Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/branch_length_calculations.R

Calculates the weightings for ILR coordinates based on branch lenghts of a phylogenetic tree via a few different methods (see details).

1 | ```
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

1 2 3 | ```
tr <- named_rtree(50)
calculate.blw(tr, method='sum.children')[1:10]
calculate.blw(tr, method='mean.descendants')[1:10]
``` |

jsilve24/philr documentation built on Aug. 1, 2019, 5:48 p.m.

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