Nothing
qvcalc.lm <- function(object, factorname = NULL, coef.indices = NULL,
dispersion = NULL, ...)
{
coef.indices.saved <- coef.indices
if (is.null(factorname) && is.null(coef.indices)) {
stop("arguments 'factorname' and 'coef.indices' are both NULL")
}
if (is.null(coef.indices)) { ## try to use factorname
term.index <- which(attr(terms(object),"term.labels") == factorname)
modelmat <- model.matrix(object)
has.coef <- colnames(modelmat) %in% names(coef(object))
coef.indices <- which(attr(modelmat, "assign")[has.coef] == term.index)
if (length(object$xlevels[[factorname]]) == length(coef.indices)){
## factor has no constraint applied, eg if no intercept in model
contmat <- diag(length(coef.indices))}
else
contmat <- eval(call(object$contrasts[[factorname]],
object$xlevels[[factorname]]))
estimates <- contmat %*% coef(object)[coef.indices]
covmat <- vcov(object, dispersion = dispersion)
covmat <- covmat[coef.indices, coef.indices, drop = FALSE]
covmat <- contmat %*% covmat %*% t(contmat)
}
else {
k <- length(coef.indices)
refPos <- numeric(0)
if (0 %in% coef.indices) { ## there's a reference level to include
refPos <- which(coef.indices == 0)
coef.indices <- coef.indices[-refPos]
}
covmat <- vcov(object, dispersion = dispersion)
covmat <- covmat[coef.indices, coef.indices, drop = FALSE]
estimates <- coef(object)[coef.indices]
if (length(refPos) == 1) {
if (length(estimates) != k) estimates <- c(0, estimates)
covmat <- cbind(0, rbind(0, covmat))
names(estimates)[1] <- rownames(covmat)[1] <-
colnames(covmat)[1] <- "(reference)"
if (refPos != 1) {
if (refPos == k){
perm <- c(2:k, 1)
} else {
perm <- c(2:refPos, 1, (refPos + 1):k)
}
estimates <- estimates[perm]
covmat <- covmat[perm, perm, drop = FALSE]
}
}
}
return(qvcalc.default(covmat,
factorname = factorname,
coef.indices = coef.indices.saved,
labels = NULL,
dispersion = dispersion,
estimates = estimates,
modelcall = object$call, ...)
)
}
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