Last data update: 2014.03.03
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R: Picante utility functions
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
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x |
A data.frame, matrix or dist object
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colID |
Numeric or character ID of column to include
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int.node |
internal node number
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return.names |
TRUE or FALSE
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scaled |
Scale contrasts by branch length
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... |
Additional arguments
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Details
Various utility functions for manipulating trees, data, etc.
Value
df2vec |
A named vector
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internal2tips |
Vector of tips descended from a node
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node.age |
Phylo object with phylo$ages vector of node ages corresponding to phylo$edge
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pic.variance |
Variance of independent contrasts
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sortColumns |
A data.frame or matrix with columns sorted by name
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sortRows |
A data.frame or matrix with rows sorted by name
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taxaShuffle |
Matrix with taxa names shuffled
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tipShuffle |
Phylo object with taxa names shuffled
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Author(s)
Steven Kembel <steve.kembel@gmail.com>, Peter Cowan <pdc@berkeley.edu>, David Ackerly <dackerly@berkeley.edu>
Results
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