Modified drop.tip() from 'ape' package that also updates the recombination proportions added when loaded from CFML or Gubbins

# S3 method for useRec
drop.tip(
  phy,
  tip,
  trim.internal = TRUE,
  subtree = FALSE,
  root.edge = 0,
  rooted = is.rooted(phy),
  collapse.singles = TRUE,
  interactive = FALSE
)

Arguments

phy: Tree from loadCFML() or loadGubbins()
tip: a vector of mode numeric or character specifying the tips to delete.
trim.internal: a logical specifying whether to delete the corresponding internal branches.
subtree: a logical specifying whether to output in the tree how many tips have been deleted and where.
root.edge: an integer giving the number of internal branches to be used to build the new root edge. This has no effect if trim.internal FALSE.
rooted: a logical indicating whether the tree must be treated as rooted or not. This allows to force the tree to be considered as unrooted.
collapse.singles: a logical specifying whether to delete the internal nodes of degree 2.
interactive: if TRUE the user is asked to select the tips or the node by clicking on the tree which must be plotted.

Value

tree with rec data