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[jaspMixedModels] Fix parametric bootstrap error in Generalized Linear Mixed Models. ... #285

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[jaspMixedModels] Fix parametric bootstrap error in Generalized Linear Mixed Models. ... #285

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24 changes: 24 additions & 0 deletions R/MixedModelsCommon.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,30 @@
# TODO: Expose priors specification to users in Bxxx?
# TODO: Add 3rd level random effects grouping factors ;) (not that difficult actually)

# Workaround for afex::mixed with parametric bootstrap calling glmer with REML argument
# glmer() does not accept REML (GLMMs are always fit with ML), but afex passes REML = FALSE
# Patch lme4::glmer to accept but ignore REML argument
# This runs via .onLoad to ensure namespace is properly unlocked
.glmerPatchEnv <- new.env()
assign(".glmer_patched", FALSE, envir = .glmerPatchEnv)

.onLoad <- function(libname, pkgname) {
# Only patch once
if (!get(".glmer_patched", envir = .glmerPatchEnv)) {
ns <- asNamespace("lme4")
if (unlockBinding("glmer", ns)) {
.glmer_orig <<- get("glmer", envir = ns, inherits = FALSE)
ns$glmer <- function(...) {
args <- list(...)
args$REML <- NULL
do.call(.glmer_orig, args)
}
lockBinding("glmer", ns)
assign(".glmer_patched", TRUE, envir = .glmerPatchEnv)
}
}
}

.mmRunAnalysis <- function(jaspResults, dataset, options, type) {

.setOptions()
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