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utility

Picante utility functions


Description

Picante utility functions for tree and data manipulation

Usage

df2vec(x, colID=1)
internal2tips(phy, int.node, return.names = FALSE)
node.age(phy)
pic.variance(x, phy, scaled = TRUE)
sortColumns(x)
sortRows(x)
taxaShuffle(x)
tipShuffle(phy)

Arguments

phy

phylo object

x

A data.frame, matrix or dist object

colID

Numeric or character ID of column to include

int.node

internal node number

return.names

TRUE or FALSE

scaled

Scale contrasts by branch length

Details

Various utility functions for manipulating trees, data, etc.

Value

df2vec

A named vector

internal2tips

Vector of tips descended from a node

node.age

Phylo object with phylo\$ages vector of node ages corresponding to phylo\$edge

pic.variance

Variance of independent contrasts

sortColumns

A data.frame or matrix with columns sorted by name

sortRows

A data.frame or matrix with rows sorted by name

taxaShuffle

Matrix with taxa names shuffled

tipShuffle

Phylo object with taxa names shuffled

Author(s)

Steven Kembel <steve.kembel@gmail.com>, Peter Cowan <pdc@berkeley.edu>, David Ackerly <dackerly@berkeley.edu>


picante

Integrating Phylogenies and Ecology

v1.8.2
GPL-2
Authors
Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>
Initial release
2020-06-08

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