R: Extract conditional modes and conditional variances from clmm...
ranef
R Documentation
Extract conditional modes and conditional variances from clmm objects
Description
The ranef function extracts the conditional modes of the random
effects from a clmm object. That is, the modes of the distributions
for the random effects given the observed data and estimated model
parameters. In a Bayesian language they are posterior modes.
The conditional variances are computed from the second order
derivatives of the conditional distribution of the random
effects. Note that these variances are computed at a fixed value of
the model parameters and thus do not take the uncertainty of the
latter into account.
Usage
ranef(object, ...)
condVar(object, ...)
## S3 method for class 'clmm'
ranef(object, condVar=FALSE, ...)
## S3 method for class 'clmm'
condVar(object, ...)
Arguments
object
a clmm object.
condVar
an optional logical argument indicating of conditional variances
should be added as attributes to the conditional modes.
...
currently not used by the clmm methods.
Details
The ranef method returns a list of data.frames; one for
each distinct grouping factor. Each data.frame has as many rows
as there are levels for that grouping factor and as many columns as
there are random effects for each level. For example a model can
contain a random intercept (one column) or a random
intercept and a random slope (two columns) for the same grouping
factor.
If conditional variances are requested, they are returned in the same
structure as the conditional modes (random effect
estimates/predictions).
Value
The ranef method returns a list of data.frames with the
random effects predictions/estimates computed as conditional
modes. If condVar = TRUE a data.frame with the
conditional variances is stored as an attribute on each
data.frame with conditional modes.
The condVar method returns a list of data.frames with
the conditional variances. It is a convenience function that simply
computes the conditional modes and variances, then extracts and
returns only the latter.
Author(s)
Rune Haubo B Christensen
Examples
fm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine)
## Extract random effect estimates/conditional modes:
re <- ranef(fm1, condVar=TRUE)
## Get conditional variances:
attr(re$judge, "condVar")
## Alternatively:
condVar(fm1)