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Handle infinite values in effectiveSizeEquivalentError() #2

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Handle infinite values in effectiveSizeEquivalentError() #2

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13 changes: 11 additions & 2 deletions R/effectiveSizeEquivalentError.R
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Original file line number Diff line number Diff line change
Expand Up @@ -103,13 +103,22 @@ effectiveSizeEquivalentError <- function(simulated.samples,tree.dist="RF",measur
if ( verbose ) {
cat("\nDrawing n_eff iid samples for all measures and all chains\n")
}
iid_n_samples_max <- round(max(all_ess))
if (any(!is.finite(all_ess))) {
warning("Infinite values in ",
paste(colnames(all_ess)[colSums(!is.finite(all_ess)) > 0],
collapse = ", "),
" replaced with NA",
immediate. = TRUE
)
all_ess[!is.finite(all_ess)] <- NA
}
iid_n_samples_max <- round(max(all_ess,na.rm=TRUE))
iid_samples <- lapply(ess.methods,function(this_method) {
these_ess <- round(all_ess[,colnames(all_ess) == this_method])
iid <- simulated.samples
drawn_indices <- lapply(these_ess,function(n_eff){
# Some ESS may be in [0,1], but we can't compute any measures without trees
n_eff <- max(1,n_eff)
n_eff <- max(1,n_eff,na.rm=TRUE)
drawn <- sample.int(ntrees,n_eff,replace=TRUE,prob=topo_probs)
if (n_eff < iid_n_samples_max) {
drawn <- c(drawn,rep(NA,iid_n_samples_max - n_eff))
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