Analysis of Evolutionary Diversification

aicm | Akaike's Information Criterion for MCMC samples (AICM) |

aicw | determining Akaike weights |

aov.phylo | phylogenetic ANOVA and MANOVA |

bd.ms | estimate net diversification rate |

calibrate.mecca | calibrating MECCA |

calibrate.rjmcmc | initialize proposal width |

congruify.phylo | ultrametricization of trees from a supplied timetree |

dcount | prior densities for truncated discrete random variable |

drop.extinct | prune specified taxa from a phylogenetic tree |

dtt | disparity-through-time |

fitContinuous | model fitting for continuous comparative data |

fitContinuousMCMC | Fit models of continuous trait evolution to comparative data... |

fitDiscrete | model fitting for discrete comparative data |

gbresolve | NCBI taxonomy |

geiger-data | example datasets |

geiger-defunct | deprecated functions in GEIGER |

geiger-examples | internal geiger functions |

geiger-internal | internal geiger functions |

geiger-package | GEIGER |

load.rjmcmc | posterior samples from single or multiple MCMC runs |

make.gbm | tailor reversible-jump Markov chain Monte Carlo sampling |

mecca | running a MECCA analysis |

medusa | MEDUSA: modeling evolutionary diversification using stepwise... |

name.check | Compares taxa in data and tree |

nh.test | using the Freckleton and Harvey node-height test |

nodelabel.phylo | Blending information from taxonomies and trees |

plot.medusa | MEDUSA: modeling evolutionary diversification using stepwise... |

pp.mcmc | using posterior predictive MCMC for modeling quantitative... |

r8s.phylo | call r8s from geiger |

ratematrix | evolutionary VCV matrix |

rc | relative cladogenesis test |

rescale | Tree transformations |

rjmcmc.bm | Bayesian sampling of shifts in trait evolution: relaxed... |

sim.bd | birth-death population simulator |

sim.bdtree | birth-death tree simulator |

sim.char | simulate character evolution |

startingpt.mecca | starting values for MECCA |

subset.phylo | blending information from taxonomies and trees |

tips | descendents of a given node in a phylogenetic tree |

to.auteur | conversion of MCMC samples between auteur and coda |

treedata | compare taxa in data and tree |

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