GetClosestSamples: Get n samples

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

Description

Get n samples

Usage

GetClosestSamples(
  n,
  phy_full,
  taxa_feasible,
  replace_full = TRUE,
  replace_feasible = FALSE,
  truncate_full_to_mrca = FALSE,
  less_memory = FALSE,
  descendant_labeled = FALSE,
  fast_ultrametric = FALSE,
  verbose = TRUE
)

Arguments

n	How many taxa to sample
phy_full	A phylo object with all feasible taxa to sample from
taxa_feasible	A vector of taxon names that are feasible to study (often on another tree)
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
less_memory	If TRUE, uses a much slower approach that will not create giant matrices
descendant_labeled	If TRUE, assumes the phy_full has been labeled with LabelNodesWithFeasibleDescendants
fast_ultrametric	If TRUE, uses a fast algorithm for ultrametric trees
verbose	If TRUE, all the output will print to the screen

Value

A data.frame of chosen taxa, closest feasible match, and distance between them

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