plot.gls {nlme}  R Documentation 
Diagnostic plots for the linear model 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. If form
is a onesided formula, histograms of the
variable on the right hand side of the formula, before a 
operator, are displayed (the Trellis function histogram
is
used). If form
is twosided and both its left and
right hand side variables are numeric, scatter plots are displayed
(the Trellis function xyplot
is used). Finally, if form
is twosided and its left had side variable is a factor, boxplots of
the right hand side variable by the levels of the left hand side
variable are displayed (the Trellis function bwplot
is used).
## S3 method for class 'gls' plot(x, form, abline, id, idLabels, idResType, grid, ...)
x 
an object inheriting from class 
form 
an optional formula specifying the desired type of
plot. Any variable present in the original data frame used to obtain

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 onesided formula. If given as
a value, it is used as a significance level for a twosided outlier
test for the standardized residuals. Observations with
absolute standardized residuals greater than the 1  value/2
quantile of the standard normal distribution are identified in the
plot using 
idLabels 
an optional vector, or onesided formula. If given as a
vector, it is converted to character mode and used to label the
observations identified according to 
idResType 
an optional character string specifying the type of
residuals to be used in identifying outliers, when 
grid 
an optional logical value indicating whether a grid should
be added to plot. Default depends on the type of Trellis plot used:
if 
... 
optional arguments passed to the Trellis plot function. 
a diagnostic Trellis plot.
JosÃ© Pinheiro and Douglas Bates bates@stat.wisc.edu
gls
, xyplot
,
bwplot
, histogram
fm1 < gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary, correlation = corAR1(form = ~ 1  Mare)) # standardized residuals versus fitted values by Mare plot(fm1, resid(., type = "p") ~ fitted(.)  Mare, abline = 0) # boxplots of residuals by Mare plot(fm1, Mare ~ resid(.)) # observed versus fitted values by Mare plot(fm1, follicles ~ fitted(.)  Mare, abline = c(0,1))