Nothing
calchelpers.brprob <-
function(sTree, gTree, assoc, ploidy, dmvD, node) {
# Descr: organising likelihood calculations for particular branches
# Calculate prob of gene tree part, which is a subset
# of the species tree.
# More general: Calculate the prob of subtrees defined
# by their MRCA (i.e. their node).
# Deps: calchelpers.gtreeparse
# calchelpers.probcalc
# I/p: sTree
# gTree
# assoc
# ploidy
# dmvD = demographic data
# node
# Note: branching times = distance from each node to the tips,
# under the assumption that the tree is ultrametric
debugBool = get("P2C2M_flg_dbgBool", envir=P2C2M_globalVars)
if (debugBool) {
cat("\n", xtermStyle::style("DEBUG> calchelpers.brprob", fg="red"),
sep="")
}
ind = calchelpers.gtreeparse(sTree, gTree, assoc, dmvD, node)
gBt = ind$gBt
fBt = ind$fBt
lBt = ind$lBt
fNd = ind$fNd
lNd = ind$lNds
if(fBt!=0) {prob=1}
else
{
# Retain those gTree branching times (i.e. column 1) whose node names
# (i.e. column 2) fall within "fBt" and "lBt"
gBt = gBt[gBt[,1]>=fBt & gBt[,1]<=lBt,]
# Add lNd row at bottom of gBt-matrix
gBt = rbind(gBt, c(lBt, lNd))
# Perform actual prob calculation
prob = calchelpers.probcalc(gBt, dmvD, ploidy, node, fBt, lBt, fNd, lNd)
}
return(prob)
}
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