rank.partitionedRAD: Bin trees into 'suppported' or 'disfavored' by locus.
In RADami: Phylogenetic Analysis of RADseq Data

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

This function takes output from match.lnL.to.trees and scores trees as favored or disfavored for all loci that satisfy the criteria specified

rank.partitionedRAD(radMat, minTrees = 10,
	                  min.overall.diff.lnL = 5,
		threshold.lnL = 2,
                    discardDoubleCounts = TRUE)

`radMat`	matrix output from `match.lnL.to.trees`
`minTrees`	integer, minimum number of unique trees required per locus
`min.overall.diff.lnL`	minimum log-likelihood difference required between the most poorly- supported tree and the best supported tree for each locus
`threshold.lnL`	the log-likelihood window for binning a tree into favored or disfavored
`discardDoubleCounts`	determines whether that place any tree within both the favored and disfavored bins should be counted (`TRUE`) or not (`FALSE`)

This function works by first filtering loci by the minimum number of trees and the overall range in log-likelihood, then binning trees into supported if they are within threshold.lnL of the best-supported tree for each locus, and disfavored if they are within threshold.lnL of the least supported tree for each locus. Overlapping trees can occur when the range in log-likelihood is set to less than twice the threshold log-likelihood or quite near it.

A list composed of 7 matrices and one numeric vector. The matrices all have loci as the rows and trees as the columns:

`bestMat`	boolean; which trees are supported by which loci
`worstMat`	boolean; which trees are disfavored by which loci
`doubleCountMat`	boolean; which trees are double-counted by which loci
`radMat`	the final likelihood matrix corresponding with `bestMat` and `worstMat`
`radMat.preLnLDiff`	the likelihood matrix before filtering by lnL range
`radMat.preMinTrees`	the likelihood matrix before filtering by minimum number of trees
`radMat.preDoubleCounts`	the likelihood matrix before filtering by double counts
`params`	the analysis parameters, in this order: minTrees, min.overall.diff.lnL, threshold.lnL, discardDoubleCounts

Andrew Hipp

Hipp A.L., Eaton D.A.R., Cavender-Bares J., Fitzek E., Nipper R. & Manos P.S. (Accepted pending revision). A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE.

match.lnL.to.trees, plot.rankedPartitionedRAD

RADami documentation built on May 30, 2017, 8:23 a.m.