EVOLUTION-MANAGER
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Plot an lme or nls object</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" type="text/css" href="R.css" /> </head><body> <table width="100%" summary="page for plot.lme {nlme}"><tr><td>plot.lme {nlme}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot an lme or nls object</h2> <h3>Description</h3> <p>Diagnostic plots for the linear mixed-effects fit are obtained. The <code>form</code> argument gives considerable flexibility in the type of plot specification. A conditioning expression (on the right side of a <code>|</code> operator) always implies that different panels are used for each level of the conditioning factor, according to a Trellis display. If <code>form</code> is a one-sided formula, histograms of the variable on the right hand side of the formula, before a <code>|</code> operator, are displayed (the Trellis function <code>histogram</code> is used). If <code>form</code> is two-sided and both its left and right hand side variables are numeric, scatter plots are displayed (the Trellis function <code>xyplot</code> is used). Finally, if <code>form</code> is two-sided and its left had side variable is a factor, box-plots of the right hand side variable by the levels of the left hand side variable are displayed (the Trellis function <code>bwplot</code> is used). </p> <h3>Usage</h3> <pre> ## S3 method for class 'lme' plot(x, form, abline, id, idLabels, idResType, grid, ...) ## S3 method for class 'nls' plot(x, form, abline, id, idLabels, idResType, grid, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>an object inheriting from class <code>"<a href="lme.html">lme</a>"</code>, representing a fitted linear mixed-effects model, or from <code>nls</code>, representing an fitted nonlinear least squares model.</p> </td></tr> <tr valign="top"><td><code>form</code></td> <td> <p>an optional formula specifying the desired type of plot. Any variable present in the original data frame used to obtain <code>x</code> can be referenced. In addition, <code>x</code> itself can be referenced in the formula using the symbol <code>"."</code>. Conditional expressions on the right of a <code>|</code> operator can be used to define separate panels in a Trellis display. Default is <code>resid(., type = "p") ~ fitted(.) </code>, corresponding to a plot of the standardized residuals versus fitted values, both evaluated at the innermost level of nesting.</p> </td></tr> <tr valign="top"><td><code>abline</code></td> <td> <p>an optional numeric value, or numeric vector of length two. If given as a single value, a horizontal line will be added to the plot at that coordinate; else, if given as a vector, its values are used as the intercept and slope for a line added to the plot. If missing, no lines are added to the plot.</p> </td></tr> <tr valign="top"><td><code>id</code></td> <td> <p>an optional numeric value, or one-sided formula. If given as a value, it is used as a significance level for a two-sided outlier test for the standardized, or normalized residuals. Observations with absolute standardized (normalized) residuals greater than the <i>1 - value/2</i> quantile of the standard normal distribution are identified in the plot using <code>idLabels</code>. If given as a one-sided formula, its right hand side must evaluate to a logical, integer, or character vector which is used to identify observations in the plot. If missing, no observations are identified.</p> </td></tr> <tr valign="top"><td><code>idLabels</code></td> <td> <p>an optional vector, or one-sided formula. If given as a vector, it is converted to character and used to label the observations identified according to <code>id</code>. If given as a one-sided formula, its right hand side must evaluate to a vector which is converted to character and used to label the identified observations. Default is the innermost grouping factor.</p> </td></tr> <tr valign="top"><td><code>idResType</code></td> <td> <p>an optional character string specifying the type of residuals to be used in identifying outliers, when <code>id</code> is a numeric value. If <code>"pearson"</code>, the standardized residuals (raw residuals divided by the corresponding standard errors) are used; else, if <code>"normalized"</code>, the normalized residuals (standardized residuals pre-multiplied by the inverse square-root factor of the estimated error correlation matrix) are used. Partial matching of arguments is used, so only the first character needs to be provided. Defaults to <code>"pearson"</code>.</p> </td></tr> <tr valign="top"><td><code>grid</code></td> <td> <p>an optional logical value indicating whether a grid should be added to plot. Default depends on the type of Trellis plot used: if <code>xyplot</code> defaults to <code>TRUE</code>, else defaults to <code>FALSE</code>.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>optional arguments passed to the Trellis plot function.</p> </td></tr> </table> <h3>Value</h3> <p>a diagnostic Trellis plot. </p> <h3>Author(s)</h3> <p>José Pinheiro and Douglas Bates <a href="mailto:bates@stat.wisc.edu">bates@stat.wisc.edu</a></p> <h3>See Also</h3> <p><code><a href="lme.html">lme</a></code>, <code><a href="../../lattice/html/xyplot.html">xyplot</a></code>, <code><a href="../../lattice/html/xyplot.html">bwplot</a></code>, <code><a href="../../lattice/html/histogram.html">histogram</a></code></p> <h3>Examples</h3> <pre> fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject) # standardized residuals versus fitted values by gender plot(fm1, resid(., type = "p") ~ fitted(.) | Sex, abline = 0) # box-plots of residuals by Subject plot(fm1, Subject ~ resid(.)) # observed versus fitted values by Subject plot(fm1, distance ~ fitted(.) | Subject, abline = c(0,1)) </pre> <hr /><div style="text-align: center;">[Package <em>nlme</em> version 3.1-139 <a href="00Index.html">Index</a>]</div> </body></html>