qqnorm.lme {nlme}

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(.))