phylo2sbp: Create Sequential Binary Partition from Phylogenetic Tree

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

Description

This function converts a binary phylogenetic tree to sequential binary parition to be used to then build an ILR basis for compositional metagenomic data.

Usage

1

Arguments

tr

a phylo tree object with n leaves

Details

The choice of orientation for a balance (i.e., which of the two descendant clades of an internal node is in the numerator or denominator of the log-ratio) is given by the default of the function phangorn::Children and that choise is used consistently throughout the philr package.

Value

a n by n-1 matrix of the sequential binary partition sign matrix

Author(s)

Justin Silverman

References

Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

See Also

philr

Examples

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2
tr <- named_rtree(5)
phylo2sbp(tr)

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