Position Leverage
Provides a rough heuristic for determining the degree to which each position in the DNA matrix affects the resulting tree.
position.leverage(data, F, to = NULL, rep = 50, by = 1)
data |
A DNA matrix in |
F |
A tree estimation function, accepting a DNA matrix of class |
to |
The tree with which distances are measured in respect to, or |
rep |
The number of times to replicate the position in question. |
by |
The function will perform the calculation on every |
This function takes a DNA matrix and, for every by-th position,
replicates that position rep times, randomly removing
rep other positions to keep all sequences the same length
other positions to keep all sequences the same length. For each new DNA
matrix created in this way, F is used to estimate the corresponding
tree, and the distance to tree to is computed and stored. This
distance can be thought of as somewhat analogous to the leverage of that
position.
Returns a numeric vector of distances from tree to for each position
sampled.
John Chakerian
Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.
data(woodmouse) f.est <- function(x) root(nj(dist.dna(x)), "No305", resolve.root = TRUE) position.leverage(woodmouse, f.est, by = 10)
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