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## modified from contribution by Sanford Weisberg
##' @rdname downstream_methods
##' @param focal.predictors a character vector of one or more predictors in the
##' model in any order.
##'
##' @rawNamespace if(getRversion() >= "3.6.0") { S3method(effects::Effect, glmmTMB) } else { export(Effect.glmmTMB) }
Effect.glmmTMB <- function (focal.predictors, mod, ...) {
fam <- family(mod)
## code to make the 'truncated_*' families work
if (grepl("^truncated", fam$family))
fam <- c(fam, make.link(fam$link))
## dummy functions to make Effect.default work
dummyfuns <- list(variance=function(mu) mu,
initialize=expression(mustart <- y + 0.1),
dev.resids=function(...) poisson()$dev.res(...)
)
for (i in names(dummyfuns)) {
if (is.null(fam[[i]])) fam[[i]] <- dummyfuns[[i]]
}
## allow calculation of effects ...
if (length(formals(fam$variance))>1 || length(formals(fam$dev.resids))>3) {
warning("overriding variance function for effects/dev.resids: ",
"computed variances may be incorrect")
fam$variance <- dummyfuns$variance
fam$dev.resids <- dummyfuns$dev.resids
}
args <- list(call = getCall(mod),
coefficients = lme4::fixef(mod)[["cond"]],
vcov = vcov(mod)[["cond"]],
family=fam)
if (!requireNamespace("effects"))
stop("please install the effects package")
effects::Effect.default(focal.predictors, mod, ..., sources = args)
}
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