calc_sum_stats: calculate summary statistics of a phylogenetic tree, compared...

In nodeSub: Simulate DNA Alignments Using Node Substitutions

calculate summary statistics of a phylogenetic tree, compared with a reference tree. The following statistics are calculated: the beta statistic, gamma statistic, crown age, mean branch length, number of tips, the nLTT statistic and the laplacian difference, given by RPANDA's JSDtree. Because JSDtree can sometimes cause issues, some additional checks are performed to ensure that is possible to run this function.

Description

calculate summary statistics of a phylogenetic tree, compared with a reference tree. The following statistics are calculated: the beta statistic, gamma statistic, crown age, mean branch length, number of tips, the nLTT statistic and the laplacian difference, given by RPANDA's JSDtree. Because JSDtree can sometimes cause issues, some additional checks are performed to ensure that is possible to run this function.

Usage

calc_sum_stats(trees, true_tree, verbose = FALSE)

Arguments

trees	a phyloList object containing multiple trees
true_tree	a phylo object containing the reference tree, preferably without extinct lineages. If extinct lineages are found, these are dropped.
verbose	verbose output if true (e.g. progressbars)

Value

list with two tibbles 1) containing the summary statistics of all trees and 2) containing the difference with the true tree

nodeSub documentation built on Nov. 14, 2023, 5:10 p.m.