Man pages for geiger
Analysis of Evolutionary Diversification

aicmAkaike's Information Criterion for MCMC samples (AICM)
aicwdetermining Akaike weights
aov.phylophylogenetic ANOVA and MANOVA
bd.msestimate net diversification rate
calibrate.meccacalibrating MECCA
calibrate.rjmcmcinitialize proposal width
congruify.phyloultrametricization of trees from a supplied timetree
dcountprior densities for truncated discrete random variable
drop.extinctprune specified taxa from a phylogenetic tree
fitContinuousModel fitting for continuous comparative data
fitContinuousMCMCFit models of continuous trait evolution to comparative data...
fitDiscreteModel fitting for discrete comparative data
gbresolveNCBI taxonomy
geiger-dataexample datasets
geiger-defunctdeprecated functions in GEIGER
geiger-examplesinternal geiger functions
geiger-internalinternal geiger functions
load.rjmcmcposterior samples from single or multiple MCMC runs
make.gbmtailor reversible-jump Markov chain Monte Carlo sampling
meccarunning a MECCA analysis
medusaMEDUSA: modeling evolutionary diversification using stepwise...
name.checkCompares taxa in data and tree
nh.testusing the Freckleton and Harvey node-height test
nodelabel.phyloBlending information from taxonomies and trees
plot.medusaMEDUSA: modeling evolutionary diversification using stepwise...
pp.mcmcusing posterior predictive MCMC for modeling quantitative...
r8s.phylocall r8s from geiger
ratematrixevolutionary VCV matrix
rcrelative cladogenesis test
rescale.phyloRescale object of class '"phylo"'
rjmcmc.bmBayesian sampling of shifts in trait evolution: relaxed...
sim.bdbirth-death population simulator
sim.bdtreebirth-death tree simulator
sim.charsimulate character evolution
startingpt.meccastarting values for MECCA
subset.phyloblending information from taxonomies and trees
tipsdescendents of a given node in a phylogenetic tree
to.auteurconversion of MCMC samples between auteur and coda
treedatacompare taxa in data and tree
geiger documentation built on April 4, 2023, 1:07 a.m.