Drop Tips and Update a Phylogenetic Tree — drop_tips

This function iteratively removes specified tips (or tips matching a pattern) from a phylogenetic tree without collapsing internal nodes or singleton nodes.

drop_tips_update(tr, drop_name, pattern = NULL)

Arguments

tr: A phylogenetic tree of class phylo.
drop_name: A character vector of tip or node names to drop. If missing and pattern is provided, names matching the pattern will be dropped.
pattern: An optional regular expression pattern to match tip or node labels for dropping.

Value

A phylo object with specified tips removed.

Examples

if (requireNamespace("ape")) {
  library(ape)
  tr <- rtree(10)
  plot(tr)
  # Drop tips containing "t1" or "t2" in their label
  tr2 <- drop_tips_update(tr, pattern = "t1|t2")
  plot(tr2)

  # Alternatively, specify tips directly
  tr3 <- drop_tips_update(tr, drop_name = c("t3", "t5"))
  plot(tr3)
}
#> Loading required namespace: ape