Nothing
bpec.treeEdges = function(MCMCout) {
count = MCMCout$count
rootProbMean = MCMCout$rootProbs[1:MCMCout$count] + MCMCout$rootProbs[(MCMCout$count+1):(MCMCout$count * 2)]
root = which.max(rootProbMean)
levels = MCMCout$levels
datSiz = MCMCout$noSamples
clado = MCMCout$clado
seqLabels = MCMCout$seqsFile[MCMCout$seqLabels]
edgeList = NULL
plotheight = sqrt(2)
levels = levels + 1
if (length(seqLabels) < count) {
seqLabels = c(seqLabels, rep(0, count - length(seqLabels)))
}
counter = max(seqLabels) + 1
for(i in 1:count) {
if (seqLabels[i] == 0) {
seqLabels[i] = counter
counter = counter + 1
}
}
nodeOrder = array(0, count)
newNodeOrder = array(0, count)
maxLevel = max(levels)
nodeOrder[1] = root
newNodeOrder[1] = root
descendantCounter = 2
descendants = 0
for(i in 1:maxLevel) {
prevDescendants = descendants
descendants = 1
nodeOrder = newNodeOrder
for(j in 1:count) {
if (levels[j] == i) {
descendants = descendants + 1
}
}
prevOrd = descendantCounter - 1
# print(descendantcounter)
# print(prevord)
descendantcounter = 1
previousOne = -1
if (prevOrd > 0) {
for(j in 1:prevOrd) {
for(l in 1:count) {
if ((clado[(nodeOrder[j] - 1) * count + l] == 1 || clado[(l-1) * count + nodeOrder[j]] == 1) && levels[l] == i) {
# print(l)
# edgelist output
edgeList = rbind(edgeList, data.frame(vert.from = seqLabels[nodeOrder[j]], vert.to = seqLabels[l], level = i, ssize = datSiz[l]))
previousOne = l
newNodeOrder[descendantCounter] = l
descendantCounter = descendantCounter + 1
next
}
}
}
}
}
return(edgeList)
}
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