mvSLOUCH-internal: Internal mvSLOUCH objects

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

Internal mvSLOUCH objects

Description

Internal mvSLOUCH objects.

Details

These are not to be called by the user. They are located in the code files as follows .ape2slouch.mvsl: trees2slouch.mvsl.R .beginEstimationParams: modelparams.R .bm.estim: estimBM.R .bm.phyl.cov: sdecovariancephyl.R .bm.sim.est: bootstrap.R .bm.simulate: simulVasicekproc.R .boot.cleanup: bootstrap.R .boot.extract: bootstrap.R .boot.extract.model.components: bootstrap.R .boot.getval: bootstrap.R .calc_species_covariance: sdemoments.R .calc_species_mean: sdemoments.R .calc.cov.bm.mv: sdemoments.R .calc.cov.ouch.mv: sdemoments.R .calc.cov.slouch.mv: sdemoments.R .calc.exptA: matrixexps.R .calc.exptA.2dim: matrixexps.R .calc.integral.evAStevA: matrixexps.R .calc.integral.evAStevA.2dim: matrixexps.R .calc.mean.bm.mv: sdemoments.R .calc.mean.ouch.mv: sdemoments.R .calc.mean.slouch.mv: sdemoments.R .calc.phyl.cov: sdecovariancephyl.R .calc.phyl.halflife: modelparamssummary.R .calc.phyl.LogLik.traits: loglik.R .calc.vec.dist: phylgls.R .calcCI: ci.R .calcESSanalytical: getESS.R .calcESSsim: getESS.R .calculate_Tree_dists_forCovariance: getESS.R .CalcVlq: precalcs.R .CalcVlq2: precalcs.R .CalcVlqStat: precalcs.R .callPCMBase_mvlik: loglik.R .changeSigmatoSyy: evolmodelest.R .CheckSanityRegimes: regimes.R .check_is_better: evolmodelest.R .cleanUpModelParams: modelparamssummary.R .col.rot: matrixparametrizations.R .correct_npar0: modelparamssummary.R .correct_for_diagonalSigns_parscale: PhyloSDEestim.R .correct_phylGLS_response_by_intercept: phylgls.R .correct.names: PhyloSDEestim.R .createMeasurementError: PhyloSDEestim.R .createRegimes: regimes.R .createStartPointsASyyB: evolmodelest.R .decompEigenA.S: precalcs.R .describe.best.model: evolmodelest.R .design_matrix_bm: phylgls.R .design_matrix_construction: phylgls.R .design_matrix_mvslouch: phylgls.R .design_matrix_ouch: phylgls.R .detV: phylgls.R .do_phylGLSestimation: phylgls.R .draw.bm: simulVasicekproc.R .draw.mvslouch: simulVasicekproc.R .draw.ouch: simulVasicekproc.R .drawOneLineage: simulVasicekproc.R .dzeta.matrix.t: precalcs.R .dzeta.matrix.t1t2: precalcs.R .dzeta.matrix.t1t2v2: precalcs.R .dzeta.matrix.tv2: precalcs.R .dzetaIJ.matrix: precalcs.R .dzetaKappa.intercept: precalcs.R .dzetaKappa.matrix: precalcs.R .dzetaKappa.matrix.simp.t: precalcs.R .dzetaKappa.matrix2: precalcs.R .dzetaKappa.simp.intercept: precalcs.R .EvaluatePoint: modelparams.R .extract_from_signs: phylgls.R .extract_GLS_results: phylgls.R .extract_GLS_results_bm: phylgls.R .extract_GLS_results_mvslouch: phylgls.R .extract_GLS_results_ouch: phylgls.R .extract.model.key.properties: evolmodelest.R .generate.all.model.setups: evolmodelest.R .generate.basic.model.setups: evolmodelest.R .generate.ext.model.setups: evolmodelest.R .generate.fund.model.setups: evolmodelest.R .generate.list.of.model.setups: evolmodelest.R .generate.model.description: evolmodelest.R .generate.model.se: evolmodelest.R .generate.univ.model.setups: evolmodelest.R .generatenames: PhyloSDEestim.R .getESScriteria: getESS.R .getMVSLphylCovMatrix: getESS.R .getMVSLproc_size: getESS.R .get_fullGLSintercept: phylgls.R .get_fullGLSintercept_mvslouch: phylgls.R .givens.mult.M: matrixparametrizations.R .givens.real: matrixparametrizations.R .glsgc.estim: estimGLSGC.R .InitialRegimeSetup: regimes.R .internal_BrownianMotionModel: wrappers.R .internal_mvslouchModel: wrappers.R .internal_ouchModel: wrappers.R .inv.rho.givens.real: matrixparametrizations.R .is0_Merror: estimBM.R .Kappa.matrix: precalcs.R .Kappa.matrix.NA: precalcs.R .M.mult.givens: matrixparametrizations.R .make.states.mvsl: make.states.mvsl.R .maxlik.estim: estimMAXLIK.R .MinusPhylLogLikFunc: loglik.R .MinusPhylLogLikFuncMVslouch: loglik.R .MinusPhylLogLikFuncouch: loglik.R .ModelSetupPCMBase: regimes.R .mvslouch_to_ouch_model: modelparamstransform.R .mvslouch.phyl.cov: sdecovariancephyl.R .mvslouch.simulate: simulVasicekproc.R .norm.max: modelparamssummary.R .num.inv.transform.positive: matrixparametrizations.R .num.transform.positive: matrixparametrizations.R .oubm.sim.est: bootstrap.R .ouch.phyl.cov: sdecovariancephyl.R .ouch.simulate: simulVasicekproc.R .ouch2slouch.mvsl: trees2slouch.mvsl.R .ouou.sim.est: bootstrap.R .OUtoBM_pcmbase_model_box: estimBM.R .packageName: .par_transform_withPCMBase: modelparamstransform.R .par.inv.transform: modelparamstransform.R .par.inv.transform.decomp.matrix: matrixparametrizations.R .par.inv.transform.decomp.neg.real.matrix: matrixparametrizations.R .par.inv.transform.decomp.pos.real.matrix: matrixparametrizations.R .par.inv.transform.decomp.real.matrix: matrixparametrizations.R .par.inv.transform.decomp.sym.matrix: matrixparametrizations.R .par.inv.transform.invert.matrix: matrixparametrizations.R .par.inv.transform.invert.qr.matrix matrixparametrizations.R .par.inv.transform.invert.svd.matrix: matrixparametrizations.R .par.inv.transform.lowertri.matrix: matrixparametrizations.R .par.inv.transform.orth.matrix.cayley: matrixparametrizations.R .par.inv.transform.orth.matrix.givens: matrixparametrizations.R .par.inv.transform.symmetric.matrix: matrixparametrizations.R .par.inv.transform.twobytwo.matrix: matrixparametrizations.R .par.inv.transform.uppertri.matrix: matrixparametrizations.R .par.transform: modelparamstransform.R .par.transform.decomp.matrix: matrixparametrizations.R .par.transform.decomp.neg.real.matrix: matrixparametrizations.R .par.transform.decomp.pos.real.matrix: matrixparametrizations.R .par.transform.decomp.real.matrix: matrixparametrizations.R .par.transform.decomp.sym.matrix: matrixparametrizations.R .par.transform.invert.matrix: matrixparametrizations.R .par.transform.invert.qr.matrix: matrixparametrizations.R .par.transform.invert.svd.matrix: matrixparametrizations.R .par.transform.lowertri.matrix: matrixparametrizations.R .par.transform.orth.matrix.cayley: matrixparametrizations.R .par.transform.orth.matrix.givens: matrixparametrizations.R .par.transform.symmetric.matrix: matrixparametrizations.R .par.transform.twobytwo.matrix: matrixparametrizations.R .par.transform.uppertri.matrix: matrixparametrizations.R .Params.summary: modelparamssummary.R .params.summary.bm: modelparamssummary.R .params.summary.mvslouch: modelparamssummary.R .params.summary.ouch: modelparamssummary.R .pcmbaseDphylGaussian_RSS: phylgls.R .pcmbaseDphylOU_GLS: phylgls.R .PhyloSDEestim: PhyloSDEestim.R .phyltree_remove_path_fields: phyltree_paths.R .phyltree_remove_tips: phyltree_paths.R .postproc_estres: evolmodelest.R .return_best_model: evolmodelest.R .row.rot: matrixparametrizations.R .set_mean0_pcmbase_model_box: phygls.R .set_1var_pcmbase_model_box: estimBM.R .set.estimparams: PhyloSDEestim.R .set.maxiter: PhyloSDEestim.R .set.paramatrizationnames: PhyloSDEestim.R .set_parscale: PhyloSDEestim.R .set.tol: PhyloSDEestim.R .simulVasicekProcPhylTree: simulVasicekprocphyl.R .SummarizeFullPoint: modelparamssummary.R .sym.par: matrixparametrizations.R .sym.unpar: matrixparametrizations.R .update_pcmbase_box_params: modelparamstransform.R .update_pcmbase_box_params_bm: modelparamstransform.R .update_pcmbase_box_params_mvslouch: modelparamstransform.R .update_pcmbase_box_params_ouch: modelparamstransform.R .internal_phyltree_paths_BL: phyltree_paths.R .check_input_trait_data: PhyloSDEestim.R .is_det0: matrixexps.R .my_cov2cor: matrixexps.R .my_stop: loglik.R .my_message: loglik.R .my_warning: loglik.R .set_sing_bl_threshold: wrappers.R .my_chol: evolmodelest.R .set_pcmbase_model_box_X0: estimBM.R .matrixcalc_is.diagonal.matrix: from_matrixcalc_1_0_3_matrixcalculations.R .matrixcalc_is.positive.definite: from_matrixcalc_1_0_3_matrixcalculations.R .matrixcalc_is.positive.semi.definite: from_matrixcalc_1_0_3_matrixcalculations.R .matrixcalc_is.singular.matrix: from_matrixcalc_1_0_3_matrixcalculations.R .matrixcalc_is.square.matrix: from_matrixcalc_1_0_3_matrixcalculations.R .matrixcalc_is.symmetric.matrix: from_matrixcalc_1_0_3_matrixcalculations.R .calc.phyl.mean: sdemeanphyl.R .bm.phyl.mean: sdemeanphyl.R .ouch.phyl.mean: sdemeanphyl.R .mvslouch.phyl.mean: sdemeanphyl.R .get_phyl_mean: OUphylregression.R .OUphylreg_internal: OUphylregression.R .id_evolmodel: OUphylregression.R .f_warningsA: wrappers.R

mvSLOUCH documentation built on Nov. 21, 2023, 1:08 a.m.