CODEWITHSUNDEEP
rtreephylogeny
Daniel Swindlehurst
Daniel Swindlehurst

Reputation: 29

R - Running functions on multiple pylogenetic trees (multiPhylo objects)

I'd like to run the same function across multiple phylogenies that are stored as a multiPhylo object.

For example, lets say I have multiPhylo of 1,000 trees, and I want to sum the edge/branch lengths in each of these trees. I know for a single tree I can just use:

sum(tree$edge.length)

But I can't work out how to do this for all the trees in a multiPhylo. I'm sure this is simple, but it's beyond me. Can anyone help?

Thanks

Dan

Upvotes: 1

Views: 842

Answers (1)

nya
nya

Reputation: 2250

Class multiPhylo is a list (str(tree)) and thus provides functionality that R uses to handle lists. To sum edge lengths of individual trees, use the lapply function.

lapply(tree, FUN = function(x) sum(x$edge.length))

Upvotes: 4

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