Nothing
calc.parse <-
function(sTree, assoc) {
# Descr: parses species tree nodes for metric calculation
# Deps: calchelpers.dmvparse
# I/p: sTree
# assoc
debugBool = get("P2C2M_flg_dbgBool", envir=P2C2M_globalVars)
if (debugBool) {
cat("\n",xtermStyle::style("DEBUG> calc.parse",fg="red"),sep="")
}
# DEBUGLINES:
#cat("\nassoc\n"); print(assoc)
#cat("\nsTree$tip.label\n"); print(sTree$tip.label)
spNames = sTree$tip.label
n_sp = length(spNames)
#nBr = (2*n_sp)-1
tiplist = list()
for(i in 1:n_sp) {
tiplist[[spNames[i]]] = assoc[which(assoc[,1]==spNames[i]),2]
}
dmvD = calchelpers.dmvparse(sTree, n_sp) # returns demographic info of the species tree
n_tips_per_sp = lapply(tiplist, length) # calculate number of tips per species
if(any(n_tips_per_sp==1)) { # evaluate number of tips per species tree
tmp = dmvD[-which(n_tips_per_sp==1),] # Remove dmv values for terminals (i.e., where n_tips_per_sp==1)
} else {
tmp = dmvD
}
nodes = tmp[,"node"]
names(nodes) = NULL
outD = list()
outD$nodes = nodes
outD$dmvD = dmvD
return(outD)
}
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