calculate.blw {philr} | R Documentation |
Calculates the weightings for ILR coordinates based on branch lenghts of a phylogenetic tree via a few different methods (see details).
calculate.blw(tree, method = "sum.children")
tree |
a |
method |
options include: (default) |
ILR balances built from a binary partition of a phylogenetic tree
can be imbued with branch length information. This function is helpful in
calculating those weightings.
There are a number of methods for calculating these weightings, the default
'sum.children'
calculates the weighting for a given balance as the sum
of its two direct children's branch length. An alternative that has been as yet less
studied is 'mean.descendants'
to calculate the weighting for a given balance
as the sum of its two direct children's branch lengths PLUS for each child the average
distance from it to its descendant tips.
Note: That some trees contain tips with branch lengths of zero length. This can result
in that tip being unreasonably downweighted, as such this function automatically
adds a small pseudocount to those tips with zero length (equal to the smallest non-zero)
branch length on the tree.
vector of weightings for ILR coordinates produced via specified method.
Justin Silverman
tr <- named_rtree(50) calculate.blw(tr, method='sum.children')[1:10] calculate.blw(tr, method='mean.descendants')[1:10]