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

qqnorm.lme {nlme} | R Documentation

## 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)

Jose Pinheiro and Douglas Bates bates@stat.wisc.edu

### See Also

`lme`, `plot.lme`

### Examples

    ## Not run:
    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(.))

    ## End(Not run)

[Package nlme version 3.1-104 Index]