as.TreeNumber not identifying unique topologies about treetools HOT 4 CLOSED

Hi, thanks for the query. From a first glance, my guess would be that the trees' tip labels are not labelled in the same sequence in all trees, and thus that your value of tips is a list (rather than a character vector).

trees <- RenumberTips(trees, TipLabels(trees[[1]]) would ensure that the tips are labelled in a consistent order in all trees. If this doesn't solve your issue, then sending your tree file (as an attachment here, or by e-mail) would help me to explore further.

Either way it looks like I could improve the documentation, or adapt the function to support a list format for tipLabels, so please let me know how you get on.

Thanks

Martin

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Hi Martin,

Thank you so much for your fast response. I tried two things today, the first was your suggestion with the tip labels and the second was I first sorted each tree by tip, and then used that new tip label variable:

tips <- TipLabels(trees)
sorted <- SortTree(trees, how = "tip")
tips2 <- TipLabels(sorted)
possible <- as.TreeNumber(sorted, nTip=7, tipLabels=tips2)

Scanning thru the results it seems like your suggestion and this sorting method give the exact same score for all 299 trees. In most cases this is the same as my first attempt, but in many places they do differ.

While I was trying to figure this out, I did find some code on the phytools blog that finds unique topologies in a set of trees and gives them an arbitrary number. I'm looking to see if that also corresponds well to what I just recovered.

Thanks again for such a quick response.

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Thanks for the update. To investigate this further, I think I'll need to see the trees themselves. If you can't post them here, please send to martin.smith at durham.ac. uk

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I'm closing this issue for now as I can't reproduce the behaviour myself. If you're still seeing the issue, or if you are able to send me some sample trees, please do reopen the thread.

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