allmodel.signal.noise: A function to compute results of QIRP, QIHP, and QIPP...
In carolinafishes/PhyInformR: Rapid Calculation of Phylogenetic Information Content

Description Usage Arguments Details Value Author(s) References Examples

This function calculates QIRP, QIHP, and QIPP across an uneven quartet while allowing for a user to define a substitution model and base frequencies.

1	allmodel.signal.noise(a, b, c, d, e, f, internode, Pi_T, Pi_C, Pi_A, Pi_G, rate_vector)

`a`	substitution model parameter. a=rTC
`b`	substitution model parameter. b=rAT
`c`	substitution model parameter. c=rGT
`d`	substitution model parameter
`e`	substitution model parameter. e=rGC
`f`	substitution model parameter. f=rGA
`internode`	Four quartet branch lengths and internode c(62.49,62.49,65,65,3.2)->internode
`Pi_T`	Base Frequency of T
`Pi_C`	Base Frequency of C
`Pi_A`	Base Frequency of A
`Pi_G`	Base Frequency of G
`rate_vector`	site rate vector, converted to class 'matrix'

Please note that base frequencies must sum to 1.

Function returns a matrix of QIRP, QIHP. and QIPP values

A. Dornburg and J.N. Fisk

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. Su, Z., Zhuo, S., Zheng, W., Francesc, L.-G., and Townsend, J. P. “The Impact of Incorporating Molecular Evolutionary Model into Predictions of Phylogenetic Signal and Noise” Frontiers in Ecology and Evolution 2, (2014): doi:10.3389/fevo.2014.00011, Available at http://dx.doi.org/10.3389/fevo.2014.00011 Su, Z. and Townsend, J. P. “Utility of Characters Evolving at Diverse Rates of Evolution to Resolve Quartet Trees with Unequal Branch Lengths: Analytical Predictions of Long-Branch Effects” BMC evolutionary biology 15, (2015): 86.

as.matrix(rag1)->rates
a<-1
b<-1
c<-1
d<-1
e<-1
f<-1
Pi_T<-.25
Pi_C<-.25
Pi_A<-.25
Pi_G<-.25
internode<-c(12,12,15,15,.37)
allmodel.signal.noise(a, b, c, d, e, f, internode, Pi_T, Pi_C, Pi_A, Pi_G, rates)