Nothing
# Klaus 15.4.2013
mccrTest <- function (CladeSize, NumberMissing, NumberOfReps, ObservedGamma = NULL, fname = NULL)
{
if (is.null(fname)) {
v <- vector("list", NumberOfReps)
for (i in 1:NumberOfReps){
# v[[i]] <- birthdeath.tree(b = 0.1, d = 0, taxa.stop = CladeSize);
v[[i]] <- sim.bdtree(b = 0.1, d = 0, stop = "taxa", n = CladeSize);
if (NumberMissing > 0)
# v[[i]] <- drop.tip(v[[i]], as.character(sample((1:CladeSize), NumberMissing)));
v[[i]] <- drop.tip(v[[i]], sample(CladeSize, NumberMissing));
}
} else {
v <- read.tree(file = fname)
}
NullGamma <- unlist(lapply(v, gammaStat))
CriticalValue <- as.numeric(quantile(NullGamma, 0.05))
if (!is.null(ObservedGamma)) {
p.value <- (length(NullGamma[NullGamma <= ObservedGamma]) +
1)/(1 + length(NullGamma))
return(list(null.gamma = NullGamma, critical.value = CriticalValue,
p.value = p.value))
}
else {
return(list(null.gamma = NullGamma, critical.value = CriticalValue))
}
}
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