picante (version 0.7-1)

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

...

Additional arguments

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

Details

Various utility functions for manipulating trees, data, etc.