space.maker: Core Function required to assemble heatmaps of QIRP as in...

Description Usage Arguments Value Author(s) References Examples

Description

Core function required to create heatmaps as in Prum et al. 2015.

Usage

1
space.maker(rateVector, t, s)

Arguments

rateVector

An object containing a vector of site rates transformed to class "matrix"

t

Time of quartet (e.g, bigT from Townsend et al. 2012)

s

A number representing the character state space that generated the site rates (e.g., s=2 for binary data)

Value

Computes a range of QIRP values

Author(s)

A. Dornburg

References

Townsend, J. P., Su, Z., and Tekle, Y. I. “Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny” Systematic biology 61, no. 5 (2012): 835–849. Prum, R. O., Berv, J. S., Alex, D., Field, D. J., Townsend, J. P., Lemmon, E. M., and Lemmon, A. R. “A Comprehensive Phylogeny of Birds (Aves) Using Targeted next-Generation DNA Sequencing” Nature 526, no. 7574 (2015): 569–573.

Examples

1
2
as.matrix(rag1)->rr
space.maker(rr,15,3)

carolinafishes/PhyInformR documentation built on May 13, 2019, 12:50 p.m.