Man pages for richfitz/diversitree
Comparative 'Phylogenetic' Analyses of Diversification
| 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 |
| 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 |
| diversitree-package | Comparative 'Phylogenetic' Analyses of Diversification |
| find.mle | Maximimum Likelihood Inference |
| 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.bisseness | Binary State Speciation and Extinction (Node Enhanced State... |
| make.bisse.split | Binary State Speciation and Extinction Model: Split Models |
| make.bisse.td | Binary State Speciation and Extinction Model: Time Dependant... |
| 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... |
| make.geosse.t | Geographic State Speciation and Extinction Model: Time... |
| 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... |
| make.musse.split | Multiple State Speciation and Extinction Model: Split Models |
| make.musse.td | Multiple State Speciation and Extinction Model: Time... |
| 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... |
| 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 |
| trait.plot | Plot a Phylogeny and Traits |
| utils | Utility Functions |
