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poweRbal (version 0.0.1.1)

Phylogenetic Tree Models and the Power of Tree Shape Statistics

Description

The first goal of this package is to provide a multitude of tree models, i.e., functions that generate rooted binary trees with a given number of leaves. Second, the package allows for an easy evaluation and comparison of tree shape statistics by estimating their power to differentiate between different tree models. Please note that this R package was developed alongside the manuscript "Tree balance in phylogenetic models" by S. J. Kersting, K. Wicke, and M. Fischer (2024) , which provides further background and the respective mathematical definitions. This project was supported by the project ArtIGROW, which is a part of the WIR!-Alliance ArtIFARM – Artificial Intelligence in Farming funded by the German Federal Ministry of Education and Research (No. 03WIR4805).

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Version

Install

install.packages('poweRbal')

Monthly Downloads

164

Version

0.0.1.1

License

GPL (>= 3)

Maintainer

Sophie Kersting

Last Published

August 16th, 2024

Functions in poweRbal (0.0.1.1)

print.poweRbal_data

Print and summary method for poweRbal_data objects
showTSSdata

Function for displaying TSS distributions
genAldousBetaTree

Generation of rooted binary trees under Aldous' beta splitting model
genTrees

Generation of rooted binary trees under a given tree model
enum2cladewise

Function to modify the node enumeration in rooted binary trees
getTSSdata

Functions for generating the TSS data under a tree model
powerComp

Comparison of the power of TSS under different models
plot.poweRbal_data

Plot method for poweRbal_data objects
getAccRegion

Functions for computing the region of acceptance
genGrowTree

Generation of rooted binary trees under tree growing models (no extinction)
genFordsAlphaTree

Generation of rooted binary trees under Ford's alpha model
genMBTree

Generation of the maximally balanced tree
genCombTree

Generation of the comb or caterpillar tree
genPDATree

Generation of rooted binary trees under the PDA model
genETMTree

Generation of rooted binary trees under the equiprobable-types-model (ETM)
genDensityTree

Generation of rooted binary trees under the density model
genBiSSETree

Generation of rooted binary trees under the BiSSE model
genYuleTree

Generation of rooted binary trees under the Yule model
getTSSnames

Get information on included tree shape statistics
genAltBirthDeathTree

Generation of rooted binary trees under the alternative birth-death model
genGFBTree

Generation of the greedy from the bottom tree
tssInfo

Tree shape statistics
getPowerMultTSS

Function for computing the power given the region of acceptance