| .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
|
