Generate likelihood and parsimony scores for each tree.

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

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)
#> Generating tree for charset:12
#> Final p-score 2 after  0 nni operations