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.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 |
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.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.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 |
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