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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
| commit | a77a10ea6c607346778ba0700b3b66ac393101a2 (patch) | |
| tree | e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/nlme.mmkin.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/nlme.mmkin.html')
| -rw-r--r-- | docs/dev/reference/nlme.mmkin.html | 463 |
1 files changed, 463 insertions, 0 deletions
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html new file mode 100644 index 00000000..a6716c0f --- /dev/null +++ b/docs/dev/reference/nlme.mmkin.html @@ -0,0 +1,463 @@ +<!-- 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 an nlme model for an mmkin row object — 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="Create an nlme model for an mmkin row object — nlme.mmkin" /> +<meta property="og:description" content="This functions sets up a nonlinear mixed effects model for an mmkin row +object. 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 an nlme model for an mmkin row object</h1> + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small> + <div class="hidden name"><code>nlme.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This functions sets up a nonlinear mixed effects model for an mmkin row +object. 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='co'># S3 method for mmkin</span> +<span class='fu'>nlme</span>( + <span class='no'>model</span>, + <span class='kw'>data</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span>()), + <span class='no'>fixed</span>, + <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>fixed</span>, + <span class='no'>groups</span>, + <span class='no'>start</span>, + <span class='kw'>correlation</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>weights</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='no'>subset</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"ML"</span>, <span class='st'>"REML"</span>), + <span class='kw'>na.action</span> <span class='kw'>=</span> <span class='no'>na.fail</span>, + <span class='no'>naPattern</span>, + <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(), + <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> +) + +<span class='co'># S3 method for nlme.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for nlme.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</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>model</th> + <td><p>An <code><a href='mmkin.html'>mmkin</a></code> row object.</p></td> + </tr> + <tr> + <th>data</th> + <td><p>Ignored, data are taken from the mmkin model</p></td> + </tr> + <tr> + <th>fixed</th> + <td><p>Ignored, all degradation parameters fitted in the +mmkin model are used as fixed parameters</p></td> + </tr> + <tr> + <th>random</th> + <td><p>If not specified, all fixed effects are complemented +with uncorrelated random effects</p></td> + </tr> + <tr> + <th>groups</th> + <td><p>See the documentation of nlme</p></td> + </tr> + <tr> + <th>start</th> + <td><p>If not specified, mean values of the fitted degradation +parameters taken from the mmkin object are used</p></td> + </tr> + <tr> + <th>correlation</th> + <td><p>See the documentation of nlme</p></td> + </tr> + <tr> + <th>weights</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>subset</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>method</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>na.action</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>naPattern</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>control</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>verbose</th> + <td><p>passed to nlme</p></td> + </tr> + <tr> + <th>x</th> + <td><p>An nlme.mmkin object to print</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Update specifications passed to update.nlme</p></td> + </tr> + <tr> + <th>object</th> + <td><p>An nlme.mmkin object to update</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>Upon success, a fitted nlme.mmkin object, which is an nlme object +with additional elements</p> + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <div class='dont-index'><p><code><a href='nlme.html'>nlme_function</a></code></p></div> + + <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'><-</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='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)) +<span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) +<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f</span><span class='kw'>[[</span><span class='fl'>1</span>]])</div><div class='output co'>#> $distimes +#> DT50 DT90 +#> parent 11.96183 39.73634 +#> </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>) +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood +#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink) +#> Data: "Not shown" +#> Log-likelihood: -307.5269 +#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) +#> parent_0 log_k_parent_sink +#> 85.540979 -3.229602 +#> +#> Random effects: +#> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) +#> Level: ds +#> Structure: Diagonal +#> parent_0 log_k_parent_sink Residual +#> StdDev: 1.308245 1.288586 6.304923 +#> +#> Number of Observations: 90 +#> Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#> $distimes +#> DT50 DT90 +#> parent 17.51556 58.18543 +#> </div><div class='input'><span class='co'># \dontrun{</span> + <span class='no'>f_nlme_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)) + <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood +#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink) +#> Data: "Not shown" +#> Log-likelihood: -404.3729 +#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) +#> parent_0 log_k_parent_sink +#> 75.933480 -3.555983 +#> +#> Random effects: +#> Formula: parent_0 ~ 1 | ds +#> parent_0 Residual +#> StdDev: 0.002416802 21.63027 +#> +#> Number of Observations: 90 +#> Number of Groups: 5 </div><div class='input'> <span class='co'># Test on some real data</span> + <span class='no'>ds_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], + <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<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='no'>m_sfo_sfo</span> <span class='kw'><-</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>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>m_sfo_sfo_ff</span> <span class='kw'><-</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>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>m_fomc_sfo</span> <span class='kw'><-</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'>"FOMC"</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>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>m_dfop_sfo</span> <span class='kw'><-</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'>"DFOP"</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>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + + <span class='no'>f_2</span> <span class='kw'><-</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'>m_sfo_sfo</span>, + <span class='st'>"SFO-SFO-ff"</span> <span class='kw'>=</span> <span class='no'>m_sfo_sfo_ff</span>, + <span class='st'>"FOMC-SFO"</span> <span class='kw'>=</span> <span class='no'>m_fomc_sfo</span>, + <span class='st'>"DFOP-SFO"</span> <span class='kw'>=</span> <span class='no'>m_dfop_sfo</span>), + <span class='no'>ds_2</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/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>]) <span class='co'># Separate fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='no'>f_nlme_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) + <span class='co'># plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures</span> + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># Global mixed model: Fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='co'># With formation fractions</span> + <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ]) + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># chi2 different due to different df attribution</span></div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='co'># For more parameters, we need to increase pnlsMaxIter and the tolerance</span> + <span class='co'># to get convergence</span> + <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ], + <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> +#> **Iteration 1 +#> LME step: Loglik: -394.1603, nlminb iterations: 2 +#> reStruct parameters: +#> ds1 ds2 ds3 ds4 ds5 +#> -0.2079863 0.8563823 1.7454253 1.0917707 1.2756955 +#> Beginning PNLS step: .. completed fit_nlme() step. +#> PNLS step: RSS = 643.8814 +#> fixed effects: 94.17379 -5.473189 -0.6970234 -0.202509 2.103883 +#> iterations: 100 +#> Convergence crit. (must all become <= tolerance = 0.0001): +#> fixed reStruct +#> 0.7959873 0.1447512 +#> +#> **Iteration 2 +#> LME step: Loglik: -396.3824, nlminb iterations: 7 +#> reStruct parameters: +#> ds1 ds2 ds3 ds4 ds5 +#> -1.712406e-01 -2.278541e-05 1.842120e+00 1.073975e+00 1.322924e+00 +#> Beginning PNLS step: .. completed fit_nlme() step. +#> PNLS step: RSS = 643.8025 +#> fixed effects: 94.17385 -5.473491 -0.6970406 -0.2025139 2.103871 +#> iterations: 100 +#> Convergence crit. (must all become <= tolerance = 0.0001): +#> fixed reStruct +#> 5.51758e-05 1.26861e-03 +#> +#> **Iteration 3 +#> LME step: Loglik: -396.3825, nlminb iterations: 7 +#> reStruct parameters: +#> ds1 ds2 ds3 ds4 ds5 +#> -0.1712500923 -0.0001515734 1.8420972550 1.0739796967 1.3229177241 +#> Beginning PNLS step: .. completed fit_nlme() step. +#> PNLS step: RSS = 643.7941 +#> fixed effects: 94.17386 -5.473523 -0.6970424 -0.2025146 2.103869 +#> iterations: 100 +#> Convergence crit. (must all become <= tolerance = 0.0001): +#> fixed reStruct +#> 5.792621e-06 1.335434e-04 +#> +#> **Iteration 4 +#> LME step: Loglik: -396.3825, nlminb iterations: 7 +#> reStruct parameters: +#> ds1 ds2 ds3 ds4 ds5 +#> -0.1712517206 -0.0001651603 1.8420950864 1.0739800294 1.3229173529 +#> Beginning PNLS step: .. completed fit_nlme() step. +#> PNLS step: RSS = 643.7949 +#> fixed effects: 94.17386 -5.473521 -0.6970423 -0.2025145 2.10387 +#> iterations: 100 +#> Convergence crit. (must all become <= tolerance = 0.0001): +#> fixed reStruct +#> 4.025781e-07 9.628656e-06 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ], + <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>120</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>5e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> +#> **Iteration 1 +#> LME step: Loglik: -404.9583, nlminb iterations: 1 +#> reStruct parameters: +#> ds1 ds2 ds3 ds4 ds5 ds6 +#> -0.4114357 0.9798641 1.6990035 0.7293314 0.3354323 1.7113047 +#> Beginning PNLS step: .. completed fit_nlme() step. +#> PNLS step: RSS = 630.3642 +#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.0553284 +#> iterations: 120 +#> Convergence crit. (must all become <= tolerance = 0.0005): +#> fixed reStruct +#> 0.7879730 0.5822574 +#> +#> **Iteration 2 +#> LME step: Loglik: -407.7755, nlminb iterations: 11 +#> reStruct parameters: +#> ds1 ds2 ds3 ds4 ds5 ds6 +#> -0.371224105 0.003056163 1.789939431 0.724671132 0.301602942 1.754200482 +#> Beginning PNLS step: .. completed fit_nlme() step. +#> PNLS step: RSS = 630.364 +#> fixed effects: 93.82269 -5.455991 -0.6788958 -1.862196 -4.199671 0.05532834 +#> iterations: 120 +#> Convergence crit. (must all become <= tolerance = 0.0005): +#> fixed reStruct +#> 9.814652e-07 1.059239e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 +#> f_nlme_fomc_sfo 2 11 818.5151 853.0089 -398.2576 1 vs 2 21.33957 <.0001 +#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66697 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> + <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> $ff +#> parent_sink parent_A1 A1_sink +#> 0.5912432 0.4087568 1.0000000 +#> +#> $distimes +#> DT50 DT90 +#> parent 19.13518 63.5657 +#> A1 66.02155 219.3189 +#> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_dfop_sfo</span>)</div><div class='output co'>#> $ff +#> parent_A1 parent_sink +#> 0.2768574 0.7231426 +#> +#> $distimes +#> DT50 DT90 DT50_k1 DT50_k2 +#> parent 11.07091 104.6320 4.462384 46.20825 +#> A1 162.30518 539.1661 NA NA +#> </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> + + |