cluster.signal.noise: Quantify Quartet Resolution Probabilities Using 2012...

Description Usage Arguments Details Value Author(s) References Examples

Description

Quantify Quartet Resolution Probabilities (QIRP, QIHP, and QIPP) Using 2012 Formulation and MCMC approach, outputs results to file

Usage

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cluster.signal.noise(t, t0, rateVector, nsims, s, filename, imagename, image = "FALSE")

Arguments

t

Time from tip of tree to focal internode

t0

Focal internode length

rateVector

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

nsims

number of simulations

s

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

filename

Output file name for results of calculation

imagename

Output file name for results of visualization

image

True or False if image should visualized

Details

Please note that the two files must have different names

Value

returns QIRP, QIHP, and QIPP 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.

Examples

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as.matrix(rag1)->rr
Approximator(100,0.5,rr,3)

cluster.signal.noise(100, 2, rr, 1000,
3, filename="output_values", 
imagename="output_graphic", image = "TRUE") 

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