utility {picante}R Documentation

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)

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
... Additional arguments

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

Author(s)

Steven Kembel <skembel@uoregon.edu>, Peter Cowan <pdc@berkeley.edu>, David Ackerly <dackerly@berkeley.edu>


[Package picante version 0.6-1 Index]