diversitree-package	diversitree-package
anova.fit.mle	find.mle
argnames	argnames
argnames.constrained	argnames
argnames<-	argnames
argnames<-.constrained	argnames
asr	asr
asr.bisse	asr-bisse
asr.joint	asr
asr.marginal	asr
asr.marginal.bisse	asr-bisse
asr.marginal.musse	asr-bisse
asr.mkn	asr-mkn
asr.musse	asr-bisse
asr.stoch	asr
big.brother	big.brother
check.fftC	check
clades.from.classification	make.clade.tree
clades.from.polytomies	make.clade.tree
coef.fit.mle	find.mle
combine	combine
constant.x	quasse-common
constrain	constrain
constrain.i	constrain
diversitree	diversitree-package
diversitree-deprecated	diversitree-deprecated
drop.likelihood	utils
expand.parameters	utils
find.mle	find.mle
geosse.phy	geosse.phy
get.descendants	utils
get.likelihood	utils
history.from.sim.discrete	history.from.sim
invert	protect
logLik.fit.mle	find.mle
make.asr.joint	asr
make.asr.joint.mk2	asr-mkn
make.asr.joint.mkn	asr-mkn
make.asr.marginal	asr
make.asr.marginal.bisse	asr-bisse
make.asr.marginal.mk2	asr-mkn
make.asr.marginal.mkn	asr-mkn
make.asr.marginal.musse	asr-bisse
make.asr.stoch	asr
make.asr.stoch.mk2	asr-mkn
make.asr.stoch.mkn	asr-mkn
make.bd	make.bd
make.bd.split	make.bd.split
make.bd.t	make.bd.t
make.bisse	make.bisse
make.bisse.split	make.bisse.split
make.bisse.t	make.bisse.td
make.bisse.td	make.bisse.td
make.bisse.uneven	make.bisse.split
make.bisseness	make.bisseness
make.bm	make.bm
make.brownian.with.drift	quasse-common
make.clade.tree	make.clade.tree
make.classe	make.classe
make.eb	make.bm
make.geosse	make.geosse
make.geosse.split	make.geosse.split
make.geosse.t	make.geosse.t
make.geosse.uneven	make.geosse.split
make.lambda	make.bm
make.linear.x	quasse-common
make.mk2	make.mkn
make.mkn	make.mkn
make.mkn.meristic	make.mkn
make.mkn.multitrait	make.musse.multitrait
make.musse	make.musse
make.musse.multitrait	make.musse.multitrait
make.musse.split	make.musse.split
make.musse.t	make.musse.td
make.musse.td	make.musse.td
make.ou	make.bm
make.pgls	make.pgls
make.prior	make.prior
make.prior.exponential	make.prior
make.prior.uniform	make.prior
make.quasse	make.quasse
make.quasse.split	make.quasse.split
make.sim.character	sim.character
make.yule	make.bd
mcmc	mcmc
mcmc.default	mcmc
mkn.multitrait.translate	make.musse.multitrait
musse.multitrait.translate	make.musse.multitrait
noroptimal.x	quasse-common
plot.history	plot.history
polytomies.to.clades	diversitree-deprecated
profiles.plot	profiles.plot
protect	protect
prune	simulate
ROOT.ALL	constants
ROOT.BOTH	constants
ROOT.EQUI	constants
ROOT.FLAT	constants
ROOT.GIVEN	constants
ROOT.MAX	constants
ROOT.OBS	constants
run.cached	utils
sampler.norm	mcmc
sampler.slice	mcmc
set.defaults	set.defaults
sigmoid.x	quasse-common
sigmoid2.x	quasse-common
sim.character	sim.character
starting.point.bd	make.bd
starting.point.bisse	make.bisse
starting.point.classe	make.classe
starting.point.geosse	make.geosse
starting.point.musse	make.musse
starting.point.musse.multitrait	make.musse.multitrait
starting.point.quasse	make.quasse
stepf.x	quasse-common
trait.plot	trait.plot
tree.bd	simulate
tree.bisse	simulate
tree.bisseness	simulate
tree.classe	simulate
tree.geosse	simulate
tree.musse	simulate
tree.musse.multitrait	simulate
tree.quasse	simulate
tree.yule	simulate
trees	simulate
