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| anova.fit.mle | Maximimum Likelihood Inference |
| argnames | Argument Names for Vector-Argument Functions |
| argnames.constrained | Argument Names for Vector-Argument Functions |
| argnames<- | Argument Names for Vector-Argument Functions |
| argnames<-.constrained | Argument Names for Vector-Argument Functions |
| asr | Ancestral State Reconstruction |
| asr.bisse | Ancestral State Reconstruction Under BiSSE |
| asr.joint | Ancestral State Reconstruction |
| asr.marginal | Ancestral State Reconstruction |
| asr.marginal.bisse | Ancestral State Reconstruction Under BiSSE |
| asr.marginal.musse | Ancestral State Reconstruction Under BiSSE |
| asr.mkn | Ancestral State Reconstruction Under Mk2/Mkn |
| asr.musse | Ancestral State Reconstruction Under BiSSE |
| asr.stoch | Ancestral State Reconstruction |
| check.cvodes | Check Capabilities of the Diversitree Install |
| check.fftC | Check Capabilities of the Diversitree Install |
| clades.from.classification | Make a "Clade Tree" |
| clades.from.polytomies | Make a "Clade Tree" |
| coef.fit.mle | Maximimum Likelihood Inference |
| combine | Combine Several Likelihood Functions Multiplicatively |
| constant.t | Support Functions for Time-varying Models |
| constant.x | Support Functions for QuaSSE Models |
| constrain | Constrain Parameters of a Model |
| constrain.i | Constrain Parameters of a Model |
| exponential.t | Support Functions for Time-varying Models |
| find.mle | Maximimum Likelihood Inference |
| geosse.phy | Example GeoSSE Tree |
| history.from.sim.discrete | Extract Character Histories From Simulations |
| linear.t | Support Functions for Time-varying Models |
| logLik.fit.mle | Maximimum Likelihood Inference |
| make.asr.joint | Ancestral State Reconstruction |
| make.asr.joint.mk2 | Ancestral State Reconstruction Under Mk2/Mkn |
| make.asr.joint.mkn | Ancestral State Reconstruction Under Mk2/Mkn |
| make.asr.marginal | Ancestral State Reconstruction |
| make.asr.marginal.bisse | Ancestral State Reconstruction Under BiSSE |
| make.asr.marginal.mk2 | Ancestral State Reconstruction Under Mk2/Mkn |
| make.asr.marginal.mkn | Ancestral State Reconstruction Under Mk2/Mkn |
| make.asr.marginal.musse | Ancestral State Reconstruction Under BiSSE |
| make.asr.stoch | Ancestral State Reconstruction |
| make.asr.stoch.mk2 | Ancestral State Reconstruction Under Mk2/Mkn |
| make.asr.stoch.mkn | Ancestral State Reconstruction Under Mk2/Mkn |
| 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.t | Binary State Speciation and Extinction Model: Time Dependant 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.brownian.with.drift | Support Functions for QuaSSE Models |
| 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.linear.x | Support Functions for QuaSSE Models |
| make.mk2 | Mk2 and Mk-n Models of character evolution |
| make.mkn | Mk2 and Mk-n Models of character evolution |
| make.mkn.deriv | Mk2 and Mk-n Models of character evolution [temporary extension with derivatives] |
| make.mkn.multitrait | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version) |
| 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.t | Multiple State Speciation and Extinction Model: Time Dependent Models |
| make.musse.td | Multiple State Speciation and Extinction Model: Time Dependent Models |
| make.ou | Brownian Motion and Ornstein-Uhlenbeck Character Evolution |
| make.pars.t | Support Functions for Time-varying Models |
| make.prior | Simple Prior Functions |
| make.prior.exponential | Simple Prior Functions |
| make.prior.uniform | Simple Prior Functions |
| make.quasse | Quantitative State Speciation and Extinction Model |
| make.quasse.split | Quantitative State Speciation and Extinction Model: Split Models |
| make.yule | Constant Rate Birth-Death Models |
| mcmc | Simple Markov Chain Monte Carlo with Slice Sampling |
| mcmc.default | Simple Markov Chain Monte Carlo with Slice Sampling |
| mkn.multitrait.translate | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version) |
| musse.multitrait.translate | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version) |
| noroptimal.x | Support Functions for QuaSSE Models |
| plot.history | Plot Character History |
| profiles.plot | Plot Marginal Distributions from MCMC |
| prune | Evolve Birth-Death Trees |
| sampler.norm | Simple Markov Chain Monte Carlo with Slice Sampling |
| sampler.slice | Simple Markov Chain Monte Carlo with Slice Sampling |
| set.defaults | Set Default Arguments of a Function |
| sigmoid.t | Support Functions for Time-varying Models |
| sigmoid.x | Support Functions for QuaSSE Models |
| sigmoid2.x | Support Functions for QuaSSE Models |
| sim.character | Simulate a Character Distribution on a Tree |
| starting.point.bd | Constant Rate Birth-Death Models |
| starting.point.bisse | Binary State Speciation and Extinction Model |
| starting.point.classe | Cladogenetic State change Speciation and Extinction Model |
| starting.point.geosse | Geographic State Speciation and Extinction Model |
| starting.point.musse | MuSSE: Multi-State Speciation and Extinction |
| starting.point.musse.multitrait | MuSSE: Multi-State Speciation and Extinction (Multiple Binary Traits Version) |
| starting.point.quasse | Quantitative State Speciation and Extinction Model |
| stepf.t | Support Functions for Time-varying Models |
| stepf.x | Support Functions for QuaSSE Models |
| trait.plot | Plot a Phylogeny and Traits |
| tree.bd | Evolve Birth-Death Trees |
| tree.bisse | Evolve Birth-Death Trees |
| tree.bisseness | Evolve Birth-Death Trees |
| tree.classe | Evolve Birth-Death Trees |
| tree.geosse | Evolve Birth-Death Trees |
| tree.musse | Evolve Birth-Death Trees |
| tree.musse.multitrait | Evolve Birth-Death Trees |
| tree.quasse | Evolve Birth-Death Trees |
| tree.yule | Evolve Birth-Death Trees |
| trees | Evolve Birth-Death Trees |