<!-- 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/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> <!-- headroom.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/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="twitter:card" content="summary" /> <!-- 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> <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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</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> </ul> </li> <li> <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> </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> <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>Should the data be printed?</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 #> 85.541149 -3.229596 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent_sink Residual #> StdDev: 1.30857 1.288591 6.304906 #> #> 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'>#> $distimes #> DT50 DT90 #> parent 17.51545 58.18505 #> </div><div class='input'><span class='co'># \dontrun{</span> <span class='no'>f_nlme_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)) <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood #> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink) #> Data: "Not shown" #> Log-likelihood: -404.3729 #> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> parent_0 log_k_parent_sink #> 75.933480 -3.555983 #> #> Random effects: #> Formula: parent_0 ~ 1 | ds #> parent_0 Residual #> StdDev: 0.002416792 21.63027 #> #> Number of Observations: 90 #> Number of Groups: 5 </div><div class='input'> <span class='co'># Test on some real data</span> <span class='no'>ds_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<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/graphics/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/graphics/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/graphics/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 #> -0.2079984 0.8563873 1.7454146 1.0917723 1.2756924 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 643.8786 #> fixed effects: 94.17379 -5.473199 -0.6970239 -0.2025094 2.103883 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct #> 0.7865373 0.1448077 #> #> **Iteration 2 #> LME step: Loglik: -396.3824, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 #> -1.712408e-01 -2.680989e-05 1.842119e+00 1.073975e+00 1.322924e+00 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 643.8022 #> fixed effects: 94.17385 -5.473491 -0.6970405 -0.202514 2.103871 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct #> 5.341904e-05 1.227073e-03 #> #> **Iteration 3 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 #> -0.1712484347 -0.0001513555 1.8420964843 1.0739800649 1.3229176990 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 643.7947 #> fixed effects: 94.17386 -5.473522 -0.6970423 -0.2025142 2.10387 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct #> 5.568186e-06 1.276609e-04 #> #> **Iteration 4 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 #> -0.171251200 -0.000164506 1.842095097 1.073980200 1.322916184 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 643.7934 #> fixed effects: 94.17386 -5.473526 -0.6970426 -0.2025146 2.103869 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct #> 2.332100e-06 1.979007e-05 </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: -404.9591, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 #> -0.4114594 0.9798456 1.6990016 0.7293119 0.3353829 1.7112922 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 630.391 #> fixed effects: 93.82265 -5.455841 -0.6788837 -1.862191 -4.199654 0.05531046 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct #> 0.7872619 0.5811683 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 #> -0.371222832 0.003084754 1.789952290 0.724634064 0.301559136 1.754244638 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 630.359 #> fixed effects: 93.82269 -5.456014 -0.6788967 -1.862202 -4.199678 0.05534118 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct #> 0.0005550885 0.0007749418 #> #> **Iteration 3 #> LME step: Loglik: -407.7756, nlminb iterations: 11 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 #> -0.371217033 0.003064156 1.789935045 0.724683005 0.301622307 1.754234135 #> Beginning PNLS step: .. completed fit_nlme() step. #> PNLS step: RSS = 630.358 #> fixed effects: 93.82269 -5.456017 -0.6788969 -1.862197 -4.199677 0.05532978 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct #> 2.059533e-04 4.860085e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/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/graphics/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/graphics/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/graphics/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 13 843.8541 884.6194 -408.9270 #> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33913 <.0001 #> f_nlme_sfo_sfo 3 9 1085.1821 1113.4042 -533.5910 2 vs 3 270.66712 <.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 13 843.8541 884.6194 -408.927 #> f_nlme_sfo_sfo 2 9 1085.1821 1113.4042 -533.591 1 vs 2 249.328 <.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 #> 0.5912435 0.4087565 1.0000000 #> #> $distimes #> DT50 DT90 #> parent 19.13517 63.56565 #> A1 66.02149 219.31865 #> </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 A1_sink #> 0.2768571 0.7231429 1.0000000 #> #> $distimes #> DT50 DT90 DT50_k1 DT50_k2 #> parent 11.07092 104.6325 4.462389 46.2085 #> A1 162.30937 539.1801 NA NA #> </div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> <li><a href="#value">Value</a></li> <li><a href="#see-also">See also</a></li> <li><a href="#examples">Examples</a></li> </ul> </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> 1.4.1.</p> </div> </footer> </div> </body> </html>