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-rw-r--r--_pkgdown.yml2
-rw-r--r--docs/dev/articles/web_only/multistart.html2
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.pngbin61772 -> 59606 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.pngbin56540 -> 55167 bytes
-rw-r--r--docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.pngbin39866 -> 21474 bytes
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/anova.saem.mmkin.html161
-rw-r--r--docs/dev/reference/index.html14
-rw-r--r--docs/dev/reference/llhist.html15
-rw-r--r--docs/dev/reference/logLik.saem.mmkin.html135
-rw-r--r--docs/dev/reference/multistart-1.pngbin0 -> 59254 bytes
-rw-r--r--docs/dev/reference/multistart-2.pngbin0 -> 54149 bytes
-rw-r--r--docs/dev/reference/multistart.html31
-rw-r--r--docs/dev/reference/parhist.html28
-rw-r--r--docs/dev/reference/saem.html133
-rw-r--r--docs/dev/reference/set_nd_nq.html258
-rw-r--r--docs/dev/sitemap.xml9
-rw-r--r--tests/testthat/test_multistart.R24
18 files changed, 741 insertions, 73 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e2b2c0c3..6a357e05 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -53,6 +53,8 @@ reference:
- plot.mixed.mmkin
- summary.nlme.mmkin
- summary.saem.mmkin
+ - anova.saem.mmkin
+ - logLik.saem.mmkin
- nlme_function
- get_deg_func
- saemix_model
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index 8d26e55a..4af5def0 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -109,7 +109,7 @@
<h1 data-toc-skip>Short demo of the multistart method</h1>
<h4 data-toc-skip class="author">Johannes Ranke</h4>
- <h4 data-toc-skip class="date">Last change 19 September 2022 (rebuilt 2022-09-28)</h4>
+ <h4 data-toc-skip class="date">Last change 19 September 2022 (rebuilt 2022-10-26)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small>
<div class="hidden name"><code>multistart.rmd</code></div>
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png
index 18800fb9..e3baa59b 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png
Binary files differ
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index 908989e9..d32e1214 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
Binary files differ
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index e50177cc..d72722f0 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
Binary files differ
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 22ed5aa7..c0cb9f4c 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
compiled_models: web_only/compiled_models.html
dimethenamid_2018: web_only/dimethenamid_2018.html
multistart: web_only/multistart.html
-last_built: 2022-09-30T10:35Z
+last_built: 2022-10-26T07:25Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html
new file mode 100644
index 00000000..abe77c65
--- /dev/null
+++ b/docs/dev/reference/anova.saem.mmkin.html
@@ -0,0 +1,161 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Anova method for saem.mmkin objects — anova.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="Anova method for saem.mmkin objects — anova.saem.mmkin"><meta property="og:description" content="Generate an anova object. The method to calculate the BIC is that from
+the saemix package. As in other prominent anova methods, models are sorted"><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><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
+
+ <div class="container template-reference-topic">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav"><li>
+ <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu"><li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
+ <span class="fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Anova method for saem.mmkin objects</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/anova.saem.mmkin.R" class="external-link"><code>R/anova.saem.mmkin.R</code></a></small>
+ <div class="hidden name"><code>anova.saem.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Generate an anova object. The method to calculate the BIC is that from
+the saemix package. As in other prominent anova methods, models are sorted</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span>
+<span> <span class="va">object</span>,</span>
+<span> <span class="va">...</span>,</span>
+<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"is"</span>, <span class="st">"lin"</span>, <span class="st">"gq"</span><span class="op">)</span>,</span>
+<span> test <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span> model.names <span class="op">=</span> <span class="cn">NULL</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>An <a href="saem.html">saem.mmkin</a> object</p></dd>
+
+
+<dt>...</dt>
+<dd><p>further such objects</p></dd>
+
+
+<dt>method</dt>
+<dd><p>Method for likelihood calculation: "is" (importance sampling),
+"lin" (linear approximation), or "gq" (Gaussian quadrature). Passed
+to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd>
+
+
+<dt>test</dt>
+<dd><p>Should a likelihood ratio test be performed? If TRUE,
+the alternative models are tested against the first model. Should
+only be done for nested models.</p></dd>
+
+
+<dt>model.names</dt>
+<dd><p>Optional character vector of model names</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>an "anova" data frame; the traditional (S3) result of anova()</p>
+ </div>
+
+ </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></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index cbd44762..3d9d40b7 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -217,6 +217,14 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Summary method for class "saem.mmkin"</p></td>
</tr><tr><td>
+ <p><code><a href="anova.saem.mmkin.html">anova(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Anova method for saem.mmkin objects</p></td>
+ </tr><tr><td>
+ <p><code><a href="logLik.saem.mmkin.html">logLik(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>logLik method for saem.mmkin objects</p></td>
+ </tr><tr><td>
<p><code><a href="nlme.html">nlme_function()</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>
@@ -237,7 +245,7 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
</tr><tr><td>
- <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i>&lt;multistart&gt;</i>)</a></code> </p>
+ <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i>&lt;multistart&gt;</i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> </p>
</td>
<td><p>Perform a hierarchical model fit with multiple starting values</p></td>
</tr><tr><td>
@@ -341,6 +349,10 @@ degradation models and one or more error models</p></td>
</td>
<td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td>
</tr><tr><td>
+ <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p>
+ </td>
+ <td><p>Set non-detects and unquantified values in residue series without replicates</p></td>
+ </tr><tr><td>
<p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p>
</td>
<td><p>Function to calculate maximum time weighted average concentrations from
diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html
index 2eb77a82..e110416e 100644
--- a/docs/dev/reference/llhist.html
+++ b/docs/dev/reference/llhist.html
@@ -1,7 +1,6 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot the distribution of log likelihoods from multistart objects — llhist • 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="Plot the distribution of log likelihoods from multistart objects — llhist"><meta property="og:description" content="Produces a histogram of log-likelihoods, and an overlayed kernel density
-estimate. In addition, the likelihood of the original fit is shown as
-a red vertical line."><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><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot the distribution of log likelihoods from multistart objects — llhist • 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="Plot the distribution of log likelihoods from multistart objects — llhist"><meta property="og:description" content="Produces a histogram of log-likelihoods. In addition, the likelihood of the
+original fit is shown as a red vertical line."><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><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -46,12 +45,15 @@ a red vertical line."><meta name="robots" content="noindex"><!-- mathjax --><scr
<a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
@@ -85,9 +87,8 @@ a red vertical line."><meta name="robots" content="noindex"><!-- mathjax --><scr
</div>
<div class="ref-description">
- <p>Produces a histogram of log-likelihoods, and an overlayed kernel density
-estimate. In addition, the likelihood of the original fit is shown as
-a red vertical line.</p>
+ <p>Produces a histogram of log-likelihoods. In addition, the likelihood of the
+original fit is shown as a red vertical line.</p>
</div>
<div id="ref-usage">
diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html
new file mode 100644
index 00000000..9694232c
--- /dev/null
+++ b/docs/dev/reference/logLik.saem.mmkin.html
@@ -0,0 +1,135 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>logLik method for saem.mmkin objects — logLik.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="logLik method for saem.mmkin objects — logLik.saem.mmkin"><meta property="og:description" content="logLik method for saem.mmkin objects"><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><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
+
+ <div class="container template-reference-topic">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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+ </button>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
+ </span>
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+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav"><li>
+ <a href="../reference/index.html">Functions and data</a>
+</li>
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+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu"><li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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>
+ </li>
+ <li>
+ <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ </li>
+ </ul></li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
+ <span class="fab fa-github fa-lg"></span>
+
+ </a>
+</li>
+ </ul></div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header><div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>logLik method for saem.mmkin objects</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small>
+ <div class="hidden name"><code>logLik.saem.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>logLik method for saem.mmkin objects</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"lin"</span>, <span class="st">"is"</span>, <span class="st">"gq"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>object</dt>
+<dd><p>The fitted <a href="saem.html">saem.mmkin</a> object</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd>
+
+
+<dt>method</dt>
+<dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/logLik.html" class="external-link">saemix::logLik.SaemixObject</a></p></dd>
+
+</dl></div>
+
+ </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></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png
new file mode 100644
index 00000000..ee9c1b5a
--- /dev/null
+++ b/docs/dev/reference/multistart-1.png
Binary files differ
diff --git a/docs/dev/reference/multistart-2.png b/docs/dev/reference/multistart-2.png
new file mode 100644
index 00000000..e54938ab
--- /dev/null
+++ b/docs/dev/reference/multistart-2.png
Binary files differ
diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html
index 714cb2fc..83af8dbb 100644
--- a/docs/dev/reference/multistart.html
+++ b/docs/dev/reference/multistart.html
@@ -112,7 +112,17 @@ mixed-effects models by Duchesne et al (2021).</p>
<span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, cluster <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for multistart</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for default</span></span>
+<span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for default</span></span>
+<span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
@@ -149,6 +159,12 @@ for parallel execution.</p></dd>
<p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes
'multistart.saem.mmkin' and 'multistart'.</p>
+
+
+<p>The object with the highest likelihood</p>
+
+
+<p>The index of the object with the highest likelihood</p>
</div>
<div id="details">
<h2>Details</h2>
@@ -187,11 +203,14 @@ doi: 10.1186/s12859-021-04373-4.</p>
<span class="r-in"><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">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">f_saem_full</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></span></span>
<span class="r-in"><span><span class="va">f_saem_full_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>all scheduled cores encountered errors in user code</span>
<span class="r-in"><span><span class="fu"><a href="parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"bottomright"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in UseMethod("parms", object):</span> no applicable method for 'parms' applied to an object of class "try-error"</span>
+<span class="r-plt img"><img src="multistart-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(log_k2)"</span>
<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> character(0)</span>
<span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span>
<span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span>
<span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span>
@@ -200,10 +219,8 @@ doi: 10.1186/s12859-021-04373-4.</p>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">clusterExport</a></span><span class="op">(</span><span class="va">cl</span>, <span class="st">"f_mmkin"</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in get(name, envir = envir):</span> object 'f_mmkin' not found</span>
<span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in checkForRemoteErrors(val):</span> 12 nodes produced errors; first error: object 'f_mmkin' not found</span>
<span class="r-in"><span><span class="fu"><a href="parhist.html">parhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"bottomright"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in parhist(f_saem_reduced_multi, lpos = "bottomright"):</span> object 'f_saem_reduced_multi' not found</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>calling par(new=TRUE) with no plot</span>
+<span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
diff --git a/docs/dev/reference/parhist.html b/docs/dev/reference/parhist.html
index bc230c21..27fc116f 100644
--- a/docs/dev/reference/parhist.html
+++ b/docs/dev/reference/parhist.html
@@ -1,6 +1,7 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot parameter distributions from multistart objects — parhist • 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="Plot parameter distributions from multistart objects — parhist"><meta property="og:description" content="Produces a boxplot with all parameters from the multiple runs, divided by
-using their medians as in the paper by Duchesne et al. (2021)."><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><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Plot parameter distributions from multistart objects — parhist • 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="Plot parameter distributions from multistart objects — parhist"><meta property="og:description" content="Produces a boxplot with all parameters from the multiple runs, scaled
+either by the parameters of the run with the highest likelihood,
+or by their medians as proposed in the paper by Duchesne et al. (2021)."><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><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -87,12 +88,20 @@ using their medians as in the paper by Duchesne et al. (2021)."><meta name="robo
</div>
<div class="ref-description">
- <p>Produces a boxplot with all parameters from the multiple runs, divided by
-using their medians as in the paper by Duchesne et al. (2021).</p>
+ <p>Produces a boxplot with all parameters from the multiple runs, scaled
+either by the parameters of the run with the highest likelihood,
+or by their medians as proposed in the paper by Duchesne et al. (2021).</p>
</div>
<div id="ref-usage">
- <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parhist</span><span class="op">(</span><span class="va">object</span>, lpos <span class="op">=</span> <span class="st">"bottomleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parhist</span><span class="op">(</span></span>
+<span> <span class="va">object</span>,</span>
+<span> llmin <span class="op">=</span> <span class="op">-</span><span class="cn">Inf</span>,</span>
+<span> scale <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"best"</span>, <span class="st">"median"</span><span class="op">)</span>,</span>
+<span> lpos <span class="op">=</span> <span class="st">"bottomleft"</span>,</span>
+<span> main <span class="op">=</span> <span class="st">""</span>,</span>
+<span> <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
@@ -101,6 +110,15 @@ using their medians as in the paper by Duchesne et al. (2021).</p>
<dd><p>The <a href="multistart.html">multistart</a> object</p></dd>
+<dt>llmin</dt>
+<dd><p>The minimum likelihood of objects to be shown</p></dd>
+
+
+<dt>scale</dt>
+<dd><p>By default, scale parameters using the best available fit.
+If 'median', parameters are scaled using the median parameters from all fits.</p></dd>
+
+
<dt>lpos</dt>
<dd><p>Positioning of the legend.</p></dd>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index ce3d428c..c8a7504f 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -46,12 +46,15 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
<a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
@@ -101,6 +104,10 @@ Expectation Maximisation algorithm (SAEM).</p>
<span> test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
<span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span>
<span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span>
<span> save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
@@ -118,13 +125,17 @@ Expectation Maximisation algorithm (SAEM).</p>
<span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> transformations <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span>
<span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
-<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for saem.mmkin</span></span>
<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
@@ -171,6 +182,29 @@ for parameter that are tested if requested by 'test_log_parms'.</p></dd>
automatic choice is not desired</p></dd>
+<dt>covariance.model</dt>
+<dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel()</a></code>. Per
+default, uncorrelated random effects are specified for all degradation
+parameters.</p></dd>
+
+
+<dt>covariates</dt>
+<dd><p>A data frame with covariate data for use in
+'covariate_models', with dataset names as row names.</p></dd>
+
+
+<dt>covariate_models</dt>
+<dd><p>A list containing linear model formulas with one explanatory
+variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available
+in the 'covariates' data frame.</p></dd>
+
+
+<dt>no_random_effect</dt>
+<dd><p>Character vector of degradation parameters for
+which there should be no variability over the groups. Only used
+if the covariance model is not explicitly specified.</p></dd>
+
+
<dt>nbiter.saemix</dt>
<dd><p>Convenience option to increase the number of
iterations</p></dd>
@@ -249,40 +283,43 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-in"><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></span></span>
<span class="r-in"><span><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></span></span>
<span class="r-in"><span><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></span></span>
-<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(g_qlogis)"</span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by SAEM</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Structural model:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> * parent</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Data:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 90 observations of 1 variable(s) grouped in 5 datasets</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> npar AIC BIC Lik</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_sfo 5 624.26 622.31 -307.13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_fomc 7 467.87 465.13 -226.93</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop 9 493.98 490.47 -237.99</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_dfop</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> AIC BIC logLik</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 490.6 487.5 -237.3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> npar AIC BIC Lik Chisq Df Pr(&gt;Chisq) </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_sfo 5 624.26 622.31 -307.13 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop 9 493.98 490.47 -237.99 138.28 4 &lt; 2.2e-16 ***</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ---</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span>
+<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "sd(g_qlogis)"</span>
+<span class="r-in"><span><span class="va">f_saem_dfop_red</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, no_random_effect <span class="op">=</span> <span class="st">"g_qlogis"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, <span class="va">f_saem_dfop_red</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted parameters:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> estimate lower upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 93.902 91.3695 96.4339</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1 -2.936 -3.9950 -1.8762</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2 -3.091 -4.9290 -1.2523</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis -0.366 -0.6484 -0.0836</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 2.385 2.0033 2.7664</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0 2.476 0.3890 4.5623</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1 1.195 0.4381 1.9517</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2 2.092 0.7906 3.3932</span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 493.9811</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> npar AIC BIC Lik Chisq Df Pr(&gt;Chisq)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop_red 8 490.64 487.52 -237.32 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop 9 493.98 490.47 -237.99 0 1 1</span>
<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> npar AIC BIC Lik</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_sfo 5 624.26 622.31 -307.13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_fomc 7 467.87 465.13 -226.93</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_dfop 9 493.98 490.47 -237.99</span>
<span class="r-in"><span><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span></span>
<span class="r-in"><span><span class="co"># functions from saemix</span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: npde</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Package saemix, version 3.1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Package saemix, version 3.2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Attaching package: ‘saemix’</span>
@@ -308,11 +345,12 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-in"><span></span></span>
<span class="r-in"><span><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" class="external-link">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></span>
<span class="r-in"><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></span></span>
-<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</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></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Likelihoods calculated by importance sampling</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> AIC BIC</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 467.8664 465.1324</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 469.8018 466.6773</span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_fomc</span>, <span class="va">f_saem_fomc_tc</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> npar AIC BIC Lik Chisq Df Pr(&gt;Chisq)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_fomc 7 467.87 465.13 -226.93 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_saem_fomc_tc 8 469.80 466.68 -226.90 0.0645 1 0.7995</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sfo_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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
@@ -370,11 +408,11 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting: 3.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting: 3.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.1.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Fri Sep 16 10:30:47 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Sep 16 10:30:47 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Oct 26 09:20:37 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Oct 26 09:20:37 2022 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -389,7 +427,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.651 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 8.902 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
@@ -410,13 +448,20 @@ using <a href="mmkin.html">mmkin</a>.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> 842 836.9 -408</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Optimised parameters:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> est. lower upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 93.7701 91.1458 96.3945</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_A1 -5.8116 -7.5998 -4.0234</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1 -2.5841 -3.6876 -1.4805</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2 -3.5228 -5.3254 -1.7203</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis -0.1027 -0.8719 0.6665</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> est. lower upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 93.7701 91.1458 96.3945</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_A1 -5.8116 -7.5998 -4.0234</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1 -2.5841 -3.6876 -1.4805</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2 -3.5228 -5.3254 -1.7203</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis -0.1027 -0.8719 0.6665</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 1.8856 1.6676 2.1037</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.parent_0 2.7682 0.7668 4.7695</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_A1 1.7447 0.4047 3.0848</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k1 1.2423 0.4560 2.0285</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k2 2.0390 0.7601 3.3180</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.g_qlogis 0.4439 -0.3069 1.1947</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Correlation: </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parnt_0 lg_k_A1 f_prnt_ log_k1 log_k2 </span>
diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html
new file mode 100644
index 00000000..26a28339
--- /dev/null
+++ b/docs/dev/reference/set_nd_nq.html
@@ -0,0 +1,258 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Set non-detects and unquantified values in residue series without replicates — set_nd_nq • 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="Set non-detects and unquantified values in residue series without replicates — set_nd_nq"><meta property="og:description" content="This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015)."><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><!--[if lt IE 9]>
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Set non-detects and unquantified values in residue series without replicates</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/set_nd_nq.R" class="external-link"><code>R/set_nd_nq.R</code></a></small>
+ <div class="hidden name"><code>set_nd_nq.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015).</p>
+ </div>
+
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">res_raw</span>, <span class="va">lod</span>, loq <span class="op">=</span> <span class="cn">NA</span>, time_zero_presence <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">set_nd_nq_focus</span><span class="op">(</span></span>
+<span> <span class="va">res_raw</span>,</span>
+<span> <span class="va">lod</span>,</span>
+<span> loq <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span> set_first_sample_nd <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> first_sample_nd_value <span class="op">=</span> <span class="fl">0</span>,</span>
+<span> ignore_below_loq_after_first_nd <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>res_raw</dt>
+<dd><p>Character vector of a residue time series, or matrix of
+residue values with rows representing depth profiles for a specific sampling
+time, and columns representing time series of residues at the same depth.
+Values below the limit of detection (lod) have to be coded as "nd", values
+between the limit of detection and the limit of quantification, if any, have
+to be coded as "nq". Samples not analysed have to be coded as "na". All
+values that are not "na", "nd" or "nq" have to be coercible to numeric</p></dd>
+
+
+<dt>lod</dt>
+<dd><p>Limit of detection (numeric)</p></dd>
+
+
+<dt>loq</dt>
+<dd><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to
+stop after the first non-detection is to be applied</p></dd>
+
+
+<dt>time_zero_presence</dt>
+<dd><p>Do we assume that residues occur at time zero?
+This only affects samples from the first sampling time that have been
+reported as "nd" (not detected).</p></dd>
+
+
+<dt>set_first_sample_nd</dt>
+<dd><p>Should the first sample be set to "first_sample_nd_value"
+in case it is a non-detection?</p></dd>
+
+
+<dt>first_sample_nd_value</dt>
+<dd><p>Value to be used for the first sample if it is a non-detection</p></dd>
+
+
+<dt>ignore_below_loq_after_first_nd</dt>
+<dd><p>Should we ignore values below the LOQ after the first
+non-detection that occurs after the quantified values?</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p>
+ </div>
+ <div id="functions">
+ <h2>Functions</h2>
+
+<ul><li><p><code>set_nd_nq_focus()</code>: Set non-detects in residue time series according to FOCUS rules</p></li>
+</ul></div>
+ <div id="references">
+ <h2>References</h2>
+ <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
+J. and Pol, J. W. (2015). Leaching of plant protection products and their
+transformation products; Proposals for improving the assessment of leaching
+to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
+Wageningen UR (University &amp; Research centre)</p>
+<p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
+18 December 2014, p. 251</p>
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># FOCUS (2014) p. 75/76 and 131/132</span></span></span>
+<span class="r-in"><span><span class="va">parent_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_1</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span>
+<span class="r-in"><span><span class="va">parent_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA</span>
+<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_2</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA</span>
+<span class="r-in"><span><span class="va">parent_3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">.06</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span>
+<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">parent_3</span>, <span class="fl">0.02</span>, loq <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA</span>
+<span class="r-in"><span><span class="va">metabolite</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="fl">0.03</span>, <span class="fl">0.06</span>, <span class="fl">0.10</span>, <span class="fl">0.11</span>, <span class="fl">0.10</span>, <span class="fl">0.09</span>, <span class="fl">0.05</span>, <span class="fl">0.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span>
+<span class="r-in"><span><span class="fu">set_nd_nq_focus</span><span class="op">(</span><span class="va">metabolite</span>, <span class="fl">0.02</span>, <span class="fl">0.05</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.00 NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA</span>
+<span class="r-in"><span><span class="co">#</span></span></span>
+<span class="r-in"><span><span class="co"># Boesten et al. (2015), p. 57/58</span></span></span>
+<span class="r-in"><span><span class="va">table_8</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nq"</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">2</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fl">10</span>, <span class="st">"nq"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>,</span></span>
+<span class="r-in"><span> <span class="st">"nq"</span>, <span class="fl">10</span>, <span class="st">"nq"</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="st">"nd"</span>, <span class="st">"nq"</span>, <span class="st">"nq"</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">6</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_8</span>, <span class="fl">0.5</span>, <span class="fl">1.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [,1] [,2] [,3] [,4] [,5] [,6]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1,] 10.00 10.00 0.25 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [2,] 10.00 10.00 1.00 1.00 0.25 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [3,] 10.00 10.00 10.00 1.00 0.25 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [4,] 1.00 10.00 1.00 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [5,] 0.25 1.00 1.00 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [6,] NA 0.25 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [7,] NA NA NA NA NA NA</span>
+<span class="r-in"><span><span class="va">table_10</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fl">10</span>, <span class="fl">10</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="st">"nd"</span>, <span class="fl">10</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">4</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"nd"</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">6</span>, byrow <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">table_10</span>, <span class="fl">0.5</span>, time_zero_presence <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [,1] [,2] [,3] [,4] [,5] [,6]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1,] 10.00 10.00 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [2,] 10.00 10.00 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [3,] 10.00 10.00 10.00 0.25 NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [4,] 0.25 10.00 0.25 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [5,] NA 0.25 NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [6,] NA NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [7,] NA NA NA NA NA NA</span>
+</code></pre></div>
+ </div>
+ </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></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+ </footer></div>
+
+
+
+
+
+
+ </body></html>
+
diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index 5ba14939..86bf9185 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -100,6 +100,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/add_err.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/anova.saem.mmkin.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/aw.html</loc>
</url>
<url>
@@ -154,6 +157,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/logLik.saem.mmkin.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html</loc>
</url>
<url>
@@ -265,6 +271,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html</loc>
</url>
<url>
diff --git a/tests/testthat/test_multistart.R b/tests/testthat/test_multistart.R
index e5b44e78..e4885191 100644
--- a/tests/testthat/test_multistart.R
+++ b/tests/testthat/test_multistart.R
@@ -4,20 +4,30 @@ test_that("multistart works for saem.mmkin models", {
set.seed(123456)
saem_sfo_s_multi <- multistart(sfo_saem_1_reduced, n = 8, cores = n_cores,
no_random_effect = "parent_0")
+ anova_sfo <- anova(sfo_saem_1,
+ sfo_saem_1_reduced,
+ best(saem_sfo_s_multi),
+ test = TRUE
+ )
+ expect_true(anova_sfo[3, "Pr(>Chisq)"] > 0.5)
- llhist_sfo <- function() llhist(saem_sfo_s_multi)
- parhist_sfo <- function() parhist(saem_sfo_s_multi, ylim = c(0.5, 2))
- vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo)
- vdiffr::expect_doppelganger("parhist for sfo fit", parhist_sfo)
-
+ skip_on_cran() # Save CRAN time
set.seed(123456)
saem_biphasic_m_multi <- multistart(saem_biphasic_m, n = 8,
cores = n_cores)
expect_known_output(print(saem_biphasic_m_multi),
file = "print_multistart_biphasic.txt")
- skip_on_cran()
- skip_on_travis()
+ anova_biphasic <- anova(saem_biphasic_m,
+ best(saem_biphasic_m_multi))
+
+ expect_true(anova_biphasic[2, "AIC"] < anova_biphasic[1, "AIC"])
+ skip_on_travis() # Plots are platform dependent
+
+ llhist_sfo <- function() llhist(saem_sfo_s_multi)
+ parhist_sfo <- function() parhist(saem_sfo_s_multi, ylim = c(0.5, 2))
+ vdiffr::expect_doppelganger("llhist for sfo fit", llhist_sfo)
+ vdiffr::expect_doppelganger("parhist for sfo fit", parhist_sfo)
llhist_biphasic <- function() llhist(saem_biphasic_m_multi)
parhist_biphasic <- function() parhist(saem_biphasic_m_multi,

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