Message-ID: <39921e44-3afc-4673-83a9-12250f858145@mcmaster.ca>
Date: 2026-02-02T01:13:59Z
From: Ben Bolker
Subject: weighted.residuals()
The weighted.residuals() function has been under development
recently: the current version is
## see PR#7961,
https://stat.ethz.ch/pipermail/r-devel/2011-January/059642.html
## (Note, Jan 2026: PR# 7961 suggested use of deviance residuals but
then dfbeta et al. are
## not one-step approximations to leave-one-out coeff.)
weighted.residuals <- function(obj, drop0 = TRUE)
{
# w <- weights(obj, type="working")
# r <- residuals(obj, type="working")
w <- naresid(obj$na.action, obj$weights)
r <- naresid(obj$na.action, obj$residuals)
if (!is.null(w)) r <- r * sqrt(w)
if (inherits(obj, "glm")) w <- weights(obj, "prior")
if(drop0 && !is.null(w)) {
if(is.matrix(r)) r[w != 0, , drop = FALSE] # e.g. mlm fit
else r[w != 0]
} else r
}
The previous version was, as per
https://bugs.r-project.org/show_bug.cgi?id=7961,
## see PR#7961
weighted.residuals <- function(obj, drop0 = TRUE)
{
w <- weights(obj)
r <- residuals(obj, type="deviance")
if(drop0 && !is.null(w)) r[w != 0] else r
}
The problem with the current version is that it only works with
list-like objects that have $na.action, $weights, and $residuals
components. Among other things
* lme4's merMod objects, which are objects with an S4 class, throw an
error (because you can't access an S4 object element with $; even if you
used getElement() you'd get an error because those slots don't exist).
* glmmTMB objects return NULL (they're list-like but don't have the
appropriate elements).
A robust solution would use na.action(), residuals(), weights()
accessor methods. However, we can't count on working weights being the
default type, and some residuals.* or weights.* methods might not have
type="working" allowed (an intermediate version of weighted.residuals()
used weights(., type = "working"); lme4 throws an error for type =
"working" with GLMMs ... glmmTMB takes a type argument but ignores it ...
Another solution to this would be to make weighted.residuals() an S3
method and let other packages provide a method if they liked ...
Thoughts welcome.
Ben Bolker