Nothing
##' @importFrom progress progress_bar
##' @importFrom Rcpp loadRcppModules
##' @importFrom stats na.omit
collapse_singles <- function(tree, show_progress) {
if (is.null(tree$edge.length)) {
elen <- numeric(0)
} else {
elen <- tree$edge.length
}
res <- collapse_single_cpp(
ances = tree$edge[, 1],
desc = tree$edge[, 2],
elen = elen,
nnode = tree$Nnode,
show_progress = show_progress
)
new_mat <- matrix(c(res$ances, res$desc), ncol = 2)
tree$edge <- new_mat
if (length(res$edge.length) > 1) {
tree$edge.length <- res$edge.length
}
tree$Nnode <- res$Nnode
if (!is.null(tree$node.label)) {
idx_nd_lbl <- res$position_singletons + 1 - length(tree$tip.label)
warning("Dropping singleton nodes with labels: ",
paste(stats::na.omit(tree$node.label[idx_nd_lbl]), collapse = ", "))
tree$node.label <- tree$node.label[- idx_nd_lbl]
}
tree
}
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