# NOT RUN {
## Detecting diversification rate variation in bird families (135 tips)
data(bird.families)
tree.birds <- as.treeshape(bird.families, model = "yule")
class(tree.birds) <- "treeshape"
pv <- sapply(1:135, FUN = function(i) shift.test(tree.birds, i, lambda1 = 1,
lambda2 = 100, nrep = 1000, silent = TRUE))
## Significant shifts detected at nodes = 67 and 78
pv[c(67,78)]
shift.test(tree.birds, node = 67, lambda1 = 1, lambda2 = 100, nrep = 10000, silent = TRUE)
shift.test(tree.birds, node = 78, lambda1 = 1, lambda2 = 100, nrep = 10000, silent = TRUE)
## visualize the shifts
par(mfrow=c(2,1))
plot(cutreeshape(tree.birds, ancestor(tree.birds, 67) , "bottom"))
plot(cutreeshape(tree.birds, 78 , "bottom"))
# }
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