diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-08-10 16:04:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-08-10 16:04:48 +0200 |
| commit | fcef764f3688b01a4c6e92915ed68c5e54bc165f (patch) | |
| tree | 7d5f0b43485d2e99e1e0ea999d0ce47b6914839d /docs/dev/reference/summary.nlme.mmkin.html | |
| parent | bc8ce24677e953e003f7904564b7767537e01ca2 (diff) | |
| parent | 6178249bbb5e9de7cb7f34287ee7de28a68fed6c (diff) | |
Merge branch 'v1.1.2'
Diffstat (limited to 'docs/dev/reference/summary.nlme.mmkin.html')
| -rw-r--r-- | docs/dev/reference/summary.nlme.mmkin.html | 658 |
1 files changed, 311 insertions, 347 deletions
diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index b2f6624a..067efcfe 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Summary method for class "nlme.mmkin" — summary.nlme.mmkin • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Summary method for class "nlme.mmkin" — summary.nlme.mmkin" /> -<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters +<!-- 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>Summary method for class "nlme.mmkin" — summary.nlme.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summary method for class " nlme.mmkin summary.nlme.mmkin><meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting endpoints such as formation fractions and DT50 values. Optionally -(default is FALSE), the data are listed in full." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +(default is FALSE), the data are listed in full."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[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]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </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"> + <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"> @@ -76,23 +21,21 @@ endpoints such as formation fractions and DT50 values. Optionally </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">1.0.3.9000</span> + <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> + <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"> + <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> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,6 +45,9 @@ endpoints such as formation fractions and DT50 values. Optionally <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -116,34 +62,27 @@ endpoints such as formation fractions and DT50 values. Optionally <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</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/"> + </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 --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Summary method for class "nlme.mmkin"</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.nlme.mmkin.R'><code>R/summary.nlme.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.nlme.mmkin.R" class="external-link"><code>R/summary.nlme.mmkin.R</code></a></small> <div class="hidden name"><code>summary.nlme.mmkin.Rd</code></div> </div> @@ -155,295 +94,320 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.</p> </div> - <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span> -<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span> - <span class='va'>object</span>, - data <span class='op'>=</span> <span class='cn'>FALSE</span>, - verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, - distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, - alpha <span class='op'>=</span> <span class='fl'>0.05</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='co'># S3 method for summary.nlme.mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>an object of class <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td> - </tr> - <tr> - <th>data</th> - <td><p>logical, indicating whether the full data should be included in -the summary.</p></td> - </tr> - <tr> - <th>verbose</th> - <td><p>Should the summary be verbose?</p></td> - </tr> - <tr> - <th>distimes</th> - <td><p>logical, indicating whether DT50 and DT90 values should be -included.</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>error level for confidence interval estimation from the t -distribution</p></td> - </tr> - <tr> - <th>...</th> - <td><p>optional arguments passed to methods like <code>print</code>.</p></td> - </tr> - <tr> - <th>x</th> - <td><p>an object of class summary.nlme.mmkin</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to use for printing</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The summary function returns a list based on the <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a> object + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nlme.mmkin</span></span> +<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> +<span> <span class="va">object</span>,</span> +<span> data <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> distimes <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> alpha <span class="op">=</span> <span class="fl">0.05</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for summary.nlme.mmkin</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>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>an object of class <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> + + +<dt>data</dt> +<dd><p>logical, indicating whether the full data should be included in +the summary.</p></dd> + + +<dt>verbose</dt> +<dd><p>Should the summary be verbose?</p></dd> + + +<dt>distimes</dt> +<dd><p>logical, indicating whether DT50 and DT90 values should be +included.</p></dd> + + +<dt>alpha</dt> +<dd><p>error level for confidence interval estimation from the t +distribution</p></dd> + + +<dt>...</dt> +<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd> + + +<dt>x</dt> +<dd><p>an object of class summary.nlme.mmkin</p></dd> + + +<dt>digits</dt> +<dd><p>Number of digits to use for printing</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a> object obtained in the fit, with at least the following additional components</p> -<dt>nlmeversion, mkinversion, Rversion</dt><dd><p>The nlme, mkin and R versions used</p></dd> -<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were +<dl><dt>nlmeversion, mkinversion, Rversion</dt> +<dd><p>The nlme, mkin and R versions used</p></dd> + +<dt>date.fit, date.summary</dt> +<dd><p>The dates where the fit and the summary were produced</p></dd> -<dt>diffs</dt><dd><p>The differential equations used in the degradation model</p></dd> -<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> -<dt>data</dt><dd><p>The data</p></dd> -<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd> -<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd> -<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted + +<dt>diffs</dt> +<dd><p>The differential equations used in the degradation model</p></dd> + +<dt>use_of_ff</dt> +<dd><p>Was maximum or minimum use made of formation fractions</p></dd> + +<dt>data</dt> +<dd><p>The data</p></dd> + +<dt>confint_trans</dt> +<dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd> + +<dt>confint_back</dt> +<dd><p>Backtransformed parameters, with confidence intervals if available</p></dd> + +<dt>ff</dt> +<dd><p>The estimated formation fractions derived from the fitted model.</p></dd> -<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> -<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> -The print method is called for its side effect, i.e. printing the summary. - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +<dt>distimes</dt> +<dd><p>The DT50 and DT90 values for each observed variable.</p></dd> + +<dt>SFORB</dt> +<dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> +</dl><p>The print method is called for its side effect, i.e. printing the summary.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke for the mkin specific parts José Pinheiro and Douglas Bates for the components inherited from nlme</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># Generate five datasets following SFO kinetics</span> -<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> -<span class='va'>dt50_sfo_in_pop</span> <span class='op'><-</span> <span class='fl'>50</span> -<span class='va'>k_in_pop</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in_pop</span> -<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span> -<span class='va'>k_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>SFO</span> <span class='op'><-</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='op'>)</span><span class='op'>)</span> - -<span class='va'>pred_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> -<span class='op'>}</span> - -<span class='va'>ds_sfo_mean</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span> - -<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>12345</span><span class='op'>)</span> -<span class='va'>ds_sfo_syn</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, - sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, - n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> -<span class='op'>}</span><span class='op'>)</span> - -<span class='co'># Evaluate using mmkin and nlme</span> -<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> -<span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> nlme version used for fitting: 3.1.152 -#> mkin version used for pre-fitting: 1.0.3.9000 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 17:13:12 2021 -#> Date of summary: Mon Feb 15 17:13:12 2021 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> -#> Data: -#> 90 observations of 1 variable(s) grouped in 5 datasets -#> -#> Model predictions using solution type analytical -#> -#> Fitted in 0.544 s using 4 iterations -#> -#> Variance model: Two-component variance function -#> -#> Mean of starting values for individual parameters: -#> parent_0 log_k_parent -#> 101.569 -4.454 -#> -#> Fixed degradation parameter values: -#> None -#> -#> Results: -#> -#> AIC BIC logLik -#> 584.5 599.5 -286.2 -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> lower est. upper -#> parent_0 99.371 101.592 103.814 -#> log_k_parent -4.973 -4.449 -3.926 -#> -#> Correlation: -#> prnt_0 -#> log_k_parent 0.051 -#> -#> Random effects: -#> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) -#> Level: ds -#> Structure: Diagonal -#> parent_0 log_k_parent Residual -#> StdDev: 6.924e-05 0.5863 1 -#> -#> Variance function: -#> Structure: Constant plus proportion of variance covariate -#> Formula: ~fitted(.) -#> Parameter estimates: -#> const prop -#> 0.0001208853 0.0789968036 -#> -#> Backtransformed parameters with asymmetric confidence intervals: -#> lower est. upper -#> parent_0 99.370882 101.59243 103.81398 -#> k_parent 0.006923 0.01168 0.01972 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 59.32 197.1 -#> -#> Data: -#> ds name time observed predicted residual std standardized -#> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451 -#> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594 -#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313 -#> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725 -#> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796 -#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812 -#> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081 -#> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065 -#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987 -#> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480 -#> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857 -#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364 -#> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008 -#> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898 -#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252 -#> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335 -#> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423 -#> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549 -#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943 -#> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245 -#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361 -#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626 -#> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297 -#> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874 -#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251 -#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647 -#> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366 -#> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571 -#> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748 -#> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002 -#> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679 -#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485 -#> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198 -#> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171 -#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595 -#> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547 -#> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009 -#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739 -#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858 -#> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921 -#> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603 -#> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360 -#> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813 -#> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620 -#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848 -#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722 -#> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842 -#> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046 -#> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676 -#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664 -#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199 -#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776 -#> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178 -#> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282 -#> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057 -#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784 -#> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025 -#> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205 -#> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218 -#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886 -#> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706 -#> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270 -#> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357 -#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521 -#> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001 -#> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017 -#> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526 -#> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571 -#> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733 -#> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591 -#> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058 -#> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530 -#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485 -#> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531 -#> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413 -#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655 -#> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477 -#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382 -#> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267 -#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304 -#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295 -#> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141 -#> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178 -#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062 -#> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835 -#> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174 -#> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913 -#> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273 -#> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259 -#> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Generate five datasets following SFO kinetics</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</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">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dt50_sfo_in_pop</span> <span class="op"><-</span> <span class="fl">50</span></span></span> +<span class="r-in"><span><span class="va">k_in_pop</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span> <span class="op">/</span> <span class="va">dt50_sfo_in_pop</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1234</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">k_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="va">k_in_pop</span><span class="op">)</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</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="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">pred_sfo</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">k</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">SFO</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>k_parent <span class="op">=</span> <span class="va">k</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>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">ds_sfo_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">k_in</span>, <span class="va">pred_sfo</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds_sfo_mean</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"ds"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">12345</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds_sfo_syn</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_sfo_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span></span> +<span class="r-in"><span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="fl">0.07</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># Evaluate using mmkin and nlme</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"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> +<span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</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_nlme</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">#></span> nlme version used for fitting: 3.1.158 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:27:32 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:27:32 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Equations:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.534 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent </span> +<span class="r-out co"><span class="r-pr">#></span> 101.569 -4.454 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> +<span class="r-out co"><span class="r-pr">#></span> None</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Results:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 584.5 599.5 -286.2</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Optimised, transformed parameters with symmetric confidence intervals:</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.371 101.592 103.814</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -4.973 -4.449 -3.926</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Correlation: </span> +<span class="r-out co"><span class="r-pr">#></span> parnt_0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 0.0507 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent ~ 1)</span> +<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.924e-05 0.5863 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Variance function:</span> +<span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> +<span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> +<span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> +<span class="r-out co"><span class="r-pr">#></span> const prop </span> +<span class="r-out co"><span class="r-pr">#></span> 0.0001208853 0.0789968036 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters with asymmetric confidence intervals:</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.370882 101.59243 103.81398</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.006923 0.01168 0.01972</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 59.32 197.1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></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> + <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> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <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> + </footer></div> - </body> -</html> + + </body></html> |