Skip to content

sup-t option for p_adjust #1127

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
strengejacke merged 9 commits into from
Jul 7, 2025
Merged

sup-t option for p_adjust #1127

Changes from 1 commit
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
3f0cf6f
`sup-t` option for `p_adjust`
strengejacke Jul 5, 2025
b247043
finalize
strengejacke Jul 6, 2025
210a04d
fix
strengejacke Jul 6, 2025
4eb65a0
wordlist
strengejacke Jul 6, 2025
4e957f3
refactor, tests
strengejacke Jul 7, 2025
e28810f
add tests
strengejacke Jul 7, 2025
28cb641
add test
strengejacke Jul 7, 2025
7859254
works with glmmTMB
strengejacke Jul 7, 2025
d40703d
fix
strengejacke Jul 7, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 11 additions & 1 deletion R/format_p_adjust.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ format_p_adjust <- function(method) {
## TODO add "mvt" method from emmeans

# prepare arguments
all_methods <- c(stats::p.adjust.methods, "tukey", "scheffe", "sidak")
all_methods <- c(stats::p.adjust.methods, "tukey", "scheffe", "sidak", "sup-t")

# for interaction terms, e.g. for "by" argument in emmeans
# pairwise comparison, we have to adjust the rank resp. the
Expand Down Expand Up @@ -107,6 +107,16 @@ format_p_adjust <- function(method) {
} else if (tolower(p_adjust) == "sidak") {
# sidak adjustment
params$p <- 1 - (1 - params$p)^(nrow(params) / rank_adjust)
} else if (tolower(p_adjust) == "sup-t") {
insight::check_if_installed("mvtnorm")
vc <- .safe(cov2cor(insight::get_vcov(model)))
if (is.null(vc)) {
insight::format_warning("Could not calculate covariance matrix for `sup-t` adjustment.")
return(params)
}
ci_level <- mvtnorm::qmvt(0.95, df = params$df, tail = "both.tails", corr = vc)$quantile
crit <- 1 - 2 * pt(-abs(ci_level), df = params$df)
params$p <- .p_value_dof()
}

if (isTRUE(all(old_p_vals == params$p)) && !identical(p_adjust, "none") && verbose) {
Expand Down
Loading