argnames                Argument Names for Vector-Argument Functions
asr                     Ancestral State Reconstruction
asr.bisse               Ancestral State Reconstruction Under BiSSE
asr.mkn                 Ancestral State Reconstruction Under Mk2/Mkn
check.fftC              Check Capabilities of the Diversitree Install
combine                 Combine Several Likelihood Functions
                        Multiplicatively
constant.x              Support Functions for QuaSSE Models
constrain               Constrain Parameters of a Model
diversitree-package     Comparative 'Phylogenetic' Analyses of
                        Diversification
find.mle                Maximimum Likelihood Inference
get.descendants         Utility Functions
history.from.sim.discrete
                        Extract Character Histories From Simulations
make.bd                 Constant Rate Birth-Death Models
make.bd.split           Constant Rate Birth-Death Models: Split Models
make.bd.t               Time-varing Birth-Death Models
make.bisse              Binary State Speciation and Extinction Model
make.bisse.split        Binary State Speciation and Extinction Model:
                        Split Models
make.bisse.td           Binary State Speciation and Extinction Model:
                        Time Dependant Models
make.bisseness          Binary State Speciation and Extinction (Node
                        Enhanced State Shift) Model
make.bm                 Brownian Motion and Related Models of Character
                        Evolution
make.clade.tree         Make a "Clade Tree"
make.classe             Cladogenetic State change Speciation and
                        Extinction Model
make.geosse             Geographic State Speciation and Extinction
                        Model
make.geosse.split       Geographic State Speciation and Extinction
                        Model: Split Models
make.geosse.t           Geographic State Speciation and Extinction
                        Model: Time Dependent Models
make.mkn                Mk2 and Mk-n Models of character evolution
make.musse              MuSSE: Multi-State Speciation and Extinction
make.musse.multitrait   MuSSE: Multi-State Speciation and Extinction
                        (Multiple Binary Traits Version)
make.musse.split        Multiple State Speciation and Extinction Model:
                        Split Models
make.musse.td           Multiple State Speciation and Extinction Model:
                        Time Dependent Models
make.pgls               Phylogenetic Generalised Least Squares
make.prior              Simple Prior Functions
make.quasse             Quantitative State Speciation and Extinction
                        Model
make.quasse.split       Quantitative State Speciation and Extinction
                        Model: Split Models
mcmc                    Simple Markov Chain Monte Carlo with Slice
                        Sampling
plot.history            Plot Character History
profiles.plot           Plot Marginal Distributions from MCMC
set.defaults            Set Default Arguments of a Function
sim.character           Simulate a Character Distribution on a Tree
trait.plot              Plot a Phylogeny and Traits
trees                   Evolve Birth-Death Trees
