API for diversitree
Comparative 'Phylogenetic' Analyses of Diversification

Global functions
.print.constraints	Source code
.print.func.args	Source code
.print.func.phy	Source code
.print.func.reference	Source code
ROOT.ALL	Man page
ROOT.BOTH	Man page
ROOT.EQUI	Man page
ROOT.FLAT	Man page
ROOT.GIVEN	Man page
ROOT.MAX	Man page
ROOT.OBS	Man page
`argnames<-.constrained`	Source code
`argnames<-.dtlik`	Source code
`argnames<-`	Source code
add.alpha	Source code
add.profile.outline	Source code
add.profile.shading	Source code
all.models.bisse	Source code
all_branches.list	Source code
all_branches_matrix	Source code
ancestors	Source code
ancestors2	Source code
anova.fit.mle	Man page Source code
arcs	Source code
argnames	Man page Source code
argnames.constrained	Man page Source code
argnames.dtlik	Source code
argnames<-	Man page
argnames<-.constrained	Man page
argnames_twopart	Source code
as.mcmcsamples	Source code
asr	Man page
asr.bisse	Man page
asr.joint	Man page Source code
asr.marginal	Man page Source code
asr.marginal.bisse	Man page
asr.marginal.musse	Man page
asr.mkn	Man page
asr.musse	Man page
asr.stoch	Man page Source code
average.over.mcmc	Source code
big.brother	Man page Source code
bisect.int1d	Source code
block.diagonal	Source code
boxconstrain	Source code
bracket.1d	Source code
bracket.int1d	Source code
branches.bm.pruning	Source code
branches.eb	Source code
branches.lambda	Source code
branches.unresolved.bisse	Source code
branches.unresolved.bisse.split	Source code
branches.unresolved.bisseness	Source code
branching.depth	Source code
branching.heights	Source code
branching.times.edge	Source code
bucexp	Source code
bucexp.n	Source code
bucexpl	Source code
caching.branches.set.pars	Source code
caching.integer	Source code
check.bounds	Source code
check.control.bd	Source code
check.control.continuous	Source code
check.control.expokit	Source code
check.control.mk2	Source code
check.control.mkn	Source code
check.control.ode	Source code
check.control.pgls	Source code
check.control.quasse	Source code
check.control.split	Source code
check.data.pgls	Source code
check.depth	Source code
check.f.quasse	Source code
check.f.quasse.split	Source code
check.fftC	Man page Source code
check.info.ode	Source code
check.integer	Source code
check.loaded.symbol	Source code
check.n.epoch	Source code
check.nonnegative	Source code
check.nonpositive	Source code
check.par.length	Source code
check.pars.bd.split	Source code
check.pars.bisse	Source code
check.pars.bisse.split	Source code
check.pars.bisseness	Source code
check.pars.classe	Source code
check.pars.eb	Source code
check.pars.geosse	Source code
check.pars.geosse.split	Source code
check.pars.lambda	Source code
check.pars.multipart	Source code
check.pars.musse	Source code
check.pars.nonnegative	Source code
check.pars.ou	Source code
check.pars.quasse	Source code
check.ptr	Source code
check.sampling.f	Source code
check.sampling.f.split	Source code
check.scalar	Source code
check.spline.data	Source code
check.split	Source code
check.states	Source code
check.states.musse.multitrait	Source code
check.states.quasse	Source code
check.tree	Source code
check.unresolved	Source code
check.unresolved.bd	Source code
clades.from.classification	Man page Source code
clades.from.polytomies	Man page Source code
clades.from.sample	Source code
coef.fit.mle	Man page Source code
coef.mcmcsamples	Source code
collapse	Source code
combine	Man page Source code
combine.branches.quasse	Source code
constant.x	Man page Source code
constrain	Man page Source code
constrain.i	Man page Source code
constrain.i2	Source code
constrain.parse	Source code
count.eval	Source code
default.argnames.bd	Source code
default.argnames.bisse	Source code
default.argnames.bisseness	Source code
default.argnames.bm	Source code
default.argnames.classe	Source code
default.argnames.eb	Source code
default.argnames.geosse	Source code
default.argnames.lambda	Source code
default.argnames.mk2	Source code
default.argnames.mkn	Source code
default.argnames.mkn.meristic	Source code
default.argnames.musse	Source code
default.argnames.ou	Source code
default.argnames.pgls	Source code
default.argnames.quasse	Source code
default.argnames.yule	Source code
derivs.bd	Source code
derivs.bisse	Source code
derivs.bisseness	Source code
derivs.classe	Source code
derivs.for.deSolve	Source code
derivs.geosse	Source code
derivs.mkn.ode	Source code
derivs.musse	Source code
descendants	Source code
descendants.C	Source code
descendants.flag.C	Source code
descendants.idx.C	Source code
discretize	Source code
diversitree	Man page
diversitree-deprecated	Man page
diversitree-package	Man page
dmvnorm2	Source code
dmvnorm3	Source code
do.asr.joint	Source code
do.asr.marginal.R	Source code
do.constrain	Source code
do.mle.search	Source code
do.mle.search.int1d	Source code
do.mle.search.minqa	Source code
do.mle.search.mixed	Source code
do.mle.search.nlm	Source code
do.mle.search.nlminb	Source code
do.mle.search.optim	Source code
do.mle.search.optimize	Source code
do.mle.search.subplex	Source code
do.mle.search.subplexR	Source code
drop.likelihood	Man page Source code
drop_tip_fixed	Source code
dt.tips.grouped	Source code
dt.tips.ordered	Source code
expand.parameters	Man page Source code
expand.pars.quasse	Source code
expm.dense	Source code
expm.expokit.sparse.pars	Source code
expmv.expokit.dense	Source code
expmv.expokit.sparse	Source code
extractAIC.fit.mle	Source code
fftR.make.kern	Source code
fftR.propagate.t	Source code
fftR.propagate.x	Source code
filled.arcs	Source code
find.mle	Man page Source code
find.mle.default	Source code
find.mle.dtlik	Source code
find.mle.mixed	Source code
fitted.fit.mle.pgls	Source code
fitted.mcmcsamples.pgls	Source code
fitted.pgls.dt	Source code
flatten.pars.classe	Source code
get.cache	Source code
get.children	Source code
get.descendants	Man page Source code
get.info	Source code
get.likelihood	Man page Source code
get.ordering	Source code
get.par.td	Source code
group.label.tip	Source code
group.label.tip.rad	Source code
guess.constrained.start	Source code
hdr	Source code
hdr.new	Source code
hdr.uniroot	Source code
history.bin	Source code
history.from.sim.discrete	Man page Source code
hyperg	Source code
index	Source code
inflate.pars.classe	Source code
initial.conditions.bd.ode	Source code
initial.conditions.bisse	Source code
initial.conditions.bisseness	Source code
initial.conditions.bm.pruning	Source code
initial.conditions.geosse	Source code
initial.conditions.mkn	Source code
initial.conditions.musse	Source code
initial.tip.bd.ode	Source code
initial.tip.bm.pruning	Source code
initial.tip.mkn.ode	Source code
initial.tip.musse.multitrait	Source code
initial.tip.quasse	Source code
initial.tip.quasse.split	Source code
initial.tip.xxsse	Source code
invert	Man page Source code
is.constrained	Source code
load.wisdom	Source code
logLik.fit.mle	Man page Source code
lsoda.trim	Source code
make.all_branches.bd.nee	Source code
make.all_branches.bd.split	Source code
make.all_branches.bm.contrasts	Source code
make.all_branches.bm.pruning	Source code
make.all_branches.bm.vcv	Source code
make.all_branches.continuous	Source code
make.all_branches.dtlik	Source code
make.all_branches.eb.pruning	Source code
make.all_branches.lambda.pruning	Source code
make.all_branches.mkn	Source code
make.all_branches.mkn.expokit	Source code
make.all_branches.mkn.pij	Source code
make.all_branches.ou.pruning	Source code
make.all_branches.pgls.contrasts	Source code
make.all_branches.pgls.pruning	Source code
make.all_branches.pgls.pruning.phylo	Source code
make.all_branches.pgls.vcv	Source code
make.all_branches.quasse	Source code
make.all_branches.quasse.split	Source code
make.all_branches.rescale.contrasts	Source code
make.all_branches.rescale.vcv	Source code
make.all_branches.split.dtlik	Source code
make.all_branches.t.dtlik	Source code
make.all_branches.td.dtlik	Source code
make.asr.joint	Man page Source code
make.asr.joint.constrained	Source code
make.asr.joint.mk2	Man page
make.asr.joint.mkn	Man page Source code
make.asr.marginal	Man page Source code
make.asr.marginal.bisse	Man page Source code
make.asr.marginal.bisse.split	Source code
make.asr.marginal.constrained	Source code
make.asr.marginal.geosse	Source code
make.asr.marginal.mk2	Man page
make.asr.marginal.mkn	Man page Source code
make.asr.marginal.musse	Man page Source code
make.asr.stoch	Man page Source code
make.asr.stoch.constrained	Source code
make.asr.stoch.mk2	Man page
make.asr.stoch.mkn	Man page Source code
make.bd	Man page Source code
make.bd.split	Man page Source code
make.bd.split.part	Source code
make.bd.t	Man page Source code
make.bisse	Man page Source code
make.bisse.split	Man page Source code
make.bisse.t	Man page Source code
make.bisse.td	Man page Source code
make.bisse.uneven	Man page Source code
make.bisseness	Man page Source code
make.bm	Man page Source code
make.br.bbm	Source code
make.br.bm	Source code
make.br.meristic	Source code
make.br.mk2	Source code
make.br.mkn	Source code
make.br.ou	Source code
make.branches.aux.bisse	Source code
make.branches.aux.dtlik	Source code
make.branches.aux.geosse	Source code
make.branches.aux.musse	Source code
make.branches.aux.quasse	Source code
make.branches.aux.quasse.fftC	Source code
make.branches.bd.ode	Source code
make.branches.bisse	Source code
make.branches.bisseness	Source code
make.branches.classe	Source code
make.branches.comp	Source code
make.branches.dtlik	Source code
make.branches.geosse	Source code
make.branches.mkn.expokit	Source code
make.branches.mkn.ode	Source code
make.branches.musse	Source code
make.branches.ou	Source code
make.branches.quasse	Source code
make.branches.quasse.fftC	Source code
make.branches.quasse.fftR	Source code
make.branches.quasse.mol	Source code
make.branches.split	Source code
make.branches.td	Source code
make.branches.td.dtlik	Source code
make.brownian.with.drift	Man page Source code
make.cache	Source code
make.cache.bd	Source code
make.cache.bd.nee	Source code
make.cache.bd.ode	Source code
make.cache.bd.split	Source code
make.cache.bd.t	Source code
make.cache.bisse	Source code
make.cache.bisse.split	Source code
make.cache.bisse.t	Source code
make.cache.bisse.td	Source code
make.cache.bisseness	Source code
make.cache.bm	Source code
make.cache.classe	Source code
make.cache.eb	Source code
make.cache.geosse	Source code
make.cache.geosse.split	Source code
make.cache.geosse.t	Source code
make.cache.lambda	Source code
make.cache.mkn	Source code
make.cache.mkn.meristic	Source code
make.cache.mkn.multitrait	Source code
make.cache.musse	Source code
make.cache.musse.multitrait	Source code
make.cache.musse.split	Source code
make.cache.musse.t	Source code
make.cache.musse.td	Source code
make.cache.ou	Source code
make.cache.pgls	Source code
make.cache.quasse	Source code
make.cache.quasse.split	Source code
make.cache.split	Source code
make.cache.split.xxsse	Source code
make.caching.branches	Source code
make.caching.branches.aux	Source code
make.check.pars.pgls	Source code
make.clade.tree	Man page Source code
make.classe	Man page Source code
make.derivs.aux	Source code
make.derivs.mkn.meristic	Source code
make.derivs.mkn.pij	Source code
make.derivs.t	Source code
make.do.asr.marginal	Source code
make.eb	Man page Source code
make.every.so.often	Source code
make.geosse	Man page Source code
make.geosse.split	Man page Source code
make.geosse.t	Man page Source code
make.geosse.uneven	Man page Source code
make.history	Source code
make.info.bd	Source code
make.info.bd.split	Source code
make.info.bisse	Source code
make.info.bisseness	Source code
make.info.bm	Source code
make.info.classe	Source code
make.info.eb	Source code
make.info.geosse	Source code
make.info.lambda	Source code
make.info.mk2	Source code
make.info.mkn	Source code
make.info.mkn.meristic	Source code
make.info.mkn.multitrait	Source code
make.info.musse	Source code
make.info.musse.multitrait	Source code
make.info.ou	Source code
make.info.pgls	Source code
make.info.quasse	Source code
make.info.yule	Source code
make.initial.conditions.classe	Source code
make.initial.conditions.quasse	Source code
make.initial.conditions.split	Source code
make.initial.conditions.t	Source code
make.initial.conditions.td	Source code
make.initial.tip.xxsse.split	Source code
make.lambda	Man page Source code
make.linear.x	Man page Source code
make.matrix	Source code
make.matrix.ness	Source code
make.mixed	Source code
make.mk2	Man page Source code
make.mkn	Man page Source code
make.mkn.meristic	Man page Source code
make.mkn.multitrait	Man page Source code
make.musse	Man page Source code
make.musse.multitrait	Man page Source code
make.musse.split	Man page Source code
make.musse.t	Man page Source code
make.musse.td	Man page Source code
make.ode	Source code
make.ode.deSolve	Source code
make.ode.gslode	Source code
make.ou	Man page Source code
make.pars.bisse.td	Source code
make.pars.classe	Source code
make.pars.mkn	Source code
make.pars.mkn.multitrait	Source code
make.pars.musse	Source code
make.pars.musse.multitrait	Source code
make.pars.musse.split	Source code
make.pars.musse.td	Source code
make.pars.quasse	Source code
make.pars.quasse.split	Source code
make.pde.quasse.fftC	Source code
make.pde.quasse.fftR	Source code
make.pde.quasse.mol	Source code
make.pgls	Man page Source code
make.pij.mkn	Source code
make.prior	Man page
make.prior.ExpBeta	Source code
make.prior.exponential	Man page Source code
make.prior.uniform	Man page Source code
make.quasse	Man page Source code
make.quasse.split	Man page Source code
make.rescale.phylo	Source code
make.rescale.phylo.eb	Source code
make.rescale.phylo.lambda	Source code
make.rescale.phylo.ou	Source code
make.rootfunc.bd.split	Source code
make.rootfunc.quasse	Source code
make.rootfunc.split	Source code
make.rootfunc.t	Source code
make.rootfunc.td	Source code
make.sim.character	Man page Source code
make.time.machine	Source code
make.tips.quasse.fftC	Source code
make.tree.bd	Source code
make.tree.bisse	Source code
make.tree.bisse.C	Source code
make.tree.bisse.C.core	Source code
make.tree.bisse.R	Source code
make.tree.bisse.R.core	Source code
make.tree.bisseness	Source code
make.tree.classe	Source code
make.tree.musse	Source code
make.tree.quasse	Source code
make.unipar	Source code
make.unresolved.bd	Source code
make.unresolved.bisse	Source code
make.yule	Man page Source code
make_asr_marginal_dtlik_t	Source code
matrix.to.list	Source code Source code
mcmc	Man page Source code
mcmc.default	Man page Source code
mcmc.dtlik	Source code
mcmc.lowerzero	Source code
mcmc_norm_1d	Source code
mcmcsamples.index	Source code
me.to.ape.bd	Source code
me.to.ape.bisse	Source code
me.to.ape.quasse	Source code
minimise.int1d	Source code
mkn.Q	Source code
mkn.meristic.Q	Source code
mkn.multitrait.translate	Man page Source code
mrca.tipset	Source code
musse.Q	Source code
musse.multitrait.translate	Man page Source code
node.depth	Source code
node.depth.edgelength	Source code
node.height	Source code
normalise	Source code
noroptimal.x	Man page Source code
nucexp	Source code
nucexpl	Source code
pars.ge.to.cl	Source code
partition	Source code
partition2	Source code
pgls.root.mean.bm	Source code
pgls.root.var.bm	Source code
pij.mk2	Source code
plot.clade.tree	Source code
plot.dtlik.t	Source code
plot.history	Man page Source code
plot2.phylo	Source code
plot_history_coords	Source code
polytomies.to.clades	Man page Source code
pp.clades.fan	Source code
pp.clades.phylogram	Source code
pp.coords.fan	Source code
pp.coords.fix.xy	Source code
pp.coords.phylogram	Source code
pp.lim.fan	Source code
pp.lim.phylogram	Source code
pp.node.coords	Source code
pp.nodelabel.phylogram	Source code
pp.segments.fan	Source code
pp.segments.phylogram	Source code
pp.tiplabel.fan	Source code
pp.tiplabel.phylogram	Source code
predict.dtlik.t	Source code
print.dtlik	Source code
profiles.plot	Man page Source code
projection.matrix.classe	Source code
protect	Man page Source code
prune	Man page Source code
prune.hist	Source code
quadratic.roots	Source code
quasse.extent	Source code
quasse.integrate.fftR	Source code
radial.text	Source code
repack	Source code
reparam.1	Source code
reparam.q	Source code
rescale.phylo.se	Source code
residuals.fit.mle.pgls	Source code
residuals.pgls.dt	Source code
root_p_calc	Source code
root_p_quasse	Source code
rootfunc.bd.nee	Source code
rootfunc.bd.ode	Source code
rootfunc.bisseness	Source code
rootfunc.bm.contrasts	Source code
rootfunc.bm.pruning	Source code
rootfunc.bm.vcv	Source code
rootfunc.classe	Source code
rootfunc.geosse	Source code
rootfunc.mkn	Source code
rootfunc.musse	Source code
rootfunc.pgls.pruning	Source code
round_to_grid	Source code
run.cached	Man page Source code
run.until.change	Source code
sampler.hmc.bounded	Source code
sampler.norm	Man page Source code
sampler.slice	Man page Source code
save.wisdom	Source code
sectors	Source code
set.argnames	Source code
set.defaults	Man page Source code
set.info	Source code
sigmoid.x	Man page Source code
sigmoid2.x	Man page Source code
sim.character	Man page Source code
simplex	Source code
simplex.grid	Source code
slice.1d	Source code
slice.isolate	Source code
slice.sample	Source code
speciate	Source code
split_group	Source code
starting.point.bd	Man page Source code
starting.point.bisse	Man page Source code
starting.point.classe	Man page Source code
starting.point.geosse	Man page Source code
starting.point.musse	Man page Source code
starting.point.musse.multitrait	Man page Source code
starting.point.quasse	Man page Source code
stationary.freq.bisse	Source code
stationary.freq.bisseness	Source code
stationary.freq.classe	Source code
stationary.freq.classe.ev	Source code
stationary.freq.geosse	Source code
stationary.freq.mkn	Source code
stepf.x	Man page Source code
subplex.mixed	Source code
subplexR	Source code
summarise.histories.mk2	Source code
time.machine.argnames	Source code
toC.cache.continuous	Source code
toC.int	Source code
trait.plot	Man page Source code
trans.mixed	Source code
tree.bd	Man page Source code
tree.bisse	Man page Source code
tree.bisseness	Man page Source code
tree.classe	Man page Source code
tree.geosse	Man page Source code
tree.musse	Man page Source code
tree.musse.multitrait	Man page Source code
tree.quasse	Man page Source code
tree.yule	Man page Source code
trees	Man page Source code
update.cache.t	Source code
update.info.split	Source code
update.info.t	Source code
update.info.td	Source code
update.info.uneven	Source code