## utilities, these *exported*:
##' @export getL
setGeneric("getL", function(x) standardGeneric("getL"))
fixed.effects <- function(object, ...) {
## fixed.effects was an alternative name for fixef
.Deprecated("fixef")
mCall = match.call()
mCall[[1]] = as.name("fixef")
eval(mCall, parent.frame())
}
random.effects <- function(object, ...) {
## random.effects was an alternative name for ranef
.Deprecated("ranef")
mCall = match.call()
mCall[[1]] = as.name("ranef")
eval(mCall, parent.frame())
}
## Create a Markov chain Monte Carlo sample from the posterior
## distribution of the parameters
##
##
## @title Create an MCMC sample
## @param object a fitted model object
## @param n number of samples to generate. Defaults to 1; for real use values of 200-1000 are more typical
## @param verbose should verbose output be given?
## @param ... additional, optional arguments (not used)
## @return a Markov chain Monte Carlo sample as a matrix
mcmcsamp <- function(object, n = 1L, verbose = FALSE, ...) UseMethod("mcmcsamp")
if(getRversion() < "3.3") {
sigma <- function(object, ...) UseMethod("sigma")
}
isREML <- function(x, ...) UseMethod("isREML")
isLMM <- function(x, ...) UseMethod("isLMM")
isGLMM <- function(x, ...) UseMethod("isGLMM")
isNLMM <- function(x, ...) UseMethod("isNLMM")
##' Refit a model using the maximum likelihood criterion
##'
##' This function is primarily used to get a maximum likelihood fit of
##' a linear mixed-effects model for an \code{\link{anova}} comparison.
##'
##' @title Refit a model by maximum likelihood criterion
##' @param x a fitted model, usually of class \code{"\linkS4class{lmerMod}"},
##' to be refit according to the maximum likelihood criterion
##' @param ... optional additional parameters. None are used at present.
##' @return an object like \code{x} but fit by maximum likelihood
##' @export
refitML <- function(x, ...) UseMethod("refitML")
refit <- function(object, newresp, ...) UseMethod("refit")
if (FALSE) {
setGeneric("HPDinterval",
function(object, prob = 0.95, ...) standardGeneric("HPDinterval"))
}
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