NAMESPACE

###########################################################################
# Shared object library load directives.
#
# The use of the "useDynLib(qbtl)" directive means that the qbtl shared
# object library does not need to be called in the .onLoad function in
# zzz.r.
#

useDynLib(qtlbim)

############################################################################
# Export directives.  These directives export functions.  S3 methods for
# classes declared in the package should be declared with the "S3method"
# directive.
#

export(covar.mean)
export(qb.intcov)
export(qb.split.chr)
export(qb.best)

export(qb.coda)
export(qb.cross)
export(qb.data)
export(qb.genoprob)
export(qb.get)
export(qb.hpdchr)
export(qb.legacy)
export(qb.cross.class)
export(qb.mcmc)
export(qb.model)
export(qb.recover)
export(qb.remove)
export(qb.reorder)
export(qb.sim.cross)
export(qb.sweave)


export(qb.demo)
export(qb.load)
export(qb.save)
export(pull.grid)  ## new routine usable (?) in R/qtl
export(pull.loci)

export(anova.step.fitqtl)
export(sim.data)
export(step.fitqtl)


#*****************************
#******************************

## The following have S3 methods:
export(plot.qb)

export(qb.arch)
export(qb.bf)
export(qb.BayesFactor)
export(qb.close)
export(qb.BestPattern)
export(qb.confound)
export(qb.covar)
export(qb.diag)
export(qb.epimodes)
export(qb.epistasis)
export(qb.hpdone)
export(qb.loci)
export(qb.mainmodes)
export(qb.meancomp)
export(qb.multloci)
export(qb.pairloci)
export(qb.scanone)
export(qb.scantwo)
export(qb.sliceone)
export(qb.slicetwo)
export(qb.varcomp)

##############################################################################
# S3method declarations.  These will allow generic methods to function properly
# with functions such as "plot.qb" declared in the package.
#

S3method(qb.arch, default)
S3method(qb.arch, step.fitqtl)
S3method(qb.arch, qb.BestPattern)

S3method(anova, step.fitqtl)

S3method(summary, qb.sim)

S3method(subset, qb)

S3method(plot, qb)
S3method(print,qb)
S3method(summary,qb)

S3method(print,qb.arch)
S3method(summary,qb.arch)

S3method(plot, qb.BayesFactor)
S3method(print, qb.BayesFactor)
S3method(summary, qb.BayesFactor)

S3method(plot, qb.close)
S3method(print, qb.close)
S3method(summary, qb.close)
S3method(print, summary.qb.close)

S3method(plot, qb.BestPattern)
S3method(print, qb.BestPattern)
S3method(summary, qb.BestPattern)
S3method(print, summary.qb.BestPattern)



S3method(plot, qb.confound)
S3method(print, qb.confound)
S3method(summary, qb.confound)

S3method(plot, qb.covar)
S3method(print, qb.covar)
S3method(summary, qb.covar)

S3method(plot, qb.diag)
S3method(print, qb.diag)
S3method(summary, qb.diag)

S3method(plot, qb.epistasis)
S3method(print, qb.epistasis)
S3method(summary, qb.epistasis)


S3method(plot, qb.hpdone)
S3method(print, qb.hpdone)
S3method(summary, qb.hpdone)
S3method(print, summary.qb.hpdone)

S3method(plot, qb.loci)
S3method(print, qb.loci)
S3method(summary, qb.loci)

S3method(summary, qb.mainmodes)

S3method(plot, qb.meancomp)
S3method(print, qb.meancomp)
S3method(summary, qb.meancomp)

S3method(plot, qb.multloci)
S3method(print, qb.multloci)
S3method(summary, qb.multloci)
S3method(print, summary.qb.multloci)

S3method(plot, qb.pairloci)
S3method(print, qb.pairloci)
S3method(summary, qb.pairloci)

S3method(plot, qb.scanone)
S3method(print, qb.scanone)
S3method(summary, qb.scanone)
S3method(print, summary.qb.scanone)

S3method(plot, qb.scantwo)
S3method(print, qb.scantwo)
S3method(summary, qb.scantwo)
S3method(print, summary.qb.scantwo)

S3method(plot, qb.sliceone)
S3method(print, qb.sliceone)
S3method(summary, qb.sliceone)

S3method(plot, qb.slicetwo)
S3method(print, qb.slicetwo)
S3method(summary, qb.slicetwo)

S3method(plot, qb.varcomp)
S3method(print, qb.varcomp)
S3method(summary, qb.varcomp)