Diversitree

Comparative phylogenetic analysis of diversification in R. The "diversitree" package includes a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution. Contains implementations of BiSSE (Binary State Speciation and Extinction; Maddison et al. 2007: Syst. Biol. 56: 701) and its unresolved tree extensions (FitzJohn et al. 2009: Syst. Biol. 58: 595), MuSSE (Multiple State Speciation and Extinction), and QuaSSE (Quantitative State Speciation and Extinction; FitzJohn 2010: Syst. Biol. in press), and GeoSSE (Geographic State Speciation and Extinction; Goldberg et al. 2010: Syst. Biol.). The package also includes support for Markov models of character evolution (e.g., Pagel 1994, and Brownian motion) and character-independent speciation/extinction (Nee et al. 1994).

Diversitree has been used in a number of studies. If you use diversitree in a paper, please let me know!

Installation

The simplest route is to install the package through R:

      install.packages("diversitree")
    

will install diversitree from CRAN (current CRAN version: 0.7-2).

Download and installation from source

The source package can be downloaded from here.

It is important that this file is not uncompressed by your browser. If the file is downloaded without the "gz" extension, try right-clicking the file and selecting "Save file as" (or similar depending on your browser). Mac users might try

      curl -O http://www.zoology.ubc.ca/prog/diversitree/diversitree_0.7-7.tar.gz
    

from the command line.

This download is a source package only; you will need a working C and Fortran compiler to install the package. (Xcode + gfortran is sufficient on Mac OS X, most Linux systems are probably fine as-is, and on windows consider MinGW or the tools here). First, install the packages deSolve, ape, and subplex From within R, run

      install.packages("diversitree_0.7-7.tar.gz", repos=NULL, type="source")
    

which will compile and install the package.

See here for more information, for known problems with Mac OS X 10.5 (leopard), and for information about using QuaSSE.

Documentation

A preliminary tutorial is available here, which outlines use of the main models. Most of the examples here use simulated data, but to run the shorebird example, you will need a number of files from here. Additional help is available through R's online help system - type library(help=diversitree) for a list of topics.

Frequently asked questions and answers are here.

Licence

Diversitree is released under the GPL, version 2.

It uses the excellent Expokit library for matrix exponential calculations for using BiSSE with terminally unresolved clades.

Releases / Changes

• 18 July 2011 [0.7-6]
  • Works with deSolve 1.10-2.
• 11 July 2011 [0.7-6]
  • New parametrisation of MuSSE available where the multi-state trait is really combinations of binary states. This allows expressing speciation and extinction rates as main effects and interations of the underlying binary traits, and easily restricting trait evolution to a single trait at a time.
  • Some internal streamlining that should speed up most models slightly
  • Faster stochastic character mapping
  • Various bugs fixed (mcmc not passing additional arguments properly, make.bd.split not using unresolved clade information).
• 12 May 2011 [0.7-2]
  • Fixed bug that prevented use on Windows
• 11 May 2011 [0.7-1]
  • New Sundials based solver CVODE available (switch with control=list(backend="CVODES")). In some cases this is 8x faster than the previous version.
  • Bug fixes. In particular, the equilibrium root state treatment (ROOT.EQUI) was incorrect.
  • Works with deSolve 1.10.
• 20 April 2011 [0.6-5] Bug fixes mostly:
  • Better integration control for all ODE-based solvers.
  • Slightly altered root state treatment (exact calculations will change with condition.surv=TRUE)
  • Very basic mixed integer nonlinear optimisation approach for finding ML point for some QuaSSE models that involve a character space variable (poorly documented at present).
  • Assorted minor bug fixes.
• 26 January 2011 [0.6-3]. Bug fixes and some new features/models:
  • Includes Emma Goldberg's GeoSSE model
  • New numerical method-of-lines integrator for QuaSSE, which may be more robust in some situations.
  • Marginal ancestral state reconstructions for MuSSE models.
  • Better support for MuSSE/mkn models with >9 states
  • Works with deSolve 1.9
  • Builds on CRAN for windows!
• 21 October 2010 [0.6-1]. A number of new models.
  • "QuaSSE" (Quantitative Trait Speciation and Extinction): new method is now released. This tests for correlation between a continuous/quantitative character and rates of speciation and/or extinction. Includes support for "split" QuaSSE analyses.
  • Improved support for time dependent models: now, speciation, extinction, and (for BiSSE only) character change rates may be arbitrary functions of time. This is implemented for birth-death models, BiSSE, and MuSSE.
• 23 September 2010 [0.5-3]. A couple of model extensions, documentation improvements, and bug fixes.
  • Now works with deSolve 1.8
  • Time-dependent and "split" MuSSE models are now included. The interface for both is similar to their BiSSE analogues.
  • A new tutorial document.
• 12 August 2010 [0.5-2]. A number of new models and bug fixes.
  • "MuSSE" (Multi-State Speciation and Extinction): the multiple-character extension to BiSSE is now implemented. This allows modelling characters with more than two states, or combinations of characters (similar to the Pagel 1994 method for rates of character evolution). Likelihood calculations and tree simulation are supported.
  • Simple support for Brownian Motion models of continuous trait evolution (single trait only).
  • "Split BiSSE" model: this combines aspects of the MEDUSA model (Alfaro et al. 2009) with the BiSSE model to allow different parts of the tree to have different rates of speciation, extinction, and/or character evolution. For completeness a "Split BD" model is also implemented. None of these assist in searching for positions in the tree where rates shift.
  • "Time-dependent" BiSSE, where different chunks of time have different rates of speciation, extinction, and/or character evolution.
  The new models' documentation is still very preliminary and these are not yet in the tutorial document.
  Other new features:
  • Interrupting a mcmc run will return a truncated set of samples.
  • Constrained functions can be constrained (though this is still limited)
  • subplex is now the default ML search algorithm for BiSSE and MuSSE models.
• 2 March 2010 [0.4-5]. Some important bug fixes (BiSSE likelihood calculations were very slightly incorrect at root and unresolved clade calculations were incorrect when no species within a clade had a known state). Other changes:
  • Added support for sampling and unresolved clades in constant rate birth-death models.
  • Fixes to the Mk2 ancestral state reconstructions
  • Works with deSolve version 1.7
  • Assorted small bug fixes and documentation improvements
• 2 Febrary 2010 [0.4-4]. New features include:
  • Ancestral state reconstruction and stochastic character mapping under Mk2 (?asr.mk2) (slow, but will get faster in future versions)
  • Much faster Mk2 likelihood calculation (speed increase of 20-50x)
  • Ancestral state reconstruction under BiSSE (?asr.marginal.bisse)
  The ancestral state reconstruction code should be regarded as experimental.
• 19 January 2010 [0.4-3]. Mostly a few bug fixes.
• 11 January 2010 [0.4-2]. New features include:
  • Remembering and plotting character histories on simulated trees (see ?tree.bisse
  • Works with deSolve 1.6
  • Support for simulating Yule trees and estimating Yule model parameters
  • Bug fixes and improvements to the MLE code
• 02 December 2009 [0.4-1]. New features include
  • Constant rate birth death model (make.bd) and Mk2/Mk-n (make.mk2, make.mkn) models implemented
  • Now works with the current deSolve package
  • Node states now retained during tree simulation (see ?trees for an example)
  • Simple MCMC plots with profiles.plot
  • Several bugs fixes, documentation improvements, additional examples, and minor features
• 16 October 2009 [0.3-2]:: Minor bugfix
• 15 October 2009 [0.3-1]:
  • New formula-based constraint interface (through function constrain())
  • Subplex available to do ML searches
  • Simple hypothesis testing convenience functions added (anova(), logLik()).
• 5 May 2009 [0.2-1]: Initial public release

References

• Alfaro M.E., Santini F., Brock C., Alamillo H., Dornburg A., Rabosky D.L., Carnevale G., and Harmon L.J. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. U.S.A. 106:13410-13414.
• FitzJohn, R.G., W.P. Maddison, and S.P. Otto. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58: 595-611.
• FitzJohn R.G. 2010. Quantitative traits and diversification. Systematic Biology 59: 619-633.
• Goldberg E.E., Lancaster L.T., and Ree R.H. 2011. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology in press.
• Maddison, W.P., P.E. Midford, and S.P. Otto. 2007. Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56: 701-710.
• Nee S., May R.M., and Harvey P.H. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344:305-311.
• Pagel M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B Biol. Sci. 255:37-45.