Thanks to Emmanuel for adding the equiprob=TRUE option to multi2di. However,
I’m not convinced that it’s working correctly - I still get more balanced trees
than unbalanced trees in ape 5.4.1
> library(phytools)
> library(phangorn)
> library(ape)
> packageVersion("ape")
[1] '5.4.1'
> reps <- do.call(c, lapply(1:100000, function(x)
+ multi2di(starTree(c('a','b','c','d')), equiprob=TRUE)))
> balanced = read.tree(text="((a,c),(b,d));”) # test one of 15 4-tomy
> resolutions
> test <- sapply(reps, function(x) RF.dist(x, balanced, rooted=TRUE) == 0)
> mean(test) # should be ~ 1/15 ~ 0.0667
[1] 0.16625
By the way, there is a spelling mistake on the ape homepage too ("ape souce
code” - is missing an “r” in “source”).
Cheers
Yan
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