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diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html new file mode 100644 index 00000000..e3c13f48 --- /dev/null +++ b/docs/dev/reference/nlme.html @@ -0,0 +1,197 @@ +<!DOCTYPE html> +<!-- 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, shrink-to-fit=no"><title>Helper functions to create nlme models from mmkin row objects — nlme_function • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Helper functions to create nlme models from mmkin row objects — nlme_function"><meta name="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 +datasets. They are used internally by the nlme.mmkin() method."><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 +datasets. They are used internally by the nlme.mmkin() method."><meta name="robots" content="noindex"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item dropdown"> + <button 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class="external-link"><code>R/nlme.R</code></a></small> + <div class="d-none name"><code>nlme.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>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 +datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.mmkin()</a></code> method.</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> +<dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + <p>A function that can be used with nlme</p> +<p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">nlme::groupedData</a></code> object</p> + </div> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> + <div class="dont-index"><p><code><a href="nlme.mmkin.html">nlme.mmkin</a></code></p></div> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><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">m_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 class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_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="fl">0.1</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">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_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="fl">0.05</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">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_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="fl">0.02</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">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds</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>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f</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</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># These assignments are necessary for these objects to be</span></span></span> +<span class="r-in"><span><span class="co"># visible to nlme and augPred when evaluation is done by</span></span></span> +<span class="r-in"><span><span class="co"># pkgdown to generate the html docs.</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</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="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">m_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">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">grouped_data</span>,</span></span> +<span class="r-in"><span> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Nonlinear mixed-effects model fit by maximum likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) </span> +<span class="r-out co"><span class="r-pr">#></span> Data: grouped_data </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> 266.6428 275.8935 -128.3214</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_sink ~ 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_sink Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.0003775775 0.7058039 3.065183</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> +<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07257 0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0</span> +<span class="r-out co"><span class="r-pr">#></span> Correlation: </span> +<span class="r-out co"><span class="r-pr">#></span> prnt_0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.031 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> +<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> +<span class="r-out co"><span class="r-pr">#></span> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 47</span> +<span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <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">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="nlme-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># augPred does not work on fits with more than one state</span></span></span> +<span class="r-in"><span><span class="co"># variable</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span></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</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> +</div> + + </footer></div> + + + + + + </body></html> + |