API for mwpennell/geiger-v2
Analysis of Evolutionary Diversification

Global functions
.CI Source code
.Qmatrix.from.gfit Source code
.acegram Source code
.adjustjump Source code
.adjustrate Source code
.adjustshift Source code
.adjustvalue Source code
.ard.matrix Source code
.area.between.curves Source code
.assess.lnR Source code
.assigndescendants Source code
.basename.noext Source code
.bf.interpreter Source code
.bm.lik.fn.reml Source code
.bm.lik.fn.vcv Source code
.bm.phylo Source code
.bm.rate.mle Source code
.bm.smartstart Source code
.bnd.hessian Source code
.branching.depth Source code
.branching.heights Source code
.build_calibrations Source code
.build_classification Source code
.cache.descendants Source code
.cache.y.nodes Source code
.check.Qmatrix Source code
.check.control.mkn Source code
.check.control.ode Source code
.check.gbm Source code
.check.info.ode Source code
.check.integer Source code
.check.lim Source code
.check.loaded.symbol Source code
.check.parallel Source code
.check.pars.nonnegative Source code
.check.prior Source code
.check.root Source code
.check.scalar Source code
.check.states Source code
.check.states.quasse Source code
.check.stoppingcrit Source code
.check.tree Source code
.cleanup.rjmcmc Source code
.compile_taxonomy Source code
.constrain Source code
.constrain.k Source code
.constrain.m Source code
.constrain.parse Source code
.cont.foo Source code
.default.argn.bm Source code
.default.argn.mk2 Source code
.default.argn.mkn Source code
.defunctify Source code
.delta.cache Source code
.delta.phylo Source code
.deprecate Source code
.depth.phylo Source code
.detachDiversitree Source code
.disparity Source code
.dlnratio Source code
.drop.tip Source code
.dt.tips.ordered Source code
.dtt Source code
.dtt.polygon Source code
.dunifn Source code
.eb.cache Source code
.eb.phylo Source code
.edger Source code
.er.matrix Source code
.error.rjmcmc Source code
.ests.parlog.rjmcmc Source code
.exemplar.default Source code
.fetch_gbhierarchy.above Source code
.fill.taxonomy Source code
.fix.rjmcmc.matrix Source code
.fix.root.bm Source code
.format.levels.print Source code
.gb_anc_worker Source code
.gb_des_worker Source code
.gbm.prior.lik Source code
.geigerwarn Source code
.get.ancestor.of.node Source code
.get.ancestors.of.node Source code
.get.children Source code
.get.desc.of.node Source code
.get.descendants.of.node Source code
.get.ordering Source code
.get.simulation.matrix Source code
.hash.tip Source code
.ic.sigma Source code
.initial.tip.bm.pruning Source code
.intercalate.rjmcmc Source code
.is.wholenumber Source code
.jumps.edgewise Source code
.jumps.plot Source code
.kappa.cache Source code
.kappa.phylo Source code
.kendallmoran.rate Source code
.lambda.cache Source code
.lambda.phylo Source code
.link.root Source code
.lnpriorhastings_ratio.merge Source code
.lnpriorhastings_ratio.split Source code
.load.rjmcmc Source code
.lrate.phylo Source code
.make.bm.relaxed.pic Source code
.make.bm.relaxed.vcv Source code
.make.cache Source code
.make.cache.bm Source code
.make.cache.mkn Source code
.make.info.bm Source code
.make.info.mkn Source code
.make.modelmatrix Source code
.make.ode.deSolve Source code
.make.pars.mkn Source code
.make.pij.mkn Source code
.matrix.to.list Source code
.md5 Source code
.meristic.matrix Source code
.mrca Source code
.namespace Source code
.nodefind.phylo Source code
.nrate.phylo Source code
.null.cache Source code
.null.phylo Source code
.oldestyle.gfit.continuous Source code
.oldestyle.gfit.discrete Source code
.ou.cache Source code
.ou.phylo Source code
.ou.smartstart Source code
.ou.vcv Source code
.parlog.rjmcmc Source code
.paths.cache Source code
.paths.phylo Source code
.pic_variance.phylo Source code
.polytomy.phylo Source code
.pp.getproposal Source code
.prep.glomogram Source code
.prepare.bm.univariate Source code
.prepare.gbm.univariate Source code
.print.table Source code
.proc.lnR Source code
.process.jumps Source code
.process.shifts Source code
.proposal.multiplier Source code
.proposal.slidingwindow Source code
.rate.estimate Source code
.rcount Source code
.rcp Source code
.read.ests.rjmcmc Source code
.reml.lk Source code
.repars Source code
.replace.tip.with.subtree Source code
.reshape.constraint.m Source code
.resolve.executable Source code
.rjmcmc.bm.multi Source code
.root.bm.direct Source code
.root.p.calc Source code
.rootfunc.mkn Source code
.samples.plot Source code
.scale.brlen Source code
.scale.edge.tree Source code
.set.seed.clock Source code
.shifts.plot Source code
.slot.attribute Source code
.splitormerge Source code
.standardize.prior Source code
.startingpt.bm Source code
.subset.auteurRAW Source code
.sym.matrix Source code
.toC.int Source code
.traceplot Source code
.treeslide Source code
.trend.cache Source code
.trend.phylo Source code
.tune.SE Source code
.tune.rate Source code
.tune.value Source code
.unique.phylo Source code
.uniquify_hashes Source code
.white.cache Source code
.white.phylo Source code
BDsim Man page Source code
Linnaean Man page
PATHd8.phylo Man page Source code
`argn<-` Source code
aicm Man page
aicw Man page
amphibia Man page
aov.phylo Man page Source code
area.between.curves Man page
argn Man page Source code
argn.bm Man page Source code
argn.default Man page Source code
argn.mkn Man page Source code
argn<- Man page
argn<-.bm Man page
as.phylo.hphylo Man page Source code
bd.km Man page Source code
bd.ms Man page Source code
bf Man page Source code
birthdeath.tree Man page Source code
bm.lik Man page Source code
calibrate.mecca Man page
calibrate.proposalwidth Man page
calibrate.rjmcmc Man page Source code
caniformia Man page
carnivores Man page
caudata Man page
chelonia Man page
cherries Man page Source code
coef.gfit Man page Source code
coef.gfits Man page Source code
compare.rates Man page
congruify.phylo Man page Source code
constrain Man page
constrain.k Man page
constrain.m Man page
crown.limits Man page Source code
crown.p Man page Source code
dcount Man page Source code
deltaTree Man page Source code
disp.calc Man page
disparity Man page Source code
dlunif Man page Source code
drop.extinct Man page
drop.random Man page
drop.tip Man page
dtpois Man page Source code
dtt Man page Source code
dtt.full Man page
edgelabels.auteur Man page
edges.phylo Man page Source code
ess Man page Source code
ex.jumpsimulator Man page Source code
ex.ratesimulator Man page Source code
ex.traitgram Man page Source code
exemplar.phylo Man page Source code
exponentialchangeTree Man page Source code
fitContinuous Man page Source code
fitContinuousMCMC Man page Source code
fitDiscrete Man page Source code
fitDiversification Man page
fitSplitModel Man page
gbcontain Man page Source code
gbresolve Man page Source code
gbresolve.default Man page Source code
gbresolve.phylo Man page Source code
gbtaxdump Man page
geiger Man page
geiger-package Man page
gen Man page
geospiza Man page
get.simulation.matrix Man page
getAncStates Man page Source code
getBD Man page
getDiversificationModel Man page
getFullSplitModel Man page
getMDIp Source code
glomogram.phylo Man page Source code
hash.node Man page Source code
hashes.phylo Man page Source code
hashes.rjmcmc Man page Source code
hdr Man page
heights Man page Source code
heights.multiPhylo Man page Source code
heights.phylo Man page Source code
hme Man page Source code
ic.sigma Man page Source code
intercalate.samples Man page
is.constrained Man page Source code
is.extinct Man page
is.phylo Man page Source code
is.root Man page
kappaTree Man page Source code
kendallmoran.rate Man page
lambdaTree Man page Source code
likfx.bm Man page
linearchangeTree Man page Source code
load Man page
load.rjmcmc Man page Source code
logLik.gfit Man page Source code
logLik.gfits Man page Source code
lookup.phylo Man page Source code
make.bm.relaxed Man page Source code
make.gbm Man page Source code
mecca Man page
medusa Man page
mkn.lik Man page Source code
name.check Man page Source code Source code
nh.test Man page Source code
node.leaves Man page Source code
node.sons Man page
nodelabel.phylo Man page Source code
ouTree Man page Source code
phy.anova Man page
phy.manova Man page
phylo.clades Man page Source code
phylo.lookup Man page Source code
plot.auteurMCMC Man page Source code
plot.auteurMCMCMC Man page Source code
plot.medusa Man page
plot.rjmcmc Man page
plot.rjmcmc.list Man page
plotDiversificationSurface Man page
pool.rjmcmcsamples Man page
pp.mcmc Man page Source code
primates Man page
print.auteurRAW Man page Source code
print.bayesfactor Man page Source code
print.bm Man page
print.constraint.m Man page Source code
print.gfit Source code
print.gfits Source code
print.glnL Man page Source code
print.gprior Man page Source code
print.mcmc.list Man page Source code
print.medusa Man page
print.mkn Man page
print.rbm Man page
print.rjmcmc Man page
print.rjmcmcmc Man page
print.taxdump Man page
print.transformer Man page
prune.extinct.taxa Man page Source code
prune.random.taxa Man page Source code
r8s.phylo Man page Source code
rate.estimate Man page Source code
ratematrix Man page Source code
rc Man page Source code
rescale Man page Source code
rescale.phylo Man page Source code
rescaleTree Man page Source code
resplitEdgeMatrixGeiger Man page
rjmcmc.bm Man page
root.phylo Man page
runMedusa Man page Source code
sem Man page Source code
shifts.plot Man page
sim.bd Man page
sim.bdtree Man page
sim.char Man page Source code
sim.mecca Man page
span.phylo Man page Source code
speciationalTree Man page Source code
splitEdgeMatrixGeiger Man page
startingpt.mecca Man page
stem.limits Man page Source code
stem.p Man page Source code
subset.phylo Man page Source code
tip.disparity Man page Source code
tips Man page Source code
to.auteur Man page Source code
to.coda Man page Source code
tracer Man page
transform.phylo Man page
treePL.phylo Source code
treedata Man page Source code
tworateTree Man page Source code
ultrametricize.phylo Man page
unique.multiPhylo Man page Source code
unique.phylo Man page Source code
vmat Man page
whales Man page
white.mkn Man page Source code
write.pathd8 Man page Source code
write.r8s Man page Source code
write.treePL Man page Source code
mwpennell/geiger-v2 documentation built on May 23, 2019, 11:58 a.m.