sumstat: calculat summary statistics for a set of gene tree and a...

In huatengh/Classiphy: Classify gene trees basing on the processes generating species-tree gene-tree discordance

Usage

sumstat(repfolder=NULL,sfile=NULL,gfile=NULL,phylonet.path,max.freq=0.1,c=T,tscore=T,mdcscore=T,subtree=T)

Arguments

repfolder	The path to the folder containing s_tree.trees, l_trees.trees, and g_trees.trees. If missing, taking following two file paths
sfile	species tree file
gfile	gene tree file, labels need to be the same as the species tree file.
phylonet.path	path to the PhyloNet program
max.freq	maximum subtree frequency. As HGT events generate rare clades on gene tree, the more common a clade is among gene trees, the less interesting it is. Not an important paramter, just to save computation time and space. Default to 10

Returns a data frame ready to be classified using DAPC

##—- Should be DIRECTLY executable !! —- ##– ==> Define data, use random, ##– or do help(data=index) for the standard data sets.

## The function is currently defined as function (x) ~kwd1 ~kwd2

huatengh/Classiphy documentation built on May 21, 2019, 7:53 a.m.