mvSLOUCH-package	mvSLOUCH-package
.ape2slouch.mvsl	mvSLOUCH-internal
.beginEstimationParams	mvSLOUCH-internal
.bm.estim	mvSLOUCH-internal
.bm.phyl.cov	mvSLOUCH-internal
.bm.sim.est	mvSLOUCH-internal
.bm.simulate	mvSLOUCH-internal
.boot.cleanup	mvSLOUCH-internal
.boot.extract	mvSLOUCH-internal
.boot.extract.model.components	mvSLOUCH-internal
.boot.getval	mvSLOUCH-internal
.calc.cov.bm.mv	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.mean.bm.mv	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.vec.dist	mvSLOUCH-internal
.calcCI	mvSLOUCH-internal
.calcESSanalytical	mvSLOUCH-internal
.calcESSsim	mvSLOUCH-internal
.calculate_Tree_dists_forCovariance	mvSLOUCH-internal
.CalcVlq	mvSLOUCH-internal
.CalcVlq2	mvSLOUCH-internal
.CalcVlqStat	mvSLOUCH-internal
.calc_species_covariance	mvSLOUCH-internal
.calc_species_mean	mvSLOUCH-internal
.callPCMBase_mvlik	mvSLOUCH-internal
.changeSigmatoSyy	mvSLOUCH-internal
.CheckSanityRegimes	mvSLOUCH-internal
.check_input_trait_data	mvSLOUCH-internal
.check_is_better	mvSLOUCH-internal
.cleanUpModelParams	mvSLOUCH-internal
.col.rot	mvSLOUCH-internal
.correct.names	mvSLOUCH-internal
.correct_for_diagonalSigns_parscale	mvSLOUCH-internal
.correct_npar0	mvSLOUCH-internal
.correct_phylGLS_response_by_intercept	mvSLOUCH-internal
.createMeasurementError	mvSLOUCH-internal
.createRegimes	mvSLOUCH-internal
.createStartPointsASyyB	mvSLOUCH-internal
.decompEigenA.S	mvSLOUCH-internal
.describe.best.model	mvSLOUCH-internal
.design_matrix_bm	mvSLOUCH-internal
.design_matrix_construction	mvSLOUCH-internal
.design_matrix_mvslouch	mvSLOUCH-internal
.design_matrix_ouch	mvSLOUCH-internal
.detV	mvSLOUCH-internal
.do_phylGLSestimation	mvSLOUCH-internal
.draw.bm	mvSLOUCH-internal
.draw.mvslouch	mvSLOUCH-internal
.draw.ouch	mvSLOUCH-internal
.drawOneLineage	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
.extract.model.key.properties	mvSLOUCH-internal
.extract_from_signs	mvSLOUCH-internal
.extract_GLS_results	mvSLOUCH-internal
.extract_GLS_results_bm	mvSLOUCH-internal
.extract_GLS_results_mvslouch	mvSLOUCH-internal
.extract_GLS_results_ouch	mvSLOUCH-internal
.generate.all.model.setups	mvSLOUCH-internal
.generate.basic.model.setups	mvSLOUCH-internal
.generate.ext.model.setups	mvSLOUCH-internal
.generate.fund.model.setups	mvSLOUCH-internal
.generate.list.of.model.setups	mvSLOUCH-internal
.generate.model.description	mvSLOUCH-internal
.generate.model.se	mvSLOUCH-internal
.generate.univ.model.setups	mvSLOUCH-internal
.generatenames	mvSLOUCH-internal
.getESScriteria	mvSLOUCH-internal
.getMVSLphylCovMatrix	mvSLOUCH-internal
.getMVSLproc_size	mvSLOUCH-internal
.get_fullGLSintercept	mvSLOUCH-internal
.get_fullGLSintercept_mvslouch	mvSLOUCH-internal
.givens.mult.M	mvSLOUCH-internal
.givens.real	mvSLOUCH-internal
.glsgc.estim	mvSLOUCH-internal
.InitialRegimeSetup	mvSLOUCH-internal
.internal_BrownianMotionModel	mvSLOUCH-internal
.internal_mvslouchModel	mvSLOUCH-internal
.internal_ouchModel	mvSLOUCH-internal
.internal_phyltree_paths_BL	mvSLOUCH-internal
.inv.rho.givens.real	mvSLOUCH-internal
.is0_Merror	mvSLOUCH-internal
.is_det0	mvSLOUCH-internal
.Kappa.matrix	mvSLOUCH-internal
.Kappa.matrix.NA	mvSLOUCH-internal
.M.mult.givens	mvSLOUCH-internal
.make.states.mvsl	mvSLOUCH-internal
.maxlik.estim	mvSLOUCH-internal
.MinusPhylLogLikFunc	mvSLOUCH-internal
.MinusPhylLogLikFuncMVslouch	mvSLOUCH-internal
.MinusPhylLogLikFuncouch	mvSLOUCH-internal
.ModelSetupPCMBase	mvSLOUCH-internal
.mvslouch.phyl.cov	mvSLOUCH-internal
.mvslouch.simulate	mvSLOUCH-internal
.mvslouch_to_ouch_model	mvSLOUCH-internal
.my_chol	mvSLOUCH-internal
.my_cov2cor	mvSLOUCH-internal
.my_message	mvSLOUCH-internal
.my_stop	mvSLOUCH-internal
.my_warning	mvSLOUCH-internal
.norm.max	mvSLOUCH-internal
.num.inv.transform.positive	mvSLOUCH-internal
.num.transform.positive	mvSLOUCH-internal
.oubm.sim.est	mvSLOUCH-internal
.ouch.phyl.cov	mvSLOUCH-internal
.ouch.simulate	mvSLOUCH-internal
.ouch2slouch.mvsl	mvSLOUCH-internal
.ouou.sim.est	mvSLOUCH-internal
.OUtoBM_pcmbase_model_box	mvSLOUCH-internal
.packageName	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.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.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	mvSLOUCH-internal
.params.summary.bm	mvSLOUCH-internal
.params.summary.mvslouch	mvSLOUCH-internal
.params.summary.ouch	mvSLOUCH-internal
.par_transform_withPCMBase	mvSLOUCH-internal
.pcmbaseDphylGaussian_RSS	mvSLOUCH-internal
.pcmbaseDphylOU_GLS	mvSLOUCH-internal
.PhyloSDEestim	mvSLOUCH-internal
.phyltree_remove_path_fields	mvSLOUCH-internal
.phyltree_remove_tips	mvSLOUCH-internal
.postproc_estres	mvSLOUCH-internal
.return_best_model	mvSLOUCH-internal
.row.rot	mvSLOUCH-internal
.set.estimparams	mvSLOUCH-internal
.set.maxiter	mvSLOUCH-internal
.set.paramatrizationnames	mvSLOUCH-internal
.set.tol	mvSLOUCH-internal
.set_1var_pcmbase_model_box	mvSLOUCH-internal
.set_mean0_pcmbase_model_box	mvSLOUCH-internal
.set_parscale	mvSLOUCH-internal
.set_pcmbase_model_box_X0	mvSLOUCH-internal
.set_sing_bl_threshold	mvSLOUCH-internal
.simulVasicekProcPhylTree	mvSLOUCH-internal
.SummarizeFullPoint	mvSLOUCH-internal
.sym.par	mvSLOUCH-internal
.sym.unpar	mvSLOUCH-internal
.update_pcmbase_box_params	mvSLOUCH-internal
.update_pcmbase_box_params_bm	mvSLOUCH-internal
.update_pcmbase_box_params_mvslouch	mvSLOUCH-internal
.update_pcmbase_box_params_ouch	mvSLOUCH-internal
BrownianMotionModel	BrownianMotionModel
drawPhylProcess	drawPhylProcess
estimate.evolutionary.model	estimate.evolutionary.model
fitch.mvsl	fitch.mvsl
generate.model.setups	generate.model.setups
mvSLOUCH	mvSLOUCH-package
mvslouchModel	mvslouchModel
ouchModel	ouchModel
parametric.bootstrap	parametric.bootstrap
phyltree_paths	phyltree_paths
plot.clustered_phylo	plot.clustered_phylo
simulate_clustered_phylogeny	simulate_clustered_phylogeny
simulBMProcPhylTree	simulBMProcPhylTree
simulMVSLOUCHProcPhylTree	simulMVSLOUCHProcPhylTree
simulOUCHProcPhylTree	simulOUCHProcPhylTree
SummarizeBM	SummarizeBM
SummarizeMVSLOUCH	SummarizeMVSLOUCH
SummarizeOUCH	SummarizeOUCH
