Ape

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.tree(text="((((((artemisia_species:44,lactuca_species:44,senecio_species:44)6:46,campanula_species:90)5:17.75,((asclepias_species:71,galium_species:71)8:18.375,plantago_species:89.375)7:18.375)4:17.75,((cerastium_species:41.833332,silene_species:41.833332)10:41.833332,chenopodium_species:83.666664)9:41.833336)3:17.75,((geum_species:47,potentilla_species:47)12:48.125,lepidium_species:95.125)11:48.125)2:17.75,(bromus_species:12,elymus_species:12)13:149)1;") dat <- treeresstats(tree) dat # Many trees example maketrees <- function(numtrees) { require(ape); require(plyr) trees <- rmtree(numtrees, 20) llply(trees, di2multi, tol = 0.5) } trees <- maketrees(30) dat <- ldply(trees, function(x) data.frame(treeresstats(x))) dat Here’s output from the gist above: ...

I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc. Please comment if you have code for doing bayesian phylogenetic inference in R. I know phyloch has function mrbayes, but can’t get it to work… Phylogenetics in R View more presentations from schamber

I did a little simulation to examine how K and lambda vary in response to tree size (and how they compare to each other on the same simulated trees). I use Liam Revell’s functions fastBM to generate traits, and phylosig to measure phylogenetic signal. Two observations: First, it seems that lambda is more sensitive than K to tree size, but then lambda levels out at about 40 species, whereas K continues to vary around a mean of 1. Second, K is more variable than lambda at all levels of tree size (compare standard error bars). Does this make sense to those smart folks out there? ...

With all the packages (and beta stage groups of functions) for comparative phylogenetics in R (tested here: picante, geiger, ape, motmot, Liam Revell’s functions), I was simply interested in which functions to use in cases where multiple functions exist to do the same thing. I only show default settings, so perhaps these functions would differ under different parameter settings. [I am using a Mac 2.4 GHz i5, 4GB RAM] Get motmot here: https://r-forge.r-project.org/R/?group_id=782 ...