qqnorm.lme: Normal Plot of Residuals or Random Effects from an lme Object

In nlme: Linear and Nonlinear Mixed Effects Models

Normal Plot of Residuals or Random Effects from an lme Object

Description

Diagnostic plots for assessing the normality of residuals and random effects in the linear mixed-effects fit are obtained. The form argument gives considerable flexibility in the type of plot specification. A conditioning expression (on the right side of a | operator) always implies that different panels are used for each level of the conditioning factor, according to a Trellis display.

Usage

## S3 method for class 'lme'
qqnorm(y, form, abline, id, idLabels, grid, ...)

Arguments

y	an object inheriting from class "lme", representing a fitted linear mixed-effects model or from class "lmList", representing a list of lm objects, or from class "lm", representing a fitted linear model, or from class "nls", representing a nonlinear least squares fitted model.
form	an optional one-sided formula specifying the desired type of plot. Any variable present in the original data frame used to obtain y can be referenced. In addition, y itself can be referenced in the formula using the symbol ".". Conditional expressions on the right of a | operator can be used to define separate panels in a Trellis display. The expression on the right hand side of form and to the left of a | operator must evaluate to a residuals vector, or a random effects matrix. Default is ~ resid(., type = "p"), corresponding to a normal plot of the standardized residuals evaluated at the innermost level of nesting.
abline	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.
id	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 residuals (random effects). Observations with absolute standardized residuals (random effects) greater than the 1 - value/2 quantile of the standard normal distribution are identified in the plot using idLabels. 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.
idLabels	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 id. 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.
grid	an optional logical value indicating whether a grid should be added to plot. Default is FALSE.
...	optional arguments passed to the Trellis plot function.

Value

a diagnostic Trellis plot for assessing normality of residuals or random effects.

Author(s)

José Pinheiro and Douglas Bates [e-mail]

See Also

lme, plot.lme

Examples

fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
## normal plot of standardized residuals by gender
qqnorm(fm1, ~ resid(., type = "p") | Sex, abline = c(0, 1))
## normal plots of random effects
qqnorm(fm1, ~ranef(.))

nlme documentation built on Nov. 27, 2023, 5:09 p.m.