R Hackathon 1/Targets and Accomplishments

From Phyloinformatics
Jump to: navigation, search

Current status of hackathon targets and accomplishments

Diversification (Alfaro, Midford, Orme, Rabosky)

  • Implementation of Binary-state speciation / extinction (BiSSE) model in R
    • Status: ?
  • Implementing Ree (2005) key innovation test
    • Status: ?
  • Major update to package laser; added set of functions to test for diversification rate shifts using combined phylogenetic and taxonomic data
    • Status: ?
  • Vignettes written for several diversification rate analyses
    • Status: ?

Divergence Time (Bell, Loarie, Swofford, Waddell)

  • Recode penalized likelihood method in ape
    • Status: ?
  • Implement new models of rate change other than Poisson approximation
    • Status: ?
  • Implement code in C for cross checking
    • Status: ?
  • New tree parameterization
    • Status: ?
  • Wrote HowTo estimate divergence times in R
    • Status: ?

Documentation (Price, Sidlauskas, Smith, Vision, Zanne)

Class Design (Bolker, Butler, Cowan, de Vienne, Jombart, Kembel, O'Meara, Paradis)

  • Phylobase package
    • Status: Online at R-Forge, to be released on CRAN?

Mesquite-R (Lapp, Maddison)

  • Installable package RMesquite
    • Status: ?
  • Vignettes and API documentation in RMesquite are still missing.
    • Status: ?
  • Provide coercion of Mesquite Tree and Character data objects to phylo4 and phylo4d S4 classes.
    • Status: ?
  • Provide coercion for Mesquite Project object to an R object or class (e.g., phylo4d?).
    • Status: ?
  • Provide way to inspect the possible options for "Employees" that Mesquite has available to hire by a particular general analysis class, and a way to pass a choice into Mesquite.
    • Status: ?
  • Getting Mesquite calling R fully working and & easily installable on Windows and Linux.
    • Status: ?

Input/Output (Desper, Hiebl, O'Meara, Zwickl)

  • Input of trees and data from Nexus files
    • Status: accomplished, part of phylobase
  • Output of trees and data from R to other formats
    • Status: ?
  • Calling other programs (MrBayes, etc.) from R
    • Status: ?

Trait Evolution (Harmon, Hipp, Hunt)

  • Compare various implementations of the same methods (ape, geiger, OUCH, Mesquite)
  • Improve functionality of character fitting in R
    • Status: Implemented in geiger package
  • Identify gaps in current implementation
    • The main gap, from an end-user perspective, is obtaining estimates of ancestral character states in R. ape does this, but only for joint likelihoods, and the function sometimes has trouble finding the ML solution. There is no way to get marginal ancestral character states for discrete characters in r other than interfacing with Mesquite
    • Status: ?
  • Implement "white noise" and Brownian motion with a trend models in geiger's fitContinuous
    • Status: ?
  • Investigate statistical properties of these methods
    • Status: ?