.810299 0.58817
+#&gt; ds 3 parent 7 81.5 79.910 1.589701 -0.33271
+#&gt; ds 3 parent 14 69.1 68.050 1.050102 -0.24845
+#&gt; ds 3 parent 14 62.4 68.050 -5.649898 1.33675
+#&gt; ds 3 parent 28 49.1 49.349 -0.248837 0.07412
+#&gt; ds 3 parent 28 47.2 49.349 -2.148837 0.64010
+#&gt; ds 3 parent 60 21.9 23.676 -1.775776 0.82085
+#&gt; ds 3 parent 60 23.6 23.676 -0.075776 0.03503
+#&gt; ds 3 parent 90 12.4 11.892 0.507660 -0.31425
+#&gt; ds 3 parent 90 13.8 11.892 1.907660 -1.18088
+#&gt; ds 3 parent 120 4.9 5.974 -1.073521 0.80099
+#&gt; ds 3 parent 120 7.5 5.974 1.526479 -1.13895
+#&gt; ds 4 parent 0 91.8 102.087 -10.287197 1.77084
+#&gt; ds 4 parent 0 104.6 102.087 2.512803 -0.43256
+#&gt; ds 4 parent 1 117.5 101.632 15.867689 -2.74145
+#&gt; ds 4 parent 1 99.3 101.632 -2.332311 0.40295
+#&gt; ds 4 parent 3 94.0 100.729 -6.728610 1.17100
+#&gt; ds 4 parent 3 98.7 100.729 -2.028610 0.35304
+#&gt; ds 4 parent 7 109.2 98.945 10.254756 -1.81080
+#&gt; ds 4 parent 7 89.2 98.945 -9.745244 1.72083
+#&gt; ds 4 parent 14 103.3 95.900 7.400009 -1.34021
+#&gt; ds 4 parent 14 103.0 95.900 7.100009 -1.28588
+#&gt; ds 4 parent 28 90.8 90.088 0.712227 -0.13563
+#&gt; ds 4 parent 28 88.7 90.088 -1.387773 0.26427
+#&gt; ds 4 parent 60 74.8 78.091 -3.291273 0.70124
+#&gt; ds 4 parent 60 75.3 78.091 -2.791273 0.59471
+#&gt; ds 4 parent 90 71.1 68.300 2.800407 -0.66075
+#&gt; ds 4 parent 90 78.0 68.300 9.700407 -2.28880
+#&gt; ds 4 parent 120 59.1 59.736 -0.635668 0.16554
+#&gt; ds 4 parent 120 53.8 59.736 -5.935668 1.54574
+#&gt; ds 5 parent 0 94.9 98.353 -3.452694 0.61266
+#&gt; ds 5 parent 0 101.8 98.353 3.447306 -0.61171
+#&gt; ds 5 parent 1 96.1 96.722 -0.621996 0.11187
+#&gt; ds 5 parent 1 97.1 96.722 0.378004 -0.06799
+#&gt; ds 5 parent 3 93.8 93.541 0.258738 -0.04781
+#&gt; ds 5 parent 3 85.8 93.541 -7.741262 1.43043
+#&gt; ds 5 parent 7 87.6 87.490 0.109848 -0.02141
+#&gt; ds 5 parent 7 94.0 87.490 6.509848 -1.26885
+#&gt; ds 5 parent 14 82.5 77.827 4.672679 -0.99818
+#&gt; ds 5 parent 14 81.7 77.827 3.872679 -0.82728
+#&gt; ds 5 parent 28 60.0 61.585 -1.585419 0.40382
+#&gt; ds 5 parent 28 61.0 61.585 -0.585419 0.14911
+#&gt; ds 5 parent 60 32.5 36.068 -3.568284 1.30251
+#&gt; ds 5 parent 60 35.5 36.068 -0.568284 0.20744
+#&gt; ds 5 parent 90 21.8 21.842 -0.042136 0.02028
+#&gt; ds 5 parent 90 24.4 21.842 2.557864 -1.23088
+#&gt; ds 5 parent 120 14.1 13.227 0.872898 -0.52035
+#&gt; ds 5 parent 120 12.1 13.227 -1.127102 0.67189</div><div class='input'><span class='co'># }</span>
+
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top">
+ <h2 data-toc-skip>Contents</h2>
+ </nav>
+ </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> 1.6.1.</p>
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+ </body>
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diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index c5f285f1..d9ef2228 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -190,6 +190,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html</loc>
</url>
<url>

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