Nothing
calchelpers.gtreeparse <-
function(sTree, gTree, assoc, dmvD, node) {
# Descr: parsing branches for likelihood calculations
# Deps: calchelpers.descend
# I/p: sTree
# gTree
# assoc
# dmvD
# node
# Note: branching times = distance from each node to the tips,
# under the assumption that the tree is ultrametric
# gBt = gene tree branching times (plural!)
# fBt = first branching time
# lBt = last branching time
# fNd = first node
# lNd = last node
debugBool = get("P2C2M_flg_dbgBool", envir=P2C2M_globalVars)
if (debugBool) {
cat("\n", xtermStyle::style("DEBUG> calchelpers.gtreeparse", fg="red"),
sep="")
}
# returns the subtree that starts at node <node>
subtree = calchelpers.descend(sTree, gTree, assoc, node)
# infers the branching times for a subtree (here the gene tree)
gBt = sort(ape::branching.times(subtree))
# generate a matrix with branching times in first column and node
# names in second column
gBt = c(0, gBt)
gBt = cbind(gBt, length(gBt):1)
# get the branching times for a node in the species tree
fBt = dmvD[node,"sbt"]
# get the branching times for a node in the species tree + the branch
# lengths for that node
lBt = (dmvD[node,"sbt"] + dmvD[node,"length"])
# get those node IDs (column 2), whose gene tree branching times (column 1)
# are equal the largest of the species tree branching times
fBtMax = max(gBt[gBt[,1]<=fBt,1])
fNd = gBt[gBt[,1]==fBtMax,2]
# get those node IDs (column 2), whose gene tree branching times (column 1)
# that equal the largest of the species tree branching times + branch lengths
lBtMax = max(gBt[gBt[,1]<=lBt,1])
lNd = gBt[gBt[,1]==lBtMax,2]
outd = list("gBt"=gBt, "fBt"=fBt, "lBt"=lBt, "fNd"=fNd, "lNd"=lNd)
return(outd)
}
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