cluster.signal.noise: Quantify Quartet Resolution Probabilities Using 2012...
In PhyInformR: Rapid Calculation of Phylogenetic Information Content

Description Usage Arguments Details Value Author(s) References Examples

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

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

`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

Please note that the two files must have different names

returns QIRP, QIHP, and QIPP values

A. Dornburg

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.

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

cluster.signal.noise(100, 2, rr, 10,
3, filename="output_values", 
imagename="output_graphic", image = "TRUE")