Comparison of functions for comparative phylogenetics

May 11, 2011
By

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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
Get Liam Revell’s functions here: http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/

> # Load 
require(motmot); require(geiger); require(picante)
source("http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/phylosig/v0.3/phylosig.R")
source("http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/fastBM/v0.4/fastBM.R")
 
# Make tree
tree <- rcoal(10)
 





# Transform branch lengths
> system.time( replicate(1000, transformPhylo(tree, model = "lambda", lambda = 0.5)) ) # motmot
user system elapsed
1.757 0.004 1.762
> system.time( replicate(1000, lambdaTree(tree, 0.9)) ) # geiger
user system elapsed
3.708 0.008 3.716
> # motmot wins!!!




# Simulate trait evolution
system.time( replicate(1000, transformPhylo.sim(tree, model = "bm")) ) # motmot
user system elapsed
3.732 0.007 3.741
> system.time( replicate(1000, rTraitCont(tree, model = "BM")) ) # ape
user system elapsed
0.312 0.009 0.321
> system.time( replicate(1000, fastBM(tree)) ) # Revell
user system elapsed
1.315 0.005 1.320
> # ape wins!!!




# Phylogenetically independent contrasts
trait <- rnorm(10)
names(trait) <- tree$tip.label
 
> system.time( replicate(10000, pic.motmot(trait, tree)$contr[,1]) ) # motmot
user system elapsed
3.062 0.007 3.070
> system.time( replicate(10000, pic(trait, tree)) ) # ape
user system elapsed
2.846 0.007 2.853
> # ape wins!!!





# Phylogenetic signal, Blomberg's K
> system.time( replicate(100, Kcalc(trait, tree)) ) # picante
user system elapsed
1.311 0.005 1.316
> system.time( replicate(100, phylosig(tree, trait, method = "K")) ) # Revell
user system elapsed
0.201 0.000 0.202
> # Liam Revell wins!!!




# Ancestral character state estimation
> system.time( replicate(100, ace(trait, tree)$ace) ) # ape
user system elapsed
4.988 0.018 5.007
> system.time( replicate(100, getAncStates(trait, tree)) ) # geiger
user system elapsed
2.253 0.005 2.258
> # geiger wins!!!

__________
It’s hard to pick an overall winner because not all functions are available in all packages, but there are definitely some functions that are faster than others.

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