aboutsummaryrefslogtreecommitdiff
path: root/docs/dev/reference/saemix.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
commita77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
treee91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/saemix.html
parent675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/saemix.html')
-rw-r--r--docs/dev/reference/saemix.html446
1 files changed, 446 insertions, 0 deletions
diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html
new file mode 100644
index 00000000..ad16a81b
--- /dev/null
+++ b/docs/dev/reference/saemix.html
@@ -0,0 +1,446 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Create saemix models from mmkin row objects — saemix_model • 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="Create saemix models from mmkin row objects — saemix_model" />
+<meta property="og:description" content="This function sets up a nonlinear mixed effects model for an mmkin row
+object for use with the saemix package. An mmkin row object is essentially a
+list of mkinfit objects that have been obtained by fitting the same model to
+a list of datasets." />
+
+
+<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-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ Articles
+
+ <span class="caret"></span>
+ </a>
+ <ul class="dropdown-menu" role="menu">
+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <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="http://github.com/jranke/mkin/">
+ <span class="fab fa 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>Create saemix models from mmkin row objects</h1>
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small>
+ <div class="hidden name"><code>saemix.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>This function sets up a nonlinear mixed effects model for an mmkin row
+object for use with the saemix package. An mmkin row object is essentially a
+list of mkinfit objects that have been obtained by fitting the same model to
+a list of datasets.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>saemix_model</span>(<span class='no'>object</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>())
+
+<span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>An mmkin row object containing several fits of the same model to different datasets</p></td>
+ </tr>
+ <tr>
+ <th>cores</th>
+ <td><p>The number of cores to be used for multicore processing.
+On Windows machines, cores &gt; 1 is currently not supported.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Further parameters passed to <a href='https://rdrr.io/pkg/saemix/man/saemixData.html'>saemix::saemixData</a></p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p>
+<p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Starting values for the fixed effects (population mean parameters, argument psi0 of
+<code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::saemixModel()</a></code> are the mean values of the parameters found using
+mmkin. Starting variances of the random effects (argument omega.init) are the
+variances of the deviations of the parameters from these mean values.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
+ <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]))
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>)
+<span class='no'>sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>),
+ <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># \dontrun{</span>
+<span class='no'>f_mmkin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_sfo</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>saemix</span>)</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
+#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='no'>m_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt;
+#&gt;
+#&gt; The following SaemixModel object was successfully created:
+#&gt;
+#&gt; Nonlinear mixed-effects model
+#&gt; Model function: Mixed model generated from mmkin object Model type: structural
+#&gt; function (psi, id, xidep)
+#&gt; {
+#&gt; uid &lt;- unique(id)
+#&gt; res_list &lt;- parallel::mclapply(uid, function(i) {
+#&gt; transparms_optim &lt;- psi[i, ]
+#&gt; names(transparms_optim) &lt;- names(degparms_optim)
+#&gt; odeini_optim &lt;- transparms_optim[odeini_optim_parm_names]
+#&gt; names(odeini_optim) &lt;- gsub("_0$", "", odeini_optim_parm_names)
+#&gt; odeini &lt;- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+#&gt; ode_transparms_optim_names &lt;- setdiff(names(transparms_optim),
+#&gt; odeini_optim_parm_names)
+#&gt; odeparms_optim &lt;- backtransform_odeparms(transparms_optim[ode_transparms_optim_names],
+#&gt; mkin_model, transform_rates = object[[1]]$transform_rates,
+#&gt; transform_fractions = object[[1]]$transform_fractions)
+#&gt; odeparms &lt;- c(odeparms_optim, odeparms_fixed)
+#&gt; xidep_i &lt;- subset(xidep, id == i)
+#&gt; if (analytical) {
+#&gt; out_values &lt;- mkin_model$deg_func(xidep_i, odeini,
+#&gt; odeparms)
+#&gt; }
+#&gt; else {
+#&gt; i_time &lt;- xidep_i$time
+#&gt; i_name &lt;- xidep_i$name
+#&gt; out_wide &lt;- mkinpredict(mkin_model, odeparms = odeparms,
+#&gt; odeini = odeini, solution_type = object[[1]]$solution_type,
+#&gt; outtimes = sort(unique(i_time)))
+#&gt; out_index &lt;- cbind(as.character(i_time), as.character(i_name))
+#&gt; out_values &lt;- out_wide[out_index]
+#&gt; }
+#&gt; return(out_values)
+#&gt; }, mc.cores = cores)
+#&gt; res &lt;- unlist(res_list)
+#&gt; return(res)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555e4213d8&gt;
+#&gt; &lt;environment: 0x55555c47cdf0&gt;
+#&gt; Nb of parameters: 4
+#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
+#&gt; distribution:
+#&gt; Parameter Distribution Estimated
+#&gt; [1,] parent_0 normal Estimated
+#&gt; [2,] log_k_parent normal Estimated
+#&gt; [3,] log_k_A1 normal Estimated
+#&gt; [4,] f_parent_ilr_1 normal Estimated
+#&gt; Variance-covariance matrix:
+#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
+#&gt; parent_0 1 0 0 0
+#&gt; log_k_parent 0 1 0 0
+#&gt; log_k_A1 0 0 1 0
+#&gt; f_parent_ilr_1 0 0 0 1
+#&gt; Error model: constant , initial values: a.1=1
+#&gt; No covariate in the model.
+#&gt; Initial values
+#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
+#&gt; Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='no'>d_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt;
+#&gt;
+#&gt; The following SaemixData object was successfully created:
+#&gt;
+#&gt; Object of class SaemixData
+#&gt; longitudinal data for use with the SAEM algorithm
+#&gt; Dataset ds_saemix
+#&gt; Structured data: value ~ time + name | ds
+#&gt; X variable for graphs: time () </div><div class='input'><span class='no'>saemix_options</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>,
+ <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>displayProgress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>nbiter.saemix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>200</span>, <span class='fl'>80</span>))
+<span class='no'>f_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>)</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Wed May 27 05:55:50 2020"
+#&gt; ..
+#&gt; Minimisation finished
+#&gt; [1] "Wed May 27 06:01:54 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
+#&gt; -----------------------------------
+#&gt; ---- Data ----
+#&gt; -----------------------------------
+#&gt; Object of class SaemixData
+#&gt; longitudinal data for use with the SAEM algorithm
+#&gt; Dataset ds_saemix
+#&gt; Structured data: value ~ time + name | ds
+#&gt; X variable for graphs: time ()
+#&gt; Dataset characteristics:
+#&gt; number of subjects: 5
+#&gt; number of observations: 170
+#&gt; average/min/max nb obs: 34.00 / 30 / 38
+#&gt; First 10 lines of data:
+#&gt; ds time name value mdv cens occ ytype
+#&gt; 1 Dataset 6 0 parent 97.2 0 0 1 1
+#&gt; 2 Dataset 6 0 parent 96.4 0 0 1 1
+#&gt; 3 Dataset 6 3 parent 71.1 0 0 1 1
+#&gt; 4 Dataset 6 3 parent 69.2 0 0 1 1
+#&gt; 5 Dataset 6 6 parent 58.1 0 0 1 1
+#&gt; 6 Dataset 6 6 parent 56.6 0 0 1 1
+#&gt; 7 Dataset 6 10 parent 44.4 0 0 1 1
+#&gt; 8 Dataset 6 10 parent 43.4 0 0 1 1
+#&gt; 9 Dataset 6 20 parent 33.3 0 0 1 1
+#&gt; 10 Dataset 6 20 parent 29.2 0 0 1 1
+#&gt; -----------------------------------
+#&gt; ---- Model ----
+#&gt; -----------------------------------
+#&gt; Nonlinear mixed-effects model
+#&gt; Model function: Mixed model generated from mmkin object Model type: structural
+#&gt; function (psi, id, xidep)
+#&gt; {
+#&gt; uid &lt;- unique(id)
+#&gt; res_list &lt;- parallel::mclapply(uid, function(i) {
+#&gt; transparms_optim &lt;- psi[i, ]
+#&gt; names(transparms_optim) &lt;- names(degparms_optim)
+#&gt; odeini_optim &lt;- transparms_optim[odeini_optim_parm_names]
+#&gt; names(odeini_optim) &lt;- gsub("_0$", "", odeini_optim_parm_names)
+#&gt; odeini &lt;- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+#&gt; ode_transparms_optim_names &lt;- setdiff(names(transparms_optim),
+#&gt; odeini_optim_parm_names)
+#&gt; odeparms_optim &lt;- backtransform_odeparms(transparms_optim[ode_transparms_optim_names],
+#&gt; mkin_model, transform_rates = object[[1]]$transform_rates,
+#&gt; transform_fractions = object[[1]]$transform_fractions)
+#&gt; odeparms &lt;- c(odeparms_optim, odeparms_fixed)
+#&gt; xidep_i &lt;- subset(xidep, id == i)
+#&gt; if (analytical) {
+#&gt; out_values &lt;- mkin_model$deg_func(xidep_i, odeini,
+#&gt; odeparms)
+#&gt; }
+#&gt; else {
+#&gt; i_time &lt;- xidep_i$time
+#&gt; i_name &lt;- xidep_i$name
+#&gt; out_wide &lt;- mkinpredict(mkin_model, odeparms = odeparms,
+#&gt; odeini = odeini, solution_type = object[[1]]$solution_type,
+#&gt; outtimes = sort(unique(i_time)))
+#&gt; out_index &lt;- cbind(as.character(i_time), as.character(i_name))
+#&gt; out_values &lt;- out_wide[out_index]
+#&gt; }
+#&gt; return(out_values)
+#&gt; }, mc.cores = cores)
+#&gt; res &lt;- unlist(res_list)
+#&gt; return(res)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555e4213d8&gt;
+#&gt; &lt;environment: 0x55555c47cdf0&gt;
+#&gt; Nb of parameters: 4
+#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
+#&gt; distribution:
+#&gt; Parameter Distribution Estimated
+#&gt; [1,] parent_0 normal Estimated
+#&gt; [2,] log_k_parent normal Estimated
+#&gt; [3,] log_k_A1 normal Estimated
+#&gt; [4,] f_parent_ilr_1 normal Estimated
+#&gt; Variance-covariance matrix:
+#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
+#&gt; parent_0 1 0 0 0
+#&gt; log_k_parent 0 1 0 0
+#&gt; log_k_A1 0 0 1 0
+#&gt; f_parent_ilr_1 0 0 0 1
+#&gt; Error model: constant , initial values: a.1=1
+#&gt; No covariate in the model.
+#&gt; Initial values
+#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
+#&gt; Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449
+#&gt; -----------------------------------
+#&gt; ---- Key algorithm options ----
+#&gt; -----------------------------------
+#&gt; Estimation of individual parameters (MAP)
+#&gt; Estimation of standard errors and linearised log-likelihood
+#&gt; Estimation of log-likelihood by importance sampling
+#&gt; Number of iterations: K1=200, K2=80
+#&gt; Number of chains: 10
+#&gt; Seed: 123456
+#&gt; Number of MCMC iterations for IS: 5000
+#&gt; Simulations:
+#&gt; nb of simulated datasets used for npde: 1000
+#&gt; nb of simulated datasets used for VPC: 100
+#&gt; Input/output
+#&gt; save the results to a file: FALSE
+#&gt; save the graphs to files: FALSE
+#&gt; ----------------------------------------------------
+#&gt; ---- Results ----
+#&gt; ----------------------------------------------------
+#&gt; ----------------- Fixed effects ------------------
+#&gt; ----------------------------------------------------
+#&gt; Parameter Estimate SE CV(%)
+#&gt; [1,] parent_0 86.14 1.61 1.9
+#&gt; [2,] log_k_parent -3.21 0.59 18.5
+#&gt; [3,] log_k_A1 -4.66 0.30 6.4
+#&gt; [4,] f_parent_ilr_1 -0.33 0.30 91.7
+#&gt; [5,] a.1 4.68 0.27 5.8
+#&gt; ----------------------------------------------------
+#&gt; ----------- Variance of random effects -----------
+#&gt; ----------------------------------------------------
+#&gt; Parameter Estimate SE CV(%)
+#&gt; parent_0 omega2.parent_0 7.71 8.14 106
+#&gt; log_k_parent omega2.log_k_parent 1.76 1.12 63
+#&gt; log_k_A1 omega2.log_k_A1 0.26 0.26 101
+#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.28 71
+#&gt; ----------------------------------------------------
+#&gt; ------ Correlation matrix of random effects ------
+#&gt; ----------------------------------------------------
+#&gt; omega2.parent_0 omega2.log_k_parent omega2.log_k_A1
+#&gt; omega2.parent_0 1 0 0
+#&gt; omega2.log_k_parent 0 1 0
+#&gt; omega2.log_k_A1 0 0 1
+#&gt; omega2.f_parent_ilr_1 0 0 0
+#&gt; omega2.f_parent_ilr_1
+#&gt; omega2.parent_0 0
+#&gt; omega2.log_k_parent 0
+#&gt; omega2.log_k_A1 0
+#&gt; omega2.f_parent_ilr_1 1
+#&gt; ----------------------------------------------------
+#&gt; --------------- Statistical criteria -------------
+#&gt; ----------------------------------------------------
+#&gt; Likelihood computed by linearisation
+#&gt; -2LL= 1064.364
+#&gt; AIC = 1082.364
+#&gt; BIC = 1078.848
+#&gt;
+#&gt; Likelihood computed by importance sampling
+#&gt; -2LL= 1063.462
+#&gt; AIC = 1081.462
+#&gt; BIC = 1077.947
+#&gt; ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span>(<span class='no'>f_saemix</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"convergence"</span>)</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'># }
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top">
+ <h2 data-toc-skip>Contents</h2>
+ </nav>
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+

Contact - Imprint