genPDATree

<code>genPDATree</code> - Generates a rooted binary tree in <code>phylo</code>
format with the given number of <code>n</code> leaves under the
proportional-to-distinguishable-arrangements model.
Given <code>n</code>, all phylogenies (trees with labeled leaves) with
<code>n</code> leaves are equiprobable under the PDA.

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).

Sophie Kersting

poweRbal

Phylogenetic Tree Models and the Power of Tree Shape Statistics

Kristina Wicke

Mareike Fischer

genPDATree function

<dl><dt>n</dt>
<dd>Integer value that specifies the desired number of leaves, i.e.,
vertices with in-degree 1 and out-degree 0. 
Due to the restrictions of the <code>phylo</code> or <code>multiphylo</code> format,
the number of leaves must be at least 2 since there must be at
least one edge.</dd></dl>

Arguments

Generation of rooted binary trees under the PDA model — genPDATree

<dl>

<dt>n</dt>
<dd>Integer value that specifies the desired number of leaves, i.e.,
vertices with in-degree 1 and out-degree 0. 
Due to the restrictions of the <code>phylo</code> or <code>multiphylo</code> format,
the number of leaves must be at least 2 since there must be at
least one edge.</dd>

</dl>

genPDATree: Generation of rooted binary trees under the PDA model

Description

Usage

Value

Arguments

References

Examples