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Merged
merged 3 commits into from
Aug 30, 2025
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Prepare CRAN release #560

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18d47e1
Prepare CRAN release
strengejacke Aug 30, 2025
5880249
styler, remove remotes
strengejacke Aug 30, 2025
6622d4c
styler
strengejacke Aug 30, 2025
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11 changes: 5 additions & 6 deletions DESCRIPTION
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@@ -1,7 +1,7 @@
Type: Package
Package: modelbased
Title: Estimation of Model-Based Predictions, Contrasts and Means
Version: 0.12.0.22
Version: 0.13.0
Authors@R:
c(person(given = "Dominique",
family = "Makowski",
Expand Down Expand Up @@ -39,10 +39,10 @@ BugReports: https://github.com/easystats/modelbased/issues
Depends:
R (>= 3.6)
Imports:
bayestestR (>= 0.16.1),
bayestestR (>= 0.17.0),
datawizard (>= 1.2.0),
insight (>= 1.3.1),
parameters (>= 0.27.0),
insight (>= 1.4.1),
parameters (>= 0.28.1),
graphics,
stats,
tools,
Expand Down Expand Up @@ -76,7 +76,7 @@ Suggests:
logspline,
MASS,
Matrix,
marginaleffects (>= 0.26.0),
marginaleffects (>= 0.29.0),
mice,
mgcv,
mvtnorm,
Expand Down Expand Up @@ -115,4 +115,3 @@ Roxygen: list(markdown = TRUE)
Config/Needs/check: stan-dev/cmdstanr
Config/Needs/website: easystats/easystatstemplate
LazyData: true
Remotes: easystats/insight, easystats/parameters, easystats/bayestestR, vincentarelbundock/marginaleffects
2 changes: 1 addition & 1 deletion NEWS.md
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# modelbased (devel)
# modelbased 0.13.0

## Changes

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2 changes: 1 addition & 1 deletion R/format.R
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Expand Up @@ -684,7 +684,7 @@ format.marginaleffects_contrasts <- function(x, model = NULL, p_adjust = NULL, c
params <- data.frame(datawizard::data_restoretype(params, model_data))

# add posterior draws?
insight::check_if_installed("marginaleffects", minimum_version = "0.28.0.22")
insight::check_if_installed("marginaleffects", minimum_version = "0.29.0")
posterior_draws <- suppressWarnings(as.data.frame(marginaleffects::get_draws(
x,
shape = "PxD"
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2 changes: 1 addition & 1 deletion R/get_marginalcontrasts.R
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Expand Up @@ -15,7 +15,7 @@ get_marginalcontrasts <- function(
...
) {
# check if available
insight::check_if_installed("marginaleffects", minimum_version = "0.25.0")
insight::check_if_installed("marginaleffects", minimum_version = "0.29.0")

# temporarily overwrite settings that error on "too many" rows
me_option <- getOption("marginaleffects_safe")
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2 changes: 1 addition & 1 deletion R/get_marginaleffects_type.R
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Expand Up @@ -122,7 +122,7 @@

# check if marginaleffects objects has posterior draws and thus is Bayesian
.is_bayesian_marginaleffects <- function(model) {
insight::check_if_installed("marginaleffects", minimum_version = "0.28.0.22")
insight::check_if_installed("marginaleffects", minimum_version = "0.29.0")
!is.null(suppressWarnings(marginaleffects::get_draws(model, "PxD")))
}

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2 changes: 1 addition & 1 deletion R/get_marginalmeans.R
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[air] reported by reviewdog 🐶

modelbased/R/get_marginalmeans.R

Lines 24 to 32 in 18d47e1

get_marginalmeans <- function(model,
by = "auto",
predict = NULL,
ci = 0.95,
estimate = NULL,
transform = NULL,
keep_iterations = FALSE,
verbose = TRUE,
...) {

Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ get_marginalmeans <- function(model,
verbose = TRUE,
...) {
# check if available
insight::check_if_installed("marginaleffects")
insight::check_if_installed("marginaleffects", minimum_version = "0.29.0")

# First step: process arguments --------------------------------------------
# --------------------------------------------------------------------------
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34 changes: 16 additions & 18 deletions R/get_marginaltrends.R
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Expand Up @@ -7,19 +7,21 @@
#' get_marginaltrends(model, trend = "Petal.Length", by = "Petal.Length")
#' get_marginaltrends(model, trend = "Petal.Length", by = c("Species", "Petal.Length"))
#' @export
get_marginaltrends <- function(model,
trend = NULL,
by = NULL,
predict = NULL,
ci = 0.95,
estimate = NULL,
transform = NULL,
p_adjust = "none",
keep_iterations = FALSE,
verbose = TRUE,
...) {
get_marginaltrends <- function(
model,
trend = NULL,
by = NULL,
predict = NULL,
ci = 0.95,
estimate = NULL,
transform = NULL,
p_adjust = "none",
keep_iterations = FALSE,
verbose = TRUE,
...
) {
# check if available
insight::check_if_installed("marginaleffects")
insight::check_if_installed("marginaleffects", minimum_version = "0.29.0")
dots <- list(...)

# set defaults
Expand Down Expand Up @@ -107,12 +109,7 @@ get_marginaltrends <- function(model,

# setup arguments again
fun_args <- insight::compact_list(c(
list(
model,
variables = myargs$trend,
by = myargs$by,
conf_level = ci
),
list(model, variables = myargs$trend, by = myargs$by, conf_level = ci),
dots
))

Expand All @@ -124,6 +121,7 @@ get_marginaltrends <- function(model,
fun_args$newdata <- datagrid
}

# fmt: skip
# handle distributional parameters
if (!is.null(predict) && inherits(model, "brmsfit") && predict %in% .brms_aux_elements(model)) {
fun_args$dpar <- predict
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2 changes: 1 addition & 1 deletion R/p_adjust.R
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Expand Up @@ -158,7 +158,7 @@

int <- paste0(pred, ":", mod)
if (inherits(x, c("marginaleffects_slopes", "slopes", "marginaleffects"))) {
insight::check_if_installed("marginaleffects", minimum_version = "0.28.0.22")
insight::check_if_installed("marginaleffects", minimum_version = "0.29.0")
model <- marginaleffects::components(x, "model")
} else {
model <- attributes(x)$model
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2 changes: 1 addition & 1 deletion tests/testthat/test-attributes_estimatefun.R
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skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("attributes_means", {
data(iris)
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2 changes: 1 addition & 1 deletion tests/testthat/test-backtransform_invlink.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("glmmTMB")

test_that("estimate_means correct inverse link for glmmTMB", {
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2 changes: 1 addition & 1 deletion tests/testthat/test-betareg.R
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skip_on_cran()
skip_if_not_installed("curl")
skip_if_offline()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("betareg")

test_that("estimate_means for betareg", {
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2 changes: 1 addition & 1 deletion tests/testthat/test-bias_correction.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("emmeans")
skip_if_not_installed("lme4")

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2 changes: 1 addition & 1 deletion tests/testthat/test-brms-marginaleffects.R
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Expand Up @@ -4,7 +4,7 @@ skip_if_offline()
skip_if_not_installed("brms")
skip_if_not_installed("BH")
skip_if_not_installed("RcppEigen")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("httr2")
skip_if_not_installed("withr")

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9 changes: 7 additions & 2 deletions tests/testthat/test-brms.R
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Expand Up @@ -4,10 +4,15 @@ skip_if_not_installed("brms")
skip_if_not_installed("BH")
skip_if_not_installed("RcppEigen")
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_means - brms", {
model <- brms::brm(Sepal.Length ~ Species * Sepal.Width, data = iris, refresh = 0, iter = 1000)
model <- brms::brm(
Sepal.Length ~ Species * Sepal.Width,
data = iris,
refresh = 0,
iter = 1000
)
estim <- estimate_means(model, backend = "emmeans")
expect_identical(dim(estim), c(3L, 5L))
})
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_contrasts-average.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")


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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_contrasts.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")

test_that("estimate_contrasts - Frequentist, one factor", {
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_contrasts_bookexamples.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")

test_that("estimate_contrasts - book examples 1", {
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_contrasts_effectsize.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("bootES")
skip_if_not_installed("lme4")
skip_on_os("mac")
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_contrasts_inequality.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")
skip_if(getRversion() < "4.5.0")
skip_if_not_installed("datawizard")
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4 changes: 2 additions & 2 deletions tests/testthat/test-estimate_expectation.R
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skip_if_not_installed("insight", minimum_version = "1.1.0")
skip_if_not_installed("insight", minimum_version = "1.4.1")

test_that("estimate_expectation", {
skip_if_not_installed("lme4")
Expand Down Expand Up @@ -77,7 +77,7 @@ test_that("estimate_expectation - error", {


test_that("estimate_relation and estimate specific", {
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
data(efc, package = "modelbased")
efc <- datawizard::to_factor(efc, c("c161sex", "c172code", "e16sex", "e42dep"))
fit <- lm(neg_c_7 ~ c12hour + barthtot + c161sex + e42dep + c172code, data = efc)
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_filter.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")

test_that("filtering for by and contrast works for different estimate options", {
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_means-average.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")


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4 changes: 2 additions & 2 deletions tests/testthat/test-estimate_means.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_means() - lm", {
data(mtcars)
Expand Down Expand Up @@ -327,7 +327,7 @@ test_that("estimate_means() - glm", {


test_that("get_marginaleffects, overall mean", {
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("emmeans")

model <- lm(Sepal.Width ~ Species * Petal.Length, data = iris)
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_means_ci.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_means() - ci frequentist", {
data(iris)
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_means_counterfactuals.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("glmmTMB")
skip_if_not_installed("lme4")

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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_means_dotargs.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_means() - estimate = average", {
data(mtcars)
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_means_marginalization.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_means() - estimate options", {
data(efc, package = "modelbased")
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_means_mixed.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_means() - mixed models", {
skip_if_not_installed("lme4")
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_predicted.R
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skip_if_not_installed("insight", minimum_version = "1.1.0")
skip_if_not_installed("insight", minimum_version = "1.4.1")

test_that("estimate_relation - shape", {
skip_if_not_installed("gamm4")
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2 changes: 1 addition & 1 deletion tests/testthat/test-estimate_slopes.R
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skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("estimate_slopes", {
data(iris)
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2 changes: 1 addition & 1 deletion tests/testthat/test-g_computation.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("nanoparquet")
skip_on_os("mac")

Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-get_marginaltrends.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("emmeans")

test_that("get_marginaltrends", {
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-glmmTMB.R
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skip_on_cran()
skip_if_not_installed("glmmTMB")
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

data <- glmmTMB::Salamanders
model <- suppressWarnings(glmmTMB::glmmTMB(
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-joint_test.R
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skip_on_cran()
skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_on_os("mac")

test_that("estimate_contrasts - joint test, 2-way", {
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2 changes: 1 addition & 1 deletion tests/testthat/test-keep_iterations.R
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skip_on_cran()
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("emmeans")
skip_if_not_installed("brms")
skip_if_not_installed("curl")
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2 changes: 1 addition & 1 deletion tests/testthat/test-mgcv.R
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skip_if_not_installed("emmeans")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("mgcv")
skip_if_not_installed("gamm4")

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2 changes: 1 addition & 1 deletion tests/testthat/test-mice.R
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skip_on_cran()
skip_if_not_installed("mice")
skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")

test_that("pool_predictions", {
set.seed(123)
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2 changes: 1 addition & 1 deletion tests/testthat/test-multivariate_response.R
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skip_if_not_installed("marginaleffects", minimum_version = "0.28.0.22")
skip_if_not_installed("marginaleffects", minimum_version = "0.29.0")
skip_if_not_installed("lme4")

test_that("multivariate response", {
Expand Down
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