API for mvSLOUCH
Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Global functions
.CalcVlq Man page Source code
.CalcVlq2 Man page Source code
.CalcVlqStat Man page Source code
.CheckSanityRegimes Man page Source code
.EvaluatePoint Man page Source code
.InitialRegimeSetup Man page Source code
.Kappa.matrix Man page Source code
.Kappa.matrix.NA Man page Source code
.M.mult.givens Man page Source code
.MinusPhylLogLikFunc Man page Source code
.MinusPhylLogLikFuncMVslouch Man page Source code
.MinusPhylLogLikFuncouch Man page Source code
.ModelSetupPCMBase Man page Source code
.OU_phylreg_internal Source code
.OUphylreg_internal Man page
.OUtoBM_pcmbase_model_box Man page Source code
.Params.summary Man page Source code
.PhyloSDEestim Man page Source code
.SummarizeFullPoint Man page Source code
.ape2slouch.mvsl Man page
.beginEstimationParams Man page Source code
.bm.estim Man page Source code
.bm.phyl.cov Man page Source code
.bm.phyl.mean Man page Source code
.bm.sim.est Man page Source code
.bm.simulate Man page Source code
.boot.cleanup Man page Source code
.boot.extract Man page Source code
.boot.extract.model.components Man page Source code
.boot.getval Man page Source code
.calc.cov.bm.mv Man page Source code
.calc.cov.ouch.mv Man page Source code
.calc.cov.slouch.mv Man page Source code
.calc.exptA Man page Source code
.calc.exptA.2dim Man page Source code
.calc.integral.evAStevA Man page Source code
.calc.integral.evAStevA.2dim Man page Source code
.calc.mean.bm.mv Man page Source code
.calc.mean.ouch.mv Man page Source code
.calc.mean.slouch.mv Man page Source code
.calc.phyl.LogLik.traits Man page Source code
.calc.phyl.cov Man page Source code
.calc.phyl.halflife Man page Source code
.calc.phyl.mean Man page Source code
.calc.vec.dist Man page Source code
.calcCI Man page Source code
.calcESSanalytical Man page Source code
.calcESSsim Man page
.calc_species_covariance Man page Source code
.calc_species_mean Man page Source code
.calculate_Tree_dists_forCovariance Man page Source code
.callPCMBase_mvlik Man page Source code
.changeSigmatoSyy Man page Source code
.check_input_trait_data Man page Source code
.check_is_better Man page Source code
.cleanUpModelParams Man page Source code
.col.rot Man page Source code
.correct.names Man page Source code
.correct_for_diagonalSigns_parscale Man page Source code
.correct_npar0 Man page Source code
.correct_phylGLS_response_by_intercept Man page Source code
.createMeasurementError Man page Source code
.createRegimes Man page Source code
.createStartPointsASyyB Man page Source code
.decompEigenA.S Man page Source code
.describe.best.model Man page Source code
.design_matrix_bm Man page Source code
.design_matrix_construction Man page Source code
.design_matrix_mvslouch Man page Source code
.design_matrix_ouch Man page Source code
.detV Man page Source code
.do_phylGLSestimation Man page Source code
.draw.bm Man page Source code
.draw.mvslouch Man page Source code
.draw.ouch Man page Source code
.drawOneLineage Man page Source code
.dzeta.matrix.t Man page Source code
.dzeta.matrix.t1t2 Man page Source code
.dzeta.matrix.t1t2v2 Man page Source code
.dzeta.matrix.tv2 Man page Source code
.dzetaIJ.matrix Man page Source code
.dzetaKappa.intercept Man page Source code
.dzetaKappa.matrix Man page Source code
.dzetaKappa.matrix.simp.t Man page Source code
.dzetaKappa.matrix2 Man page Source code
.dzetaKappa.simp.intercept Man page Source code
.extract.model.key.properties Man page Source code
.extract_GLS_results Man page Source code
.extract_GLS_results_bm Man page Source code
.extract_GLS_results_mvslouch Man page Source code
.extract_GLS_results_ouch Man page Source code
.extract_from_signs Man page Source code
.f_warningsA Man page Source code
.generate.all.model.setups Man page Source code
.generate.basic.model.setups Man page Source code
.generate.ext.model.setups Man page Source code
.generate.fund.model.setups Man page Source code
.generate.list.of.model.setups Man page Source code
.generate.model.description Man page Source code
.generate.model.se Man page Source code
.generate.univ.model.setups Man page Source code
.generatenames Man page Source code
.getESScriteria Man page Source code
.getMVSLphylCovMatrix Man page Source code
.getMVSLproc_size Man page Source code
.get_fullGLSintercept Man page Source code
.get_fullGLSintercept_mvslouch Man page Source code
.get_phyl_mean Man page Source code
.givens.mult.M Man page Source code
.givens.real Man page Source code
.glsgc.estim Man page Source code
.id_evolmodel Man page Source code
.internal_BrownianMotionModel Man page Source code
.internal_mvslouchModel Man page Source code
.internal_ouchModel Man page Source code
.internal_phyltree_paths_BL Man page Source code
.inv.rho.givens.real Man page Source code
.is0_Merror Man page Source code
.is_det0 Man page Source code
.make.states.mvsl Man page
.matrixcalc_is.diagonal.matrix Man page Source code
.matrixcalc_is.positive.definite Man page Source code
.matrixcalc_is.positive.semi.definite Man page Source code
.matrixcalc_is.singular.matrix Man page Source code
.matrixcalc_is.square.matrix Man page
.matrixcalc_is.symmetric.matrix Man page Source code
.maxlik.estim Man page Source code
.mvslouch.phyl.cov Man page Source code
.mvslouch.phyl.mean Man page Source code
.mvslouch.simulate Man page Source code
.mvslouch_to_ouch_model Man page Source code
.my_chol Man page Source code
.my_cov2cor Man page Source code
.my_message Man page Source code
.my_stop Man page Source code
.my_warning Man page Source code
.norm.max Man page Source code
.num.inv.transform.positive Man page Source code
.num.transform.positive Man page Source code
.oubm.sim.est Man page Source code
.ouch.phyl.cov Man page Source code
.ouch.phyl.mean Man page Source code
.ouch.simulate Man page Source code
.ouch2slouch.mvsl Man page
.ouou.sim.est Man page Source code
.packageName Man page
.par.inv.transform Man page Source code
.par.inv.transform.decomp.matrix Man page Source code
.par.inv.transform.decomp.neg.real.matrix Man page Source code
.par.inv.transform.decomp.pos.real.matrix Man page Source code
.par.inv.transform.decomp.real.matrix Man page Source code
.par.inv.transform.decomp.sym.matrix Man page Source code
.par.inv.transform.invert.matrix Man page Source code
.par.inv.transform.invert.qr.matrix Man page Source code
.par.inv.transform.invert.svd.matrix Man page Source code
.par.inv.transform.lowertri.matrix Man page Source code
.par.inv.transform.orth.matrix.cayley Man page Source code
.par.inv.transform.orth.matrix.givens Man page Source code
.par.inv.transform.symmetric.matrix Man page Source code
.par.inv.transform.twobytwo.matrix Man page Source code
.par.inv.transform.uppertri.matrix Man page Source code
.par.transform Man page Source code
.par.transform.decomp.matrix Man page Source code
.par.transform.decomp.neg.real.matrix Man page Source code
.par.transform.decomp.pos.real.matrix Man page Source code
.par.transform.decomp.real.matrix Man page Source code
.par.transform.decomp.sym.matrix Man page Source code
.par.transform.invert.matrix Man page Source code
.par.transform.invert.qr.matrix Man page Source code
.par.transform.invert.svd.matrix Man page Source code
.par.transform.lowertri.matrix Man page Source code
.par.transform.orth.matrix.cayley Man page Source code
.par.transform.orth.matrix.givens Man page Source code
.par.transform.symmetric.matrix Man page Source code
.par.transform.twobytwo.matrix Man page Source code
.par.transform.uppertri.matrix Man page Source code
.par_transform_withPCMBase Man page Source code
.params.summary.bm Man page Source code
.params.summary.mvslouch Man page Source code
.params.summary.ouch Man page Source code
.pcmbaseDphylGaussian_RSS Man page Source code
.pcmbaseDphylOU_GLS Man page Source code
.phyltree_remove_path_fields Man page Source code
.phyltree_remove_tips Man page Source code
.postproc_estres Man page Source code
.return_best_model Man page Source code
.row.rot Man page Source code
.set.estimparams Man page Source code
.set.maxiter Man page Source code
.set.paramatrizationnames Man page Source code
.set.tol Man page Source code
.set_1var_pcmbase_model_box Man page Source code
.set_mean0_pcmbase_model_box Man page Source code
.set_parscale Man page Source code
.set_pcmbase_model_box_X0 Man page Source code
.set_sing_bl_threshold Man page Source code
.simulVasicekProcPhylTree Man page Source code
.sym.par Man page
.sym.unpar Man page
.update_pcmbase_box_params Man page Source code
.update_pcmbase_box_params_bm Man page Source code
.update_pcmbase_box_params_mvslouch Man page Source code
.update_pcmbase_box_params_ouch Man page Source code
BrownianMotionModel Man page Source code
OU_RSS Man page Source code
OU_phylreg Man page Source code
OU_xVz Man page Source code
SummarizeBM Man page Source code
SummarizeMVSLOUCH Man page Source code
SummarizeOUCH Man page Source code
`.make.states.mvsl` Source code
drawPhylProcess Man page Source code
estimate.evolutionary.model Man page Source code
fitch.mvsl Man page
generate.model.setups Man page Source code
mvSLOUCH Man page
mvSLOUCH-package Man page
mvslouchModel Man page Source code
ouchModel Man page Source code
parametric.bootstrap Man page Source code
phyltree_paths Man page Source code
plot.clustered_phylo Man page Source code
simulBMProcPhylTree Man page Source code
simulMVSLOUCHProcPhylTree Man page Source code
simulOUCHProcPhylTree Man page Source code
simulate_clustered_phylogeny Man page Source code
mvSLOUCH documentation built on May 5, 2022, 1:05 a.m.