API for mwpennell/geiger-v2
Analysis of Evolutionary Diversification

Global functions
BDsim Man page Source code
CI Source code
Linnaean Man page
PATHd8.phylo Man page Source code
Qmatrix.from.gfit Source code
acegram Source code
adjustjump Source code
adjustrate Source code
adjustshift Source code
adjustvalue Source code
aic Source code
aicm Man page
aicw Man page Source code
amphibia Man page
aov.phylo Man page Source code
ard.matrix Source code
area.between.curves Man page Source code
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
assess.lnR Source code
assigndescendants Source code
back.step.medusa Source code
basename.noext Source code
bd.km Man page Source code
bd.ms Man page Source code
bf Man page Source code
bf.interpreter Source code
birthdeath.tree Man page Source code
bm.lik Man page 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
branchcol.plot Source code
branching.depth Source code
branching.heights Source code
build_calibrations Source code
build_classification Source code
c.sigma Source code
cache.descendants Source code
cache.tree Source code
cache.y.nodes Source code
calculate.modelfit.medusa 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
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.richness 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
chelonia Man page
cherries Man page Source code
cleanup.rjmcmc Source code
coda Source code
coef.gfit Man page Source code
coef.gfits Man page Source code
compare.rates Man page
compile_taxonomy Source code
congruify.phylo Man page Source code
constrain Man page Source code
constrain.k Man page Source code
constrain.m Man page Source code
constrain.parse Source code
cont.foo Source code
crown.limits Man page Source code
crown.p Man page Source code
dcount Man page 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
deltaTree Man page Source code
deprecate Source code
depth.phylo Source code
descendants.cutAtNode Source code
descendants.cutAtNode.idx Source code
descendants.cutAtStem Source code
descendants.cutAtStem.idx Source code
detachDiversitree Source code
disp.calc Man page
disparity Man page Source code Source code
dissolve.split.medusa Source code
dlnratio Source code
dlunif Man page Source code
drop.extinct Man page Source code
drop.random Man page Source code
drop.tip Man page Source code
dt.tips.ordered Source code
dtpois Man page Source code
dtt Man page Source code Source code
dtt.full Man page
dtt.polygon Source code
dunifn Source code
eb.cache Source code
eb.phylo Source code
edgelabels.auteur Man page Source code
edger Source code
edges.phylo Man page Source code
er.matrix Source code
error.rjmcmc Source code
ess Man page Source code
ests.parlog.rjmcmc Source code
ex.jumpsimulator Man page Source code
ex.ratesimulator Man page Source code
ex.traitgram Man page Source code
exemplar.default Source code
exemplar.phylo Man page Source code
exponentialchangeTree Man page Source code
fetch_gbhierarchy.above Source code
fill.taxonomy Source code
fit.base.medusa Source code
fit.partition.medusa Source code
fitContinuous Man page Source code
fitContinuousMCMC Man page Source code
fitDiscrete Man page Source code
fitDiversification Man page
fitSplitModel Man page
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
gbcontain Man page Source code
gbm.prior.lik 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
geigerwarn Source code
gen Man page
geospiza Man page
get.AIC Source code
get.AICc Source code
get.ancestor.of.node Source code
get.ancestors.of.node Source code
get.bd Source code
get.best.partial.model Source code
get.children Source code
get.desc.of.node Source code
get.descendants.of.node Source code
get.max.model.limit Source code
get.optimal.model.flavour Source code
get.optimal.simple Source code
get.ordering Source code
get.parallel Source code
get.profile.likelihoods Source code
get.simulation.matrix Man page Source code
getAncStates Man page Source code
getBD Man page
getDiversificationModel Man page
getFullSplitModel Man page
getMDIp Source code
glomogram.phylo Man page Source code
gui.check Source code
hash.node Man page Source code
hash.tip Source code
hashes.phylo Man page Source code
hashes.rjmcmc Man page Source code
hdr Man page Source code
heights Man page Source code
heights.cache 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 Source code
is.phylo Man page Source code
is.root Man page Source code
jumps.edgewise Source code
jumps.plot Source code
kappa.cache Source code
kappa.phylo Source code
kappaTree Man page Source code
kendallmoran.rate Man page Source code
lambda.cache Source code
lambda.phylo Source code
lambdaTree Man page Source code
lik.partition.medusa Source code
likfx.bm Man page
linearchangeTree Man page Source code
link.root Source code
lnpriorhastings_ratio.merge Source code
lnpriorhastings_ratio.split Source code
load Man page
load.rjmcmc Man page Source code Source code
logLik.gfit Man page Source code
logLik.gfits Man page Source code
lookup.phylo Man page Source code
lrate.phylo Source code
make.bm.relaxed Man page Source code
make.bm.relaxed.direct 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.medusa Source code
make.cache.mkn Source code
make.gbm Man page 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
mecca Man page
medusa Man page Source code
meristic.matrix Source code
mkn.lik Man page Source code
mrca Source code
name.check Man page Source code Source code
namespace Source code
nh.test Man page Source code
nitial.tip.bm.pruning Source code
node.leaves Man page Source code
node.sons Man page
nodefind.phylo Source code
nodelabel.phylo Man page Source code
nrate.phylo Source code
ntercalate.rjmcmc Source code
null.cache Source code
null.phylo Source code
oldestyle.gfit.continuous Source code
oldestyle.gfit.discrete Source code
opensubtree.phylo Source code
ou.cache Source code
ou.lik Source code
ou.phylo Source code
ou.smartstart Source code
ou.vcv Source code
ouTree Man page Source code
parlog.rjmcmc Source code
paths.cache Source code
paths.phylo Source code
phy.anova Man page
phy.manova Man page
phylo.clades Man page Source code
phylo.lookup Man page Source code
pic_variance.phylo Source code
plot.auteurMCMC Man page Source code
plot.auteurMCMCMC Man page Source code
plot.medusa Man page Source code
plot.rjmcmc Man page Source code
plot.rjmcmc.list Man page Source code
plotDiversificationSurface Man page
plotNN Source code
polytomy.phylo Source code
pool.rjmcmcsamples Man page
pp.acdc.prior Source code
pp.getproposal Source code
pp.mcmc Man page Source code
prefit.medusa Source code
prefit.tip.medusa Source code
prep.glomogram Source code
prepare.bm.univariate Source code
prepare.gbm.univariate Source code
primates Man page
print.auteurRAW Man page Source code
print.bayesfactor Man page Source code
print.bm Man page Source code
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 Source code
print.mkn Man page Source code
print.multimedusa Source code
print.rbm Man page Source code
print.removed.shifts Source code
print.rjmcmc Man page Source code
print.rjmcmcmc Man page Source code
print.table Source code
print.taxdump Man page
print.transformer Man page Source code
proc.lnR Source code
process.jumps Source code
process.shifts Source code
proposal.multiplier Source code
proposal.slidingwindow Source code
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 Source code
ratematrix Man page Source code
rc Man page 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
rescale Man page Source code
rescale.phylo Man page Source code
rescaleTree Man page Source code
reshape.constraint.m Source code
resolve.executable Source code
resplitEdgeMatrixGeiger Man page
rjmcmc.bm Man page Source code
rjmcmc.bm.multi Source code
root.bm.direct Source code
root.p.calc Source code
root.phylo Man page
rootfunc.mkn Source code
runMedusa Man page Source code
s.wholenumber Source code
samples.plot Source code
scale.brlen Source code
scale.edge.tree Source code
sem Man page Source code
set.mfrow Source code
set.seed.clock Source code
shifts.plot Man page Source code
sim.bd Man page Source code
sim.bdtree Man page Source code
sim.char Man page Source code
sim.mecca Man page
simple.yule.medusa Source code
slot.attribute Source code
span.phylo Man page Source code
speciationalTree Man page Source code
split.z.at.node.medusa Source code
splitEdgeMatrixGeiger Man page
splitormerge Source code
standardize.prior Source code
startingpt.bm Source code
startingpt.mecca Man page
stem.limits Man page Source code
stem.p Man page Source code
strip.stem Source code
subset.auteurRAW Source code
subset.phylo Man page Source code
summary.modelfit.medusa Source code
sym.matrix Source code
threshold.medusa 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
toC.int Source code
traceplot Source code
tracer Man page
transform.phylo Man page
transparency Source code
treePL.phylo Source code
treedata Man page Source code
treedata.medusa 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
tworateTree Man page Source code
ultrametricize.phylo Man page
unique.multiPhylo Man page Source code
unique.phylo Man page Source code Source code
uniquify_hashes Source code
update.fit.medusa Source code
updateZ Source code
vcv.anc Source code
vmat Man page
whales Man page
white.cache Source code
white.mkn Man page Source code
white.phylo Source code
withinrange 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 June 3, 2018, 11:50 p.m.