API for bayou
Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Global functions
C_threepoint Source code
C_transf_branch_lengths Source code
C_weightmatrix Source code
D.from.theta Source code
Lposterior Man page Source code
OU.asr Source code
OU.lik Man page Source code Source code
OU.repar Man page Source code
OUphenogram Man page Source code
OUwie2bayou Man page Source code
QG.alpha Man page Source code
QG.sig2 Man page Source code
addColorBar Source code
addshift2map Source code
adjustTheta Source code
allnodes.W Source code
ancestorBranches Source code
auteur.W Source code
bayou Man page
bayou-deprecated Man page Man page
bayou-package Man page
bayou.checkModel Man page Source code
bayou.lik Man page Source code
bayou.makeMCMC Man page Source code
bayou.mcmc Man page Source code
bayou2OUwie Man page Source code
branchRegime Source code
buildControl Source code
cache.descendants Source code
cache.tree Source code
cache.y.nodes Source code
cdpois Man page Source code
colorRamp Source code
combine.chains Man page Source code
computelnr Source code
countL Source code
dataSim Man page Source code
dhalfcauchy Man page Source code
discard.burnin Source code
dloc Man page Source code
dsb Man page Source code
fastbm.lik Source code
fix.root.bm Source code
gelman.R Man page Source code
get.ancestor.of.node Source code
get.ancestors.of.node Source code
getPreValues Source code
getSimDists Source code
getTipMap Source code
heights.cache Source code Source code
identifyBranches Man page Source code
jointHalflifeVyProposal Source code
load.bayou Man page Source code
make.monitorFn Source code
make.powerposteriorFn Man page Source code
make.prior Man page Source code
make.refFn Man page Source code
makeBayouModel Man page Source code
makeTransparent Man page Source code
model.OU Man page
mputePredBM Source code
mrca Source code
multiplierProposal Source code
optima.ages Source code
ou.cache.fast Source code
ou.next Source code
ouMatrix Source code
parmap.W Man page Source code Source code
pars2map Source code
pars2simmap Man page Source code
phalfcauchy Man page Source code
phenogram.density Man page Source code
plot.bayouMCMC Man page Source code
plot.ssMCMC Man page Source code
plotBayoupars Man page Source code
plotBranchHeatMap Man page Source code
plotOUtreesim Man page Source code
plotRegimes Man page Source code
plotShiftSummaries Man page Source code
plotSimmap.mcmc Man page Source code
posterior.Q Source code
powerPosteriorFn Source code
prepare.bm.univariate Source code
prepare.ou.univariate Source code
print.bayouFit Man page Source code
print.bayouMCMC Man page Source code
print.priorFn Man page Source code
print.refFn Man page Source code
print.ssMCMC Man page Source code
priorSim Man page Source code
proposalFn Source code
pruningwise.branching.times Source code
pruningwise.distFromRoot Source code
pull.pars Man page Source code
pull.rsample Source code
qhalfcauchy Man page Source code
rdpois Man page Source code
regime.plot Man page Source code
repars Source code
rhalfcauchy Man page Source code
rloc Man page Source code
rsb Man page Source code
sample Source code
set.burnin Man page Source code
set.defaults Source code
set.runpars Source code
shiftSummaries Man page Source code
sim.OU Source code
simOU.onmap Source code
simmap.W Man page Source code Source code
slide Source code
slide2 Source code
slidespace Source code
slidingWindowProposal Source code
splitmerge Source code
splitmergeGreen Source code
splitmergePrior Source code
splitmergebd Source code
steppingstone Man page Source code
steppingstone.mcmc Source code
store.bayou Source code
store.bayou2 Source code
summary.bayouMCMC Man page Source code
tipregime Source code
toSimmap Source code
tune.D Source code
updateControl Source code
vcv.asrOU Source code
vectorMultiplier Source code
vectorSlidingWindow Source code
vectorSlidingWindowSplit Source code
whichorder Source code
bayou documentation built on Oct. 9, 2018, 5:04 p.m.