## Function for phylogeny resolution

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: # calculate tree resolution stats treeresstats <- function(x) { require(phangorn) # load the phangorn package todo <- ( 1+Ntip(x)) : (Ntip(x) + Nnode(x) ) trsize_tips <- Ntip(x) trsize_nodes <- Nnode(x) polytomyvec <- sapply(todo, function(y) length(Children(x, y))) numpolys <- length(polytomyvec[polytomyvec > 2]) numpolysbytrsize_tips <- numpolys/trsize_tips numpolysbytrsize_nodes <- numpolys/trsize_nodes proptipsdescpoly <- sum(polytomyvec[polytomyvec > 2])/trsize_tips propnodesdich <- length(polytomyvec[polytomyvec == 2])/trsize_nodes list(trsize_tips = trsize_tips, trsize_nodes = trsize_nodes, numpolys = numpolys, numpolysbytrsize_tips = numpolysbytrsize_tips, numpolysbytrsize_nodes = numpolysbytrsize_nodes, proptipsdescpoly = proptipsdescpoly, propnodesdich = propnodesdich) } # Single tree example tree <- read....