SubsampleTree: Return a sampled tree

In bomeara/closesamples: Gets feasible taxon samples on a tree

Description

Return a sampled tree

Usage

SubsampleTree(
  phy_feasible,
  n,
  phy_full = NULL,
  replace_full = TRUE,
  replace_feasible = FALSE,
  truncate_full_to_mrca = FALSE,
  less_memory = FALSE,
  verbose = TRUE
)

Arguments

phy_feasible	The tree to subsample
n	The number of taxa to include
phy_full	The larger tree giving relationships
replace_full	If TRUE, will allow selecting the same taxon from the full tree more than once. If FALSE, forbids this. Both cases return n taxa
replace_feasible	If TRUE, will allow selecting the same taxon from the set of feasible taxa more than once (returning a smaller than desired tree). If FALSE, forbids this.
truncate_full_to_mrca	If TRUE, prune the full tree to the node that is the MRCA of the feasible tree
less_memory	If TRUE, uses a much slower approach that will not create giant matrices
verbose	If TRUE, all the output will print to the screen

Value

A phylo object where taxa are sampled based on representing flat sampling from taxonomy

bomeara/closesamples documentation built on Nov. 14, 2021, 9:48 a.m.