| treestats-package {treestats} | R Documentation |
Collection of phylogenetic tree statistics
Description
The 'treestats' package contains a collection of phylogenetic tree statistics, implemented in C++ to ensure high speed.
Details
Given a phylogenetic tree as a phylo object, the 'treestats' package provides a wide range of individual functions returning the relevant statistic. In addition, there are three functions available that calculate a collection of statistics at once: calc_all_statistics (which calculates all currently implemented statistics of treestats), calc_balance_stats, which calculates all (im)balance related statistics and calc_brts_stats, which calculates all branching times and branch length related statistics. Furthermore, there are a number of additional tools available that allow for phylogenetic tree manipulation: make_unbalanced_tree, which creates an imbalanced tree in a stepwise fashion. Then there are two functions related to conversion from and to an ltable, an alternative notation method used in some simulations. These are l_to_phylo which is a C++ based version of DDD::L2phylo, which converts an ltable to a phylo object, and phylo_to_l, which is a C+ based version of DDD::phylo2L, which converts a phylo object to an ltable. Lastly, the treestats package also includes a faster, C++ based, implementation of ape::branching.times (the function branching_times), which yields the same sequence of branching times, but omits the branching names in favour of speed.
Author(s)
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
References
Phylogenetic tree statistics: a systematic overview using the new R package 'treestats' Thijs Janzen, Rampal S. Etienne bioRxiv 2024.01.24.576848; doi: https://doi.org/10.1101/2024.01.24.576848