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NAMESPACE
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NAMESPACE
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import(seqinr)
useDynLib(exchange_NSE)
export(
# Data Structures
"load.codon.parms",
"load.phi",
"load.genome",
# Main Functions
"main.semppr",
# Initialization functions
"initialize",
"initialize.genome.parms",
"initialize.genome",
"initialize.gene",
"initialize.MCMC.info",
"initialize.output",
"initialize.phi",
"initialize.covariance.mat",
# SCUO
"guess.phi.scuo",
"calcScuo",
# MCMC
"update.codon.parms.all.aa",
"update.codon.parms.one.aa",
"aa.accept.ratio.all.genes",
"aa.accept.ratio.one.gene",
"update.phi.all.genes",
"update.phi.one.gene",
"update.MCMC.info",
"update.covariance.matrix",
# Simulation
"simulate.data.all.genes",
"simulate.data.one.gene",
"simulate.sequence",
# Sequence calculations
"calc.eta.NSE",
"calcMu",
"calc.moments.eta",
"opt.seq",
"pess.seq",
"rand.seq",
# Convergence
"gelman.conv",
# Old stuff from denominator approx
"calc.mean.exact"
)
S3method("plot","codon.parms")
S3method("initialize","codon.parms")
S3method("plot","phi")
S3method("initialize","phi")