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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: Pairs Plot of an lme 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 pairs.lme {nlme}"><tr><td>pairs.lme {nlme}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Pairs Plot of an lme 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. The expression on the right hand side of the formula, before a <code>|</code> operator, must evaluate to a data frame with at least two columns. If the data frame has two columns, a scatter plot of the two variables is displayed (the Trellis function <code>xyplot</code> is used). Otherwise, if more than two columns are present, a scatter plot matrix with pairwise scatter plots of the columns in the data frame is displayed (the Trellis function <code>splom</code> is used). </p> <h3>Usage</h3> <pre> ## S3 method for class 'lme' pairs(x, form, label, id, idLabels, 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.</p> </td></tr> <tr valign="top"><td><code>form</code></td> <td> <p>an optional one-sided 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. The expression on the right hand side of <code>form</code>, and to the left of the <code>|</code> operator, must evaluate to a data frame with at least two columns. Default is <code>~ coef(.) </code>, corresponding to a pairs plot of the coefficients evaluated at the innermost level of nesting.</p> </td></tr> <tr valign="top"><td><code>label</code></td> <td> <p>an optional character vector of labels for the variables in the pairs 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 an outlier test based on the Mahalanobis distances of the estimated random effects. Groups with random effects distances greater than the <i>1-value</i> percentile of the appropriate chi-square 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 points in the plot. If missing, no points 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 points 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 points. Default is the innermost grouping factor. </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 is <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="pairs.compareFits.html">pairs.compareFits</a></code>, <code><a href="pairs.lmList.html">pairs.lmList</a></code>, <code><a href="../../lattice/html/xyplot.html">xyplot</a></code>, <code><a href="../../lattice/html/splom.html">splom</a></code> </p> <h3>Examples</h3> <pre> fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject) # scatter plot of coefficients by gender, identifying unusual subjects pairs(fm1, ~coef(., augFrame = TRUE) | Sex, id = 0.1, adj = -0.5) # scatter plot of estimated random effects : pairs(fm1, ~ranef(.)) </pre> <hr /><div style="text-align: center;">[Package <em>nlme</em> version 3.1-139 <a href="00Index.html">Index</a>]</div> </body></html>