Package: poweRbal 0.0.1.1

poweRbal: Phylogenetic Tree Models and the Power of Tree Shape Statistics

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) <doi:10.48550/arXiv.2406.05185>, 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).

Authors:Sophie Kersting [aut, cre], Kristina Wicke [aut], Mareike Fischer [aut]

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poweRbal.pdf |poweRbal.html✨
poweRbal/json (API)

# Install 'poweRbal' in R:
install.packages('poweRbal', repos = c('https://sophiekersting.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.30 score 158 downloads 32 exports 54 dependencies

Last updated 3 months agofrom:ff7a8c6db5. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winOKNov 15 2024
R-4.5-linuxOKNov 15 2024
R-4.4-winOKNov 15 2024
R-4.4-macOKNov 15 2024
R-4.3-winOKNov 15 2024
R-4.3-macOKNov 15 2024

Exports:computeAccRegionenum2cladewisegenAldousBetaTreegenAltBirthDeathTreegenBiSSETreegenCombTreegenDensityTreegenETMTreegenFordsAlphaTreegenGFBTreegenGrowTreegenMBTreegenPDATreegenTreesgenYuleTreegetAccRegiongetAccRegion_exactgetAccRegion_sampledgetAllTSSgetPowerMultTSSgetTSScolorsgetTSSdatagetTSSdata_treesgetTSSnamesgetTSSonly_bingetTSSsafe_ngetTSSsimplegetTSStypepowerComppowerComp_RegAccshowTSSdatatssInfo

Dependencies:apecachemcliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdiversitreedoParallelexpmfarverfastmapfastmatchforeachgenericsgluegmpigraphiteratorslabelinglatticelifecyclemagrittrmapsMASSMatrixmemoisemnormtmunsellnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogR.methodsS3R.ooR.utilsR6RColorBrewerRcpprlangscalesscatterplot3dsubplextreebalancevctrsviridisLite

Readme and manuals

Help Manual

Help pageTopics
Function to modify the node enumeration in rooted binary treesenum2cladewise
Generation of rooted binary trees under Aldous' beta splitting modelgenAldousBetaTree
Generation of rooted binary trees under the alternative birth-death modelgenAltBirthDeathTree
Generation of rooted binary trees under the BiSSE modelgenBiSSETree
Generation of the comb or caterpillar treegenCombTree
Generation of rooted binary trees under the density modelgenDensityTree
Generation of rooted binary trees under the equiprobable-types-model (ETM)genETMTree
Generation of rooted binary trees under Ford's alpha modelgenFordsAlphaTree
Generation of the greedy from the bottom treegenGFBTree
Generation of rooted binary trees under tree growing models (no extinction)genGrowTree
Generation of the maximally balanced treegenMBTree
Generation of rooted binary trees under the PDA modelgenPDATree
Generation of rooted binary trees under a given tree modelgenTrees
Generation of rooted binary trees under the Yule modelgenYuleTree
Functions for computing the region of acceptancecomputeAccRegion getAccRegion getAccRegion_exact getAccRegion_sampled
Function for computing the power given the region of acceptancegetPowerMultTSS
Functions for generating the TSS data under a tree modelgetTSSdata getTSSdata_trees
Get information on included tree shape statisticsgetAllTSS getTSScolors getTSSnames getTSSonly_bin getTSSsafe_n getTSSsimple getTSStype
Plot method for poweRbal_data objectsplot.poweRbal_data
Comparison of the power of TSS under different modelspowerComp powerComp_RegAcc
Print and summary method for poweRbal_data objectsprint.poweRbal_data summary.poweRbal_data
Function for displaying TSS distributionsshowTSSdata
Tree shape statisticstssInfo