| pairs.lme {nlme} | R Documentation |
Diagnostic plots for 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. 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 mixed-effects model. |
form |
an optional one-sided 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 one-sided 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
1-value percentile of the appropriate chi-square 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 points in the
plot. If missing, no points 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
points 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
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)