Comparison of functions for comparative phylogenetics

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!!!

Created by Pretty R at inside-R.org


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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.

RHIPE package in R for interfacing between Hadoop and R

RHIPE: An Interface Between Hadoop and R
Presented by Saptarshi Guha

And this review of methods for interfacing with Hadoop suggests R's RHIPE is quite nice.

Treebase trees from R

UPDATE: See Carl Boettiger's functions/package at Github for searching Treebase here.



Treebase is a great resource for phylogenetic trees, and has a nice interface for searching for certain types of trees. However, if you want to simply download a lot of trees for analyses (like that in Davies et al.), then you want to be able to access trees in bulk (I believe Treebase folks are working on an API though). I wrote some simple code for extracting trees from Treebase.org.

It reads an xml file of (in this case consensus) URL's for each tree, parses the xml, makes a vector of URL's, reads the nexus files with error checking, remove trees that gave errors, then a simple plot looking at metrics of the trees.

Is there an easier way to do this?