API for richfitz/diversitree
Comparative 'Phylogenetic' Analyses of Diversification

Global functions
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
add.alpha Source code
add.profile.outline Source code
add.profile.shading Source code
all.branches.list Source code
all.branches.matrix Source code
all.models.bisse 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.twopart Source code
argnames<- Man page
argnames<-.constrained Man page
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
geosse.phy Man page
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.dtlik.t 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
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
plot.history.coords Source code
plot2.phylo 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.nodepoints.phylogram Source code
pp.segments.fan Source code
pp.segments.phylogram Source code
pp.tiplabel.fan Source code
pp.tiplabel.phylogram Source code
pp.tippoints.phylogram Source code
predict.dtlik.t Source code
print.constraints Source code
print.dtlik Source code
print.func.args Source code
print.func.phy Source code
print.func.reference 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
richfitz/diversitree documentation built on May 25, 2017, 2:11 a.m.