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# Functions to deal with bad matrix condition
# Written by Brian O'Meara
tree.kappa <- function(phy){
return(kappa(ape::vcv(phy)))
}
fix.kappa <- function(phy, data, threshold = log(40)) {
current.kappa <- tree.kappa(phy)
while(current.kappa > threshold & ape::Ntip(phy)>2) {
tree.structure <- cbind(phy$edge, phy$edge.length)
tip.structure <- tree.structure[which(tree.structure[,2]<=ape::Ntip(phy)),]
short.tip <- tip.structure[which.min(tip.structure[,3]),2]
data <- data[data[,1]!=phy$tip.label[short.tip],]
phy <- ape::drop.tip(phy, short.tip)
current.kappa <- tree.kappa(phy)
}
return(list(phy=phy, data=data))
}
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