tree_dat: Generate likelihood and parsimony scores for each tree.

In wrightaprilm/treesiftr: Visualizing The Relationship Between Phylogeny and Data

Description

Generate extra data, including likelihood and parsimony scores for each tree. Export the values as tree annotation to put into the ggplot object.

Usage

tree_dat(tree, phy_mat, start, stop, pscore = FALSE, lscore = FALSE)

Arguments

tree	Exported tree from parsimony search
phy_mat	Phylogenetic matrix
start	Which character to begin sampling characters at
stop	Which character to end sampling characters at
pscore	Boolean calculate and export parsimony scores for each character set
lscore	Boolean calculate and export likelihood scores for each character set

Value

tree Tree object with p and l scores annotated via $

Examples

data(bears)
tree <- generate_tree_vec(bears, 1, 2, tree)

wrightaprilm/treesiftr documentation built on July 15, 2019, 11:19 a.m.