R: Analysis of Evolutionary Diversification

# Analysis of Evolutionary Diversification

## Documentation for package ‘geiger’ version 2.0.12

- DESCRIPTION file.

## Help Pages

A B C D E F G I K L M N O P R S T V W

geiger-package | GEIGER

## -- A --

aicm | Akaike's Information Criterion for MCMC samples (AICM)
aicw | determining Akaike weights
amphibia | example datasets
aov.phylo | phylogenetic ANOVA and MANOVA
area.between.curves | deprecated functions in GEIGER
as.Qmatrix.gfit | Model fitting for discrete comparative data

## -- B --

bd.km | estimate net diversification rate
bd.ms | estimate net diversification rate
BDsim | deprecated functions in GEIGER
birthdeath.tree | deprecated functions in GEIGER

## -- C --

calibrate.mecca | calibrating MECCA
calibrate.proposalwidth | deprecated functions in GEIGER
calibrate.rjmcmc | initialize proposal width
caniformia | example datasets
carnivores | example datasets
caudata | example datasets
chelonia | example datasets
compare.rates | deprecated functions in GEIGER
congruify.phylo | ultrametricization of trees from a supplied timetree
crown.limits | estimate net diversification rate
crown.p | estimate net diversification rate

## -- D --

dcount | prior densities for truncated discrete random variable
deltaTree | deprecated functions in GEIGER
disp.calc | deprecated functions in GEIGER
disparity | disparity-through-time
drop.extinct | prune specified taxa from a phylogenetic tree
drop.random | prune specified taxa from a phylogenetic tree
dtt | disparity-through-time
dtt.full | deprecated functions in GEIGER

## -- E --

ex.jumpsimulator | internal geiger functions
ex.ratesimulator | internal geiger functions
ex.traitgram | internal geiger functions
exponentialchangeTree | deprecated functions in GEIGER

## -- F --

fitContinuous | Model fitting for continuous comparative data
fitContinuousMCMC | Fit models of continuous trait evolution to comparative data using MCMC
fitDiscrete | Model fitting for discrete comparative data

## -- G --

gbcontain | NCBI taxonomy
gbresolve | NCBI taxonomy
gbresolve.phylo | NCBI taxonomy
geiger | GEIGER
geiger-defunct | deprecated functions in GEIGER
geospiza | example datasets
get.simulation.matrix | deprecated functions in GEIGER
getAncStates | deprecated functions in GEIGER
glomogram.phylo | Blending information from taxonomies and trees

## -- I --

ic.sigma | deprecated functions in GEIGER
intercalate.samples | deprecated functions in GEIGER
is.extinct | prune specified taxa from a phylogenetic tree

## -- K --

kappaTree | deprecated functions in GEIGER

## -- L --

lambdaTree | deprecated functions in GEIGER
linearchangeTree | deprecated functions in GEIGER
load.rjmcmc | posterior samples from single or multiple MCMC runs
lookup.phylo | Blending information from taxonomies and trees

## -- M --

make.gbm | tailor reversible-jump Markov chain Monte Carlo sampling
mecca | running a MECCA analysis
medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC

## -- N --

name.check | Compares taxa in data and tree
nh.test | using the Freckleton and Harvey node-height test
node.leaves | deprecated functions in GEIGER
node.sons | deprecated functions in GEIGER
nodelabel.phylo | Blending information from taxonomies and trees

## -- O --

ouTree | deprecated functions in GEIGER

## -- P --

phy.anova | deprecated functions in GEIGER
phy.manova | deprecated functions in GEIGER
phylo.clades | Blending information from taxonomies and trees
phylo.lookup | Blending information from taxonomies and trees
plot.medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC
pool.rjmcmcsamples | deprecated functions in GEIGER
pp.mcmc | using posterior predictive MCMC for modeling quantitative trait evolution
primates | example datasets
print.medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC
prune.extinct.taxa | deprecated functions in GEIGER
prune.random.taxa | deprecated functions in GEIGER

## -- R --

r8s.phylo | call r8s from geiger
rate.estimate | deprecated functions in GEIGER
ratematrix | evolutionary VCV matrix
rc | relative cladogenesis test
rescale.phylo | Rescale object of class '"phylo"'
rescaleTree | deprecated functions in GEIGER
rjmcmc.bm | Bayesian sampling of shifts in trait evolution: relaxed Brownian motion
runMedusa | deprecated functions in GEIGER

## -- S --

shifts.plot | deprecated functions in GEIGER
sim.bd | birth-death population simulator
sim.bdtree | birth-death tree simulator
sim.char | simulate character evolution
speciationalTree | deprecated functions in GEIGER
startingpt.mecca | starting values for MECCA
stem.limits | estimate net diversification rate
stem.p | estimate net diversification rate
subset.phylo | blending information from taxonomies and trees

## -- T --

tip.disparity | deprecated functions in GEIGER
tips | descendents of a given node in a phylogenetic tree
to.auteur | conversion of MCMC samples between auteur and coda
to.coda | conversion of MCMC samples between auteur and coda
tracer | deprecated functions in GEIGER
transform.phylo | deprecated functions in GEIGER
treedata | compare taxa in data and tree
tworateTree | deprecated functions in GEIGER

## -- V --

vmat | deprecated functions in GEIGER

## -- W --

whales | example datasets