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diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 9ec5d65a..838265d8 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -1,74 +1,61 @@ <!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"><meta name="description" content="Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object"><title>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin • 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-5.2.2/bootstrap.min.css" 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<li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> + </ul></li> +<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1> + + <h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mixed.mmkin.R" class="external-link"><code>R/plot.mixed.mmkin.R</code></a></small> <div class="d-none name"><code>plot.mixed.mmkin.Rd</code></div> </div> @@ -79,7 +66,7 @@ <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="co"># S3 method for mixed.mmkin</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'mixed.mmkin'</span></span> <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> <span> <span class="va">x</span>,</span> <span> i <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mmkin</span><span class="op">)</span>,</span> @@ -101,7 +88,7 @@ <span> nrow.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">ceiling</a></span><span class="op">(</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span><span class="op">)</span><span class="op">/</span><span class="va">ncol.legend</span><span class="op">)</span>,</span> <span> rel.height.legend <span class="op">=</span> <span class="fl">0.02</span> <span class="op">+</span> <span class="fl">0.07</span> <span class="op">*</span> <span class="va">nrow.legend</span>,</span> <span> rel.height.bottom <span class="op">=</span> <span class="fl">1.1</span>,</span> -<span> pch_ds <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span>,</span> +<span> pch_ds <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">1</span><span class="op">:</span><span class="fl">25</span>, <span class="fl">33</span>, <span class="fl">35</span><span class="op">:</span><span class="fl">38</span>, <span class="fl">40</span><span class="op">:</span><span class="fl">41</span>, <span class="fl">47</span><span class="op">:</span><span class="fl">57</span>, <span class="fl">60</span><span class="op">:</span><span class="fl">90</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span><span class="op">]</span>,</span> <span> col_ds <span class="op">=</span> <span class="va">pch_ds</span> <span class="op">+</span> <span class="fl">1</span>,</span> <span> lty_ds <span class="op">=</span> <span class="va">col_ds</span>,</span> <span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> @@ -111,131 +98,131 @@ <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>x</dt> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An object of class <a href="mixed.html">mixed.mmkin</a>, <a href="saem.html">saem.mmkin</a> or <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> -<dt>i</dt> +<dt id="arg-i">i<a class="anchor" aria-label="anchor" href="#arg-i"></a></dt> <dd><p>A numeric index to select datasets for which to plot the individual predictions, in case plots get too large</p></dd> -<dt>obs_vars</dt> +<dt id="arg-obs-vars">obs_vars<a class="anchor" aria-label="anchor" href="#arg-obs-vars"></a></dt> <dd><p>A character vector of names of the observed variables for which the data and the model should be plotted. Defauls to all observed variables in the model.</p></dd> -<dt>standardized</dt> +<dt id="arg-standardized">standardized<a class="anchor" aria-label="anchor" href="#arg-standardized"></a></dt> <dd><p>Should the residuals be standardized? Only takes effect if <code>resplot = "time"</code>.</p></dd> -<dt>covariates</dt> +<dt id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a></dt> <dd><p>Data frame with covariate values for all variables in any covariate models in the object. If given, it overrides 'covariate_quantiles'. Each line in the data frame will result in a line drawn for the population. Rownames are used in the legend to label the lines.</p></dd> -<dt>covariate_quantiles</dt> +<dt id="arg-covariate-quantiles">covariate_quantiles<a class="anchor" aria-label="anchor" href="#arg-covariate-quantiles"></a></dt> <dd><p>This argument only has an effect if the fitted object has covariate models. If so, the default is to show three population curves, for the 5th percentile, the 50th percentile and the 95th percentile of the covariate values used for fitting the model.</p></dd> -<dt>xlab</dt> +<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt> <dd><p>Label for the x axis.</p></dd> -<dt>xlim</dt> +<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt> <dd><p>Plot range in x direction.</p></dd> -<dt>resplot</dt> +<dt id="arg-resplot">resplot<a class="anchor" aria-label="anchor" href="#arg-resplot"></a></dt> <dd><p>Should the residuals plotted against time or against predicted values?</p></dd> -<dt>pop_curves</dt> +<dt id="arg-pop-curves">pop_curves<a class="anchor" aria-label="anchor" href="#arg-pop-curves"></a></dt> <dd><p>Per default, one population curve is drawn in case population parameters are fitted by the model, e.g. for saem objects. In case there is a covariate model, the behaviour depends on the value of 'covariates'</p></dd> -<dt>pred_over</dt> +<dt id="arg-pred-over">pred_over<a class="anchor" aria-label="anchor" href="#arg-pred-over"></a></dt> <dd><p>Named list of alternative predictions as obtained from <a href="mkinpredict.html">mkinpredict</a> with a compatible <a href="mkinmod.html">mkinmod</a>.</p></dd> -<dt>test_log_parms</dt> +<dt id="arg-test-log-parms">test_log_parms<a class="anchor" aria-label="anchor" href="#arg-test-log-parms"></a></dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> -<dt>conf.level</dt> +<dt id="arg-conf-level">conf.level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> -<dt>default_log_parms</dt> +<dt id="arg-default-log-parms">default_log_parms<a class="anchor" aria-label="anchor" href="#arg-default-log-parms"></a></dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> -<dt>ymax</dt> +<dt id="arg-ymax">ymax<a class="anchor" aria-label="anchor" href="#arg-ymax"></a></dt> <dd><p>Vector of maximum y axis values</p></dd> -<dt>maxabs</dt> +<dt id="arg-maxabs">maxabs<a class="anchor" aria-label="anchor" href="#arg-maxabs"></a></dt> <dd><p>Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".</p></dd> -<dt>ncol.legend</dt> +<dt id="arg-ncol-legend">ncol.legend<a class="anchor" aria-label="anchor" href="#arg-ncol-legend"></a></dt> <dd><p>Number of columns to use in the legend</p></dd> -<dt>nrow.legend</dt> +<dt id="arg-nrow-legend">nrow.legend<a class="anchor" aria-label="anchor" href="#arg-nrow-legend"></a></dt> <dd><p>Number of rows to use in the legend</p></dd> -<dt>rel.height.legend</dt> +<dt id="arg-rel-height-legend">rel.height.legend<a class="anchor" aria-label="anchor" href="#arg-rel-height-legend"></a></dt> <dd><p>The relative height of the legend shown on top</p></dd> -<dt>rel.height.bottom</dt> +<dt id="arg-rel-height-bottom">rel.height.bottom<a class="anchor" aria-label="anchor" href="#arg-rel-height-bottom"></a></dt> <dd><p>The relative height of the bottom plot row</p></dd> -<dt>pch_ds</dt> +<dt id="arg-pch-ds">pch_ds<a class="anchor" aria-label="anchor" href="#arg-pch-ds"></a></dt> <dd><p>Symbols to be used for plotting the data.</p></dd> -<dt>col_ds</dt> +<dt id="arg-col-ds">col_ds<a class="anchor" aria-label="anchor" href="#arg-col-ds"></a></dt> <dd><p>Colors used for plotting the observed data and the corresponding model prediction lines for the different datasets.</p></dd> -<dt>lty_ds</dt> +<dt id="arg-lty-ds">lty_ds<a class="anchor" aria-label="anchor" href="#arg-lty-ds"></a></dt> <dd><p>Line types to be used for the model predictions.</p></dd> -<dt>frame</dt> +<dt id="arg-frame">frame<a class="anchor" aria-label="anchor" href="#arg-frame"></a></dt> <dd><p>Should a frame be drawn around the plots?</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>The function is called for its side effect.</p> + <p>The function is called for its side effect.</p> </div> <div class="section level2"> <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> @@ -273,7 +260,7 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-in"><span><span class="va">f_nlmix</span> <span class="op"><-</span> <span class="fu">nlmix</span><span class="op">(</span><span class="va">f_obs</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmix(f_obs):</span> could not find function "nlmix"</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_nlmix</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'f_nlmix' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'f_nlmix' not found</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We can overlay the two variants if we generate predictions</span></span></span> <span class="r-in"><span><span class="va">pred_nlme</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span></span> @@ -285,23 +272,23 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </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></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <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> |