build_consensus_tree: Build the consensus tree (i.e. the tree with the highest...

In mrajeev08/treerabid: Reconstruct Rabies Transmission Trees

Build the consensus tree (i.e. the tree with the highest proportion of consensus links)

Description

Build the consensus tree (i.e. the tree with the highest proportion of consensus links)

Usage

build_consensus_tree(
  links_consensus,
  ttrees,
  links_all,
  type = c("majority", "mcc"),
  output = c("tree", "sim")
)

Arguments

links_consensus	output from build_consensus_links
ttrees	bootstrapped trees from boot_trees
links_all	the links summarized over the trees from build_all_links
type	how to summarize the trees, either majority rule or Maximum clade credibility-ish
output	whether to output the consensus tree or the sim number of the consensus tree

Value

a data.table with the consensus tree (with score for each link, 1 if the consensus link, 0 if not.

mrajeev08/treerabid documentation built on Oct. 15, 2024, 12:14 p.m.