qqnorm.gls {nlme}R Documentation

Normal Plot of Residuals from a gls Object

Description

Diagnostic plots for assessing the normality of residuals the generalized least squares 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 'gls':
qqnorm(y, form, abline, id, idLabels, grid, ...)

Arguments

y an object inheriting from class gls, representing a generalized 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. Default is ~ resid(., type = "p"), corresponding to a normal plot of the standardized residuals.
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 depends on the type of Trellis plot used: if xyplot defaults to TRUE, else defaults to FALSE.
... optional arguments passed to the Trellis plot function.

Value

a diagnostic Trellis plot for assessing normality of residuals.

Author(s)

Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu

See Also

gls, plot.gls

Examples

fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
           correlation = corAR1(form = ~ 1 | Mare))
qqnorm(fm1, abline = c(0,1))

[Package nlme version 3.1-80 Index]