training.data: Format the training data from each simulated replicate

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

Description

A function that calcualte the summary stats for each simulated folder using function sumstat, and format the output for DAPC running

Usage

training.data(repfolder,phylonet.path)

Arguments

repfolder	The path to the folder containing s_tree.trees, l_trees.trees, and g_trees.trees. If missing, taking following three file paths
sfile	species tree file
lfile	locus tree file, labels need to be the same as the 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 dataframe that is formated for DAPC run

##—- 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.