Contains a number of comparative phylogenetic methods,
mostly focusing 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), QuaSSE (Quantitative State Speciation and Extinction;
FitzJohn 2010: Syst. Biol. 59: 619), GeoSSE (Geographic State
Speciation and Extinction; Goldberg et al. 2011: Syst. Biol. 60:
451), and BiSSE-ness (Magnuson-Ford and Otto 2012: Am. Nat.)
Other included methods include Markov models of discrete and
continuous trait evolution and constant rate speciation and
extinction.
| Version: |
0.9-7 |
| Depends: |
R (≥ 2.10), deSolve (≥ 1.7), ape, subplex, methods, Rcpp (≥
0.10.0) |
| LinkingTo: |
Rcpp |
| Suggests: |
numDeriv, minqa, lubridate, expm, caper, geiger |
| Published: |
2014-02-20 |
| Author: |
Richard G. FitzJohn, with GeoSSE and
ClaSSE by Emma E. Goldberg, and BiSSE-ness by Karen
Magnuson-Ford. |
| Maintainer: |
Richard G. FitzJohn <rich.fitzjohn at gmail.com> |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
http://www.zoology.ubc.ca/prog/diversitree |
| NeedsCompilation: |
yes |
| SystemRequirements: |
fftw3 (>= 3.1.2), gsl (>= 1.15) |
| Citation: |
diversitree citation info |
| Materials: |
README ChangeLog |
| In views: |
Phylogenetics |
| CRAN checks: |
diversitree results |