Plot Components of an lme Object
DESCRIPTION:
A method for the generic function plot() for objects inheriting from class lme.
USAGE: 
plot.lme(object, option=c("c","r","s"), which = 1:3, ...)
REQUIRED ARGUMENTS:
object:
an object inheriting from class lme, usually returned by lme() or nlme().
OPTIONAL ARGUMENTS:
option:
if "r" or "s", diagnostic plots for the fitted values and the raw ("r") or standardized ("s") residuals are returned; otherwise, if option is set to "c", the function returns plots for the random effects coefficients. Default is "c".
which:
an integer vector specifying which plots should be generated when option is set to "r" or "s". Available options include observed versus fitted values (1), residuals versus fitted values 2), and residuals by cluster (3). Default is 1:3 (all plots generated).
...:
optional plot settings arguments.
VALUE:
For either the raw residuals or the standardized residuals, three diagnostic plots are returned : response vs. fitted.values, residuals vs. fitted.values and residuals vs. cluster. For the random effects coefficients, if just one coefficient is present in the model, the normal plot of the coefficients is returned; if two coefficients are used, a scatter plot is returned; otherwise a scatter plot matrix with all pairwise combinations of the random coefficients is returned.
SEE ALSO:
lme , nlme .
EXAMPLES: 
# Ovary.fit inherits from class lme
Ovary.fit <- lme(fixed = follicles ~ sin(2*pi*Time) + cos(2*pi*Time),
                 random = ~sin(2*pi*Time) + cos(2*pi*Time), cluster = ~
                 Mare, data = Ovary, re.block = list(1, 2:3),
                 re.structure = c("i","d"), serial.structure = "ar1",
                 var.function = "power")


plot.lme(Ovary.fit)
plot.lme(Ovary.fit,"s")