qqnorm.lme               package: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 Jose.Pinheiro@pharma.novartis.com 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)

