R: Analysis of Evolutionary Diversification

# Analysis of Evolutionary Diversification

## Documentation for package ‘geiger’ version 2.0.11

- DESCRIPTION file
- Package README

## Help Pages

A B C D E F G H I K L M N O P R S T U 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
argn | internal geiger functions
argn.bm | internal geiger functions
argn.default | internal geiger functions
argn.mkn | internal geiger functions
argn<- | internal geiger functions
argn<-.bm | internal geiger functions
as.phylo.hphylo | internal geiger functions
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
bf | internal geiger functions
birthdeath.tree | deprecated functions in GEIGER
bm.lik | internal geiger functions

## -- 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
cherries | internal geiger functions
coef.gfit | internal geiger functions
coef.gfits | internal geiger functions
compare.rates | deprecated functions in GEIGER
congruify.phylo | ultrametricization of trees from a supplied timetree
constrain | internal geiger functions
constrain.k | internal geiger functions
constrain.m | internal geiger functions
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
dlunif | internal geiger functions
drop.extinct | prune specified taxa from a phylogenetic tree
drop.random | prune specified taxa from a phylogenetic tree
drop.tip | internal geiger functions
dtpois | internal geiger functions
dtt | disparity-through-time
dtt.full | deprecated functions in GEIGER

## -- E --

edgelabels.auteur | internal geiger functions
edges.phylo | internal geiger functions
ess | internal geiger functions
ex.jumpsimulator | internal geiger functions
ex.ratesimulator | internal geiger functions
ex.traitgram | internal geiger functions
exemplar.phylo | 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
fitDiversification | internal geiger functions
fitSplitModel | internal geiger functions

## -- G --

gbcontain | NCBI taxonomy
gbresolve | NCBI taxonomy
gbresolve.default | internal geiger functions
gbresolve.phylo | NCBI taxonomy
gbtaxdump | internal geiger functions
geiger | GEIGER
gen | internal geiger functions
geospiza | example datasets
get.simulation.matrix | deprecated functions in GEIGER
getAncStates | deprecated functions in GEIGER
getBD | internal geiger functions
getDiversificationModel | internal geiger functions
getFullSplitModel | internal geiger functions
glomogram.phylo | Blending information from taxonomies and trees

## -- H --

hash.node | internal geiger functions
hashes.phylo | internal geiger functions
hashes.rjmcmc | internal geiger functions
hdr | internal geiger functions
heights | internal geiger functions
heights.multiPhylo | internal geiger functions
heights.phylo | internal geiger functions
hme | internal geiger functions

## -- I --

ic.sigma | deprecated functions in GEIGER
intercalate.samples | deprecated functions in GEIGER
is.constrained | internal geiger functions
is.extinct | prune specified taxa from a phylogenetic tree
is.phylo | internal geiger functions
is.root | internal geiger functions

## -- K --

kappaTree | deprecated functions in GEIGER
kendallmoran.rate | internal geiger functions

## -- L --

lambdaTree | deprecated functions in GEIGER
likfx.bm | internal geiger functions
linearchangeTree | deprecated functions in GEIGER
Linnaean | internal geiger functions
load | internal geiger functions
load.rjmcmc | posterior samples from single or multiple MCMC runs
logLik.gfit | internal geiger functions
logLik.gfits | internal geiger functions
lookup.phylo | Blending information from taxonomies and trees

## -- M --

make.bm.relaxed | internal geiger functions
make.gbm | tailor reversible-jump Markov chain Monte Carlo sampling
mecca | running a MECCA analysis
medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC
mkn.lik | internal geiger functions

## -- 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 --

PATHd8.phylo | internal geiger functions
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.auteurMCMC | internal geiger functions
plot.auteurMCMCMC | internal geiger functions
plot.medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC
plot.rjmcmc | internal geiger functions
plot.rjmcmc.list | internal geiger functions
plotDiversificationSurface | internal geiger functions
pool.rjmcmcsamples | deprecated functions in GEIGER
pp.mcmc | using posterior predictive MCMC for modeling quantitative trait evolution
primates | example datasets
print.auteurRAW | internal geiger functions
print.bayesfactor | internal geiger functions
print.bm | internal geiger functions
print.constraint.m | internal geiger functions
print.glnL | internal geiger functions
print.gprior | internal geiger functions
print.mcmc.list | internal geiger functions
print.medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC
print.mkn | internal geiger functions
print.rbm | internal geiger functions
print.rjmcmc | internal geiger functions
print.rjmcmcmc | internal geiger functions
print.taxdump | internal geiger functions
print.transformer | internal geiger functions
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
resplitEdgeMatrixGeiger | internal geiger functions
rjmcmc.bm | Bayesian sampling of shifts in trait evolution: relaxed Brownian motion
root.phylo | internal geiger functions
runMedusa | deprecated functions in GEIGER

## -- S --

sem | internal geiger functions
shifts.plot | deprecated functions in GEIGER
sim.bd | birth-death population simulator
sim.bdtree | birth-death tree simulator
sim.char | simulate character evolution
sim.mecca | internal geiger functions
span.phylo | internal geiger functions
speciationalTree | deprecated functions in GEIGER
splitEdgeMatrixGeiger | internal geiger functions
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

## -- U --

ultrametricize.phylo | internal geiger functions
unique.phylo | internal geiger functions
uniqueMultiPhylo | internal geiger functions

## -- V --

vmat | deprecated functions in GEIGER

## -- W --

whales | example datasets
white.mkn | internal geiger functions
write.pathd8 | internal geiger functions
write.r8s | internal geiger functions
write.treePL | internal geiger functions