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| -rw-r--r-- | docs/reference/nlme.html | 32 | ||||
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| -rw-r--r-- | docs/reference/plot.nlme.mmkin.html | 252 |
5 files changed, 592 insertions, 16 deletions
diff --git a/docs/reference/index.html b/docs/reference/index.html index 31f7678c..3c5f1b38 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -270,12 +270,32 @@ of an mmkin object</p></td> <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p> </td> <td><p>Calculate the AIC for a column of an mmkin object</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-mixed-models" class="hasAnchor"><a href="#section-mixed-models" class="anchor"></a>Mixed models</h2> + <p class="section-desc"><p>Create and work with nonlinear mixed models</p></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> </p> + </td> + <td><p>Create an nlme model for an mmkin row object</p></td> + </tr><tr> + + <td> + <p><code><a href="plot.nlme.mmkin.html">plot(<i><nlme.mmkin></i>)</a></code> </p> + </td> + <td><p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p></td> </tr><tr> <td> <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> - <td><p>Estimation of parameter distributions from mmkin row objects</p></td> + <td><p>Helper functions to create nlme models from mmkin row objects</p></td> </tr> </tbody><tbody> <tr> @@ -576,6 +596,7 @@ kinetic models fitted with mkinfit</p></td> <li><a href="#section-main-functions">Main functions</a></li> <li><a href="#section-show-results">Show results</a></li> <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li> + <li><a href="#section-mixed-models">Mixed models</a></li> <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li> <li><a href="#section-nafta-guidance">NAFTA guidance</a></li> <li><a href="#section-helper-functions-mainly-used-internally">Helper functions mainly used internally</a></li> diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 1b05f882..981845fe 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Estimation of parameter distributions from mmkin row objects — nlme_function • mkin</title> +<title>Helper functions to create nlme models from mmkin row objects — nlme_function • mkin</title> <!-- jquery --> @@ -35,7 +35,7 @@ -<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — nlme_function" /> +<meta property="og:title" content="Helper functions to create nlme models from mmkin row objects — nlme_function" /> <meta property="og:description" content="These functions facilitate setting 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 @@ -130,7 +130,7 @@ datasets." /> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Estimation of parameter distributions from mmkin row objects</h1> + <h1>Helper functions to create nlme models from mmkin row objects</h1> <div class="hidden name"><code>nlme.Rd</code></div> </div> @@ -255,37 +255,39 @@ datasets.</p> <span class='no'>nlme_f_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) <span class='no'>nlme_f_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ]) <span class='no'>nlme_f_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ]) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_sfo_sfo"</span>, <span class='no'>nlme_f_sfo_sfo</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_sfo_sfo_ff"</span>, <span class='no'>nlme_f_sfo_sfo_ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f_fomc_sfo"</span>, <span class='no'>nlme_f_fomc_sfo</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) - <span class='co'># Allowing for correlations between random effects leads to non-convergence</span> + <span class='co'># Allowing for correlations between random effects (not shown)</span> + <span class='co'># leads to non-convergence</span> <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'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_k_parent_sink</span>, <span class='no'>log_k_parent_A1</span>, <span class='no'>log_k_A1_sink</span>), <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink): konnte Funktion "nlme_f_sfo_sfo" nicht finden</span></div><div class='input'> + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>) + <span class='co'># augPred does not see to work on this object, so no plot is shown</span> + <span class='co'># The same model fitted with transformed formation fractions does not converge</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'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'> - <span class='co'># It does converge with this version of reduced random effects</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'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>, - <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), - <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, - <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, - <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'> + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme.formula(value ~ nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1), data = grouped_data_2, fixed = parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1, random = pdDiag(parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1), start = mean_dp_sfo_sfo_ff): step halving factor reduced below minimum in PNLS step</span></div><div class='input'> <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'>value</span> ~ <span class='fu'>nlme_f_fomc_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_alpha</span>, <span class='no'>log_beta</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>), - <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_fomc_sfo(name, time, parent_0, log_alpha, log_beta, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_fomc_sfo" nicht finden</span></div><div class='input'> + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>) + <span class='co'># DFOP-SFO and SFORB-SFO did not converge with full random effects</span> - <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo): Objekt 'f_nlme_fomc_sfo' nicht gefunden</span></div><div class='input'># } + <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></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_fomc_sfo 1 11 932.5817 967.0755 -455.2909 +#> f_nlme_sfo_sfo 2 9 1089.2492 1117.4714 -535.6246 1 vs 2 160.6675 <.0001</div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html new file mode 100644 index 00000000..e1b1ff77 --- /dev/null +++ b/docs/reference/nlme.mmkin.html @@ -0,0 +1,301 @@ +<!-- 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. 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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> +)</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> + </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='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/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</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 ~ deg_func(name, time, parent_0, log_k_parent_sink) +#> Data: structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3)), row.names = c(NA, -90L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE) +#> Log-likelihood: -394.4901 +#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1) +#> parent_0 log_k_parent_sink +#> 73.985522 -3.869079 +#> +#> Random effects: +#> Formula: parent_0 ~ 1 | ds +#> parent_0 Residual +#> StdDev: 18.6134 18.22029 +#> +#> Number of Observations: 90 +#> Number of Groups: 5 </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='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</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 ~ deg_func(name, time, parent_0, log_k_parent_sink) +#> Data: structure(list(ds = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("1", "2", "3", "4", "5"), class = c("ordered", "factor")), name = c("parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent", "parent"), time = c(0, 0, 3, 3, 6, 6, 10, 10, 20, 20, 34, 34, 55, 55, 90, 90, 112, 112, 132, 132, 0, 0, 3, 3, 7, 7, 14, 14, 30, 30, 60, 60, 90, 90, 120, 120, 180, 180, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 0, 0, 1, 1, 3, 3, 8, 8, 14, 14, 27, 27, 48, 48, 70, 70, 91, 91, 120, 120, 0, 0, 8, 8, 14, 14, 21, 21, 41, 41, 63, 63, 91, 91, 120, 120), value = c(97.2, 96.4, 71.1, 69.2, 58.1, 56.6, 44.4, 43.4, 33.3, 29.2, 17.6, 18, 10.5, 9.3, 4.5, 4.7, 3, 3.4, 2.3, 2.7, 93.6, 92.3, 87, 82.2, 74, 73.9, 64.2, 69.5, 54, 54.6, 41.1, 38.4, 32.5, 35.5, 28.1, 29, 26.5, 27.6, 91.9, 90.8, 64.9, 66.2, 43.5, 44.1, 18.3, 18.1, 10.2, 10.8, 4.9, 3.3, 1.6, 1.5, 1.1, 0.9, 99.8, 98.3, 77.1, 77.2, 59, 58.1, 27.4, 29.2, 19.1, 29.6, 10.1, 18.2, 4.5, 9.1, 2.3, 2.9, 2, 1.8, 2, 2.2, 96.1, 94.3, 73.9, 73.9, 69.4, 73.1, 65.6, 65.3, 55.9, 54.4, 47, 49.3, 44.7, 46.7, 42.1, 41.3)), row.names = c(NA, -90L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = value ~ time | ds, FUN = function (x) max(x, na.rm = TRUE), order.groups = FALSE) +#> 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></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 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name"><code>plot.nlme.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p> + </div> + + <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( + <span class='no'>x</span>, + <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>), + <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>), + <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, + <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, + <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</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>x</th> + <td><p>An object of class <code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></td> + </tr> + <tr> + <th>i</th> + <td><p>A numeric index to select datasets for which to plot the nlme fit, +in case plots get too large</p></td> + </tr> + <tr> + <th>main</th> + <td><p>The main title placed on the outer margin of the plot.</p></td> + </tr> + <tr> + <th>legends</th> + <td><p>An index for the fits for which legends should be shown.</p></td> + </tr> + <tr> + <th>resplot</th> + <td><p>Should the residuals plotted against time, using +<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted +values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td> + </tr> + <tr> + <th>standardized</th> + <td><p>Should the residuals be standardized? This option +is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if +`resplot = "time"`.</p></td> + </tr> + <tr> + <th>cex</th> + <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</p></td> + </tr> + <tr> + <th>rel.height.middle</th> + <td><p>The relative height of the middle plot, if more +than two rows of plots are shown.</p></td> + </tr> + <tr> + <th>ymax</th> + <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and +<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function is called for its side effect.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'><-</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='co'>#plot(f) # too many panels for pkgdown</span> +<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) +<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='co'>#plot(f_nlme) # too many panels for pkgdown</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>1</span>:<span class='fl'>2</span>)</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></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="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + <p>Johannes Ranke</p> + </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> + + |
