Man pages for mwpennell/geiger-v2
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.phylo | Rescale object of class '"phylo"' |
| 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 |
