reorder.sfreemap: Reorder a 'phylo' object modified by sfreemap

In dpasqualin/sfreemap: Simulation Free Stochastic Mapping

Reorder a phylo object modified by sfreemap

Description

This function reorders the edges (and all related objects) of an object phylo modified by sfreemap.

From reorder.phylo (package ape):

In the “cladewise” order each clade is formed by a series of contiguous rows. In the “postorder” order, the rows are arranged so that computations following pruning-like algorithm the tree (or postorder tree traversal) can be done by descending along these rows (conversely, a preorder tree traversal can be performed by moving from the last to the first row). The “pruningwise” order is an alternative “pruning” order which is actually a bottom-up traversal order (Valiente 2002). (This third choice might be removed in the future as it merely duplicates the second one which is more efficient.) The possible multichotomies and branch lengths are preserved.

Usage

## S3 method for class 'sfreemap'
reorder(x, ...)

Arguments

x	A tree, result of a sfreemap execution;
...	order: The resulting order. Can be cladewise or pruningwise. index.only: logical value indicating whether only an index should be returned. other arguments, passed to reorder.phylo

Value

A phylogenetic tree of class phylo with its edges reordered.

Author(s)

Diego Pasqualin [e-mail]

See Also

sfreemap, reorder.phylo

dpasqualin/sfreemap documentation built on July 5, 2023, 10:52 a.m.