mvSLOUCH-package	mvSLOUCH-package
.beginEstimationParams	mvSLOUCH-internal
.bm.phyl.cov	mvSLOUCH-internal
.bm.phyl.mean	mvSLOUCH-internal
.calc.cov.ouch.mv	mvSLOUCH-internal
.calc.cov.slouch.mv	mvSLOUCH-internal
.calc.exptA	mvSLOUCH-internal
.calc.exptA.2dim	mvSLOUCH-internal
.calc.integral.evAStevA	mvSLOUCH-internal
.calc.integral.evAStevA.2dim	mvSLOUCH-internal
.calc.intercept	mvSLOUCH-internal
.calc.mean.ouch.mv	mvSLOUCH-internal
.calc.mean.slouch.mv	mvSLOUCH-internal
.calc.phyl.cov	mvSLOUCH-internal
.calc.phyl.halflife	mvSLOUCH-internal
.calc.phyl.LogLik.traits	mvSLOUCH-internal
.calc.phyl.mean	mvSLOUCH-internal
.calc.vec.dist	mvSLOUCH-internal
.calcAncestorTimes	mvSLOUCH-internal
.calcAprecalcMatrices	mvSLOUCH-internal
.calcCI	mvSLOUCH-internal
.calcLogLikParametrized	mvSLOUCH-internal
.calcTreeDist	mvSLOUCH-internal
.calculate.Tree.dists	mvSLOUCH-internal
.CalcVlq	mvSLOUCH-internal
.CalcVlq2	mvSLOUCH-internal
.CalcVlqStat	mvSLOUCH-internal
.ci.HL.loglikfunc	mvSLOUCH-internal
.ci.listParams	mvSLOUCH-internal
.ci.loglikfunc	mvSLOUCH-internal
.ci.vectorizeParams	mvSLOUCH-internal
.cleanUpModelParams	mvSLOUCH-internal
.col.rot	mvSLOUCH-internal
.correct.names	mvSLOUCH-internal
.decompEigenA.S	mvSLOUCH-internal
.drawRandomNiches	mvSLOUCH-internal
.drawRandomRegimes	mvSLOUCH-internal
.dzeta.matrix.t	mvSLOUCH-internal
.dzeta.matrix.t1t2	mvSLOUCH-internal
.dzeta.matrix.t1t2v2	mvSLOUCH-internal
.dzeta.matrix.tv2	mvSLOUCH-internal
.dzetaIJ.matrix	mvSLOUCH-internal
.dzetaKappa.intercept	mvSLOUCH-internal
.dzetaKappa.matrix	mvSLOUCH-internal
.dzetaKappa.matrix.simp.t	mvSLOUCH-internal
.dzetaKappa.matrix2	mvSLOUCH-internal
.dzetaKappa.simp.intercept	mvSLOUCH-internal
.EvaluatePoint	mvSLOUCH-internal
.generategrid	mvSLOUCH-internal
.generatenames	mvSLOUCH-internal
.givens.mult.M	mvSLOUCH-internal
.givens.real	mvSLOUCH-internal
.GridEvaluatePointA	mvSLOUCH-internal
.interpret.intercept	mvSLOUCH-internal
.inv.rho.givens.real	mvSLOUCH-internal
.Kappa.matrix	mvSLOUCH-internal
.Kappa.matrix.NA	mvSLOUCH-internal
.M.mult.givens	mvSLOUCH-internal
.make.states.mvsl	mvSLOUCH-internal
.min.mLogLik.BmPsi	mvSLOUCH-internal
.min.RSS.BmPsi	mvSLOUCH-internal
.MinusPhylLogLikFunc	mvSLOUCH-internal
.MinusPhylLogLikFuncMVslouch	mvSLOUCH-internal
.MinusPhylLogLikFuncouch	mvSLOUCH-internal
.num.inv.transform.positive	mvSLOUCH-internal
.num.transform.positive	mvSLOUCH-internal
.ouch.design.matrix	mvSLOUCH-internal
.ouch.GLS	mvSLOUCH-internal
.ouch2slouch.mvsl	mvSLOUCH-internal
.par.inv.transform	mvSLOUCH-internal
.par.inv.transform.decomp.matrix	mvSLOUCH-internal
.par.inv.transform.decomp.neg.real.matrix	mvSLOUCH-internal
.par.inv.transform.decomp.pos.real.matrix	mvSLOUCH-internal
.par.inv.transform.decomp.real.matrix	mvSLOUCH-internal
.par.inv.transform.decomp.sym.matrix	mvSLOUCH-internal
.par.inv.transform.invert.matrix	mvSLOUCH-internal
.par.inv.transform.invert.qr.matrix	mvSLOUCH-internal
.par.inv.transform.invert.svd.matrix	mvSLOUCH-internal
.par.inv.transform.lowertri.matrix	mvSLOUCH-internal
.par.inv.transform.normal.matrix	mvSLOUCH-internal
.par.inv.transform.orth.matrix.cayley	mvSLOUCH-internal
.par.inv.transform.orth.matrix.givens	mvSLOUCH-internal
.par.inv.transform.symmetric.matrix	mvSLOUCH-internal
.par.inv.transform.twobytwo.matrix	mvSLOUCH-internal
.par.inv.transform.uppertri.matrix	mvSLOUCH-internal
.par.transform	mvSLOUCH-internal
.par.transform.decomp.matrix	mvSLOUCH-internal
.par.transform.decomp.neg.real.matrix	mvSLOUCH-internal
.par.transform.decomp.pos.real.matrix	mvSLOUCH-internal
.par.transform.decomp.real.matrix	mvSLOUCH-internal
.par.transform.decomp.sym.matrix	mvSLOUCH-internal
.par.transform.invert.matrix	mvSLOUCH-internal
.par.transform.invert.qr.matrix	mvSLOUCH-internal
.par.transform.invert.svd.matrix	mvSLOUCH-internal
.par.transform.lowertri.matrix	mvSLOUCH-internal
.par.transform.normal.matrix	mvSLOUCH-internal
.par.transform.orth.matrix.cayley	mvSLOUCH-internal
.par.transform.orth.matrix.givens	mvSLOUCH-internal
.par.transform.symmetric.matrix	mvSLOUCH-internal
.par.transform.twobytwo.matrix	mvSLOUCH-internal
.par.transform.uppertri.matrix	mvSLOUCH-internal
.params.summary.bm	mvSLOUCH-internal
.params.summary.mvslouch	mvSLOUCH-internal
.params.summary.ouch	mvSLOUCH-internal
.resizegrid	mvSLOUCH-internal
.row.rot	mvSLOUCH-internal
.set.estimparams	mvSLOUCH-internal
.set.maxiter	mvSLOUCH-internal
.set.paramatrizationnames	mvSLOUCH-internal
.set.tol	mvSLOUCH-internal
.slouch.mv.design.matrix.YcT	mvSLOUCH-internal
.slouch.mv.iGLS	mvSLOUCH-internal
.slouch.mv.residual.covar	mvSLOUCH-internal
.solve.reg	mvSLOUCH-internal
BrownianMotionModel	BrownianMotionModel
fitch.mvsl	fitch.mvsl
mvSLOUCH	mvSLOUCH-package
mvslouchModel	mvslouchModel
ouchModel	ouchModel
simulBMProcPhylTree	simulBMProcPhylTree
simulMVSLOUCHProcPhylTree	simulMVSLOUCHProcPhylTree
simulOUCHProcPhylTree	simulOUCHProcPhylTree
SummarizeBM	SummarizeBM
SummarizeMVSLOUCH	SummarizeMVSLOUCH
SummarizeOUCH	SummarizeOUCH
