pairs.lme {nlme}  R Documentation 
Diagnostic plots for the linear mixedeffects 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. The expression on the right hand side of the formula, before
a 
operator, must evaluate to a data frame with at least two
columns. If the data frame has two columns, a scatter plot of the two
variables is displayed (the Trellis function xyplot
is
used). Otherwise, if more than two columns are present, a scatter plot
matrix with pairwise scatter plots of the columns in the data frame is
displayed (the Trellis function splom
is used).
## S3 method for class 'lme': pairs(x, form, label, id, idLabels, grid, ...)
x 
an object inheriting from class lme , representing
a fitted linear mixedeffects model. 
form 
an optional onesided formula specifying the desired type of
plot. Any variable present in the original data frame used to obtain
x can be referenced. In addition, x 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 the  operator, must evaluate to a data frame with
at least two columns. Default is ~ coef(.) , corresponding to
a pairs plot of the coefficients evaluated at the innermost level of
nesting. 
label 
an optional character vector of labels for the variables in the pairs plot. 
id 
an optional numeric value, or onesided formula. If given as
a value, it is used as a significance level for an outlier
test based on the Mahalanobis distances of the estimated random
effects. Groups with random effects distances greater than the
1value percentile of the appropriate chisquare distribution
are identified in the plot using idLabels . If given as a
onesided formula, its right hand side must evaluate to a logical,
integer, or character vector which is used to identify points in the
plot. If missing, no points are identified. 
idLabels 
an optional vector, or onesided formula. If given as a
vector, it is converted to character and used to label the
points identified according to id . If given as a
onesided formula, its right hand side must evaluate to a vector
which is converted to character and used to label the identified
points. 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. 
a diagnostic Trellis plot.
Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu
fm1 < lme(distance ~ age, Orthodont, random = ~ age  Subject) # scatter plot of coefficients by gender, identifying unusual subjects pairs(fm1, ~coef(., augFrame = TRUE)  Sex, id = 0.1, adj = 0.5) # scatter plot of estimated random effects ## Not run: pairs(fm1, ~ranef(.)) ## End(Not run)