Function for phylogeny resolution

January 13, 2012
By

(This article was first published on Recology - R, and kindly contributed to R-bloggers)

UPDATE: Yeah, so the treeresstats function had a problem in one of the calculations. I fixed that and added some more calulcations to the function.

I couldn’t find any functions to calculate number of polytomies, and related metrics.

Here’s a simple function that gives four metrics on a phylo tree object:

Here’s output from the gist above:

$trsize_tips
[1] 15

$trsize_nodes
[1] 13

$numpolys
[1] 1

$numpolysbytrsize_tips
[1] 0.06666667

$numpolysbytrsize_nodes
[1] 0.07692308

$proptipsdescpoly
[1] 0.2

$propnodesdich
[1] 0.9230769

And an example with many trees:

trsize_tips trsize_nodes numpolys numpolysbytrsize_tips numpolysbytrsize_nodes proptipsdescpoly propnodesdich
20 13 4 0.20 0.31 0.7 0.69
20 7 3 0.15 0.43 0.9 0.57
20 11 6 0.30 0.55 1.0 0.45
20 13 4 0.20 0.31 0.7 0.69
20 9 5 0.25 0.56 1.0 0.44

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