argnames Argument Names for Vector-Argument Functions
asr-bisse Ancestral State Reconstruction Under BiSSE
asr-mkn Ancestral State Reconstruction Under Mk2/Mkn
asr Ancestral State Reconstruction
big.brother Verbosely Track Function Evaluations
check Check Capabilities of the Diversitree Install
combine Combine Several Likelihood Functions Multiplicatively
Constants Constants Used by Diversitree
constrain Constrain Parameters of a Model
diversitree-deprecated Deprecated and Defunct Functions in Diversitree
find.mle Maximimum Likelihood Inference
geosse.phy Example GeoSSE Tree
history.from.sim 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 Ornstein-Uhlenbeck 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.mkn.deriv Mk2 and Mk-n Models of character evolution [temporary extension with derivatives]
make.mkn Mk2 and Mk-n Models of character evolution
make.musse.multitrait MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version)
make.musse MuSSE: Multi-State Speciation and Extinction
make.musse.split Multiple State Speciation and Extinction Model: Split Models
make.musse.td Multiple State Speciation and Extinction Model: Time Dependent Models
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
protect Protect Function Evaluations
quasse-common Support Functions for QuaSSE Models
set.defaults Set Default Arguments of a Function
sim.character Simulate a Character Distribution on a Tree
simulate Evolve Birth-Death Trees
time Support Functions for Time-varying Models
trait.plot Plot a Phylogeny and Traits
utilities Utility Functions