tests/checkTreeMatch.R

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

#Check that RERconverge will identify issues with tree topology,
#namely, ones where the trait tree is not a subset of the master gene tree.
require(devtools)
#install_github("nclark-lab/RERconverge",branch="MatchingTrees")
library('RERconverge')
repopath = '~/repos/RERconverge' #local path to repo
#repopath = '~/Documents/GitHub/RERconverge'
rerpath = find.package('RERconverge') #will files in the tests directory be installed here?

#If necessary, convert species names using 'convertSpeciesNames'
#Conversion table should be 'cctab' (or readable from 'SpeciesNamesConversionTable0818.csv')

#Use same master tree for all cases:
toytreefile = "subsetMammalGeneTrees.txt"
toyTrees=readTrees(paste(rerpath,"/extdata/",toytreefile,sep=""), max.read = 200)

#Example cases:
# -rooted trait tree
# -different tree topology
ucsctree = read.tree(paste(repopath,'tests/ucsc62mammals_commonnames.tre',sep='/'))
ttucsc = tree2Paths(ucsctree, toyTrees)

# -species in the trait tree that are not in the master tree
# -this tree also has a different tritomy (i.e., it is pseudo-rooted on a different branch)
pon1tree = read.tree(paste(repopath,'tests/PON1_addl_species.tre',sep='/'))
ttpon1 = tree2Paths(pon1tree, toyTrees)

# -different species filtered from trait tree and master tree

#Check what happens if getAllResiduals uses a different set of species from those in the trait tree