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

In dpasqualin/sfreemapr: Simulation-Free Stochastic Mapping

Description

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

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

sfreemapr.reorder(tree, order='cladewise')

Arguments

tree	A tree, result of a sfreemapr.map execution
order	The resulting order. Can be cladewise or pruningwise

Value

A phylogenetic tree of class phylo with its edges reordered.

Author(s)

Diego Pasqualin [e-mail]

See Also

sfreemapr.map

dpasqualin/sfreemapr documentation built on May 15, 2019, 10:45 a.m.