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

Global functions
.CalcVlq Man page
.CalcVlq2 Man page
.CalcVlqStat Man page
.CheckSanityRegimes Man page
.EvaluatePoint Man page
.InitialRegimeSetup Man page
.Kappa.matrix Man page
.Kappa.matrix.NA Man page
.M.mult.givens Man page
.MinusPhylLogLikFunc Man page
.MinusPhylLogLikFuncMVslouch Man page
.MinusPhylLogLikFuncouch Man page
.ModelSetupPCMBase Man page
.OUtoBM_pcmbase_model_box Man page
.Params.summary Man page
.PhyloSDEestim Man page
.SummarizeFullPoint Man page
.ape2slouch.mvsl Man page
.beginEstimationParams Man page
.bm.estim Man page
.bm.phyl.cov Man page
.bm.sim.est Man page
.bm.simulate Man page
.boot.cleanup Man page
.boot.extract Man page
.boot.extract.model.components Man page
.boot.getval Man page
.calc.cov.bm.mv Man page
.calc.cov.ouch.mv Man page
.calc.cov.slouch.mv Man page
.calc.exptA Man page
.calc.exptA.2dim Man page
.calc.integral.evAStevA Man page
.calc.integral.evAStevA.2dim Man page
.calc.mean.bm.mv Man page
.calc.mean.ouch.mv Man page
.calc.mean.slouch.mv Man page
.calc.phyl.LogLik.traits Man page
.calc.phyl.cov Man page
.calc.phyl.halflife Man page
.calc.vec.dist Man page
.calcCI Man page
.calcESSanalytical Man page
.calcESSsim Man page
.calc_species_covariance Man page
.calc_species_mean Man page
.calculate_Tree_dists_forCovariance Man page
.callPCMBase_mvlik Man page
.changeSigmatoSyy Man page
.check_input_trait_data Man page
.cleanUpModelParams Man page
.col.rot Man page
.correct.names Man page
.correct_npar0 Man page
.correct_phylGLS_response_by_intercept Man page
.createMeasurementError Man page
.createRegimes Man page
.createStartPointsASyyB Man page
.decompEigenA.S Man page
.describe.best.model Man page
.design_matrix_bm Man page
.design_matrix_construction Man page
.design_matrix_mvslouch Man page
.design_matrix_ouch Man page
.detV Man page
.do_phylGLSestimation Man page
.draw.bm Man page
.draw.mvslouch Man page
.draw.ouch Man page
.drawOneLineage Man page
.dzeta.matrix.t Man page
.dzeta.matrix.t1t2 Man page
.dzeta.matrix.t1t2v2 Man page
.dzeta.matrix.tv2 Man page
.dzetaIJ.matrix Man page
.dzetaKappa.intercept Man page
.dzetaKappa.matrix Man page
.dzetaKappa.matrix.simp.t Man page
.dzetaKappa.matrix2 Man page
.dzetaKappa.simp.intercept Man page
.extract.model.key.properties Man page
.extract_GLS_results Man page
.extract_GLS_results_bm Man page
.extract_GLS_results_mvslouch Man page
.extract_GLS_results_ouch Man page
.extract_from_signs Man page
.generate.all.model.setups Man page
.generate.basic.model.setups Man page
.generate.ext.model.setups Man page
.generate.fund.model.setups Man page
.generate.list.of.model.setups Man page
.generate.model.description Man page
.generate.model.se Man page
.generate.univ.model.setups Man page
.generatenames Man page
.getESScriteria Man page
.getMVSLphylCovMatrix Man page
.getMVSLproc_size Man page
.givens.mult.M Man page
.givens.real Man page
.glsgc.estim Man page
.internal_BrownianMotionModel Man page
.internal_mvslouchModel Man page
.internal_ouchModel Man page
.internal_phyltree_paths_BL Man page
.inv.rho.givens.real Man page
.is_det0 Man page
.make.states.mvsl Man page
.maxlik.estim Man page
.mvslouch.phyl.cov Man page
.mvslouch.simulate Man page
.mvslouch_to_ouch_model Man page
.my_cov2cor Man page
.my_message Man page
.my_stop Man page
.norm.max Man page
.num.inv.transform.positive Man page
.num.transform.positive Man page
.oubm.sim.est Man page
.ouch.phyl.cov Man page
.ouch.simulate Man page
.ouch2slouch.mvsl Man page
.ouou.sim.est Man page
.packageName Man page
.par.inv.transform Man page
.par.inv.transform.decomp.matrix Man page
.par.inv.transform.decomp.neg.real.matrix Man page
.par.inv.transform.decomp.pos.real.matrix Man page
.par.inv.transform.decomp.real.matrix Man page
.par.inv.transform.decomp.sym.matrix Man page
.par.inv.transform.invert.matrix Man page
.par.inv.transform.invert.qr.matrix Man page
.par.inv.transform.invert.svd.matrix Man page
.par.inv.transform.lowertri.matrix Man page
.par.inv.transform.symmetric.matrix Man page
.par.inv.transform.twobytwo.matrix Man page
.par.inv.transform.uppertri.matrix Man page
.par.transform Man page
.par.transform.decomp.matrix Man page
.par.transform.decomp.neg.real.matrix Man page
.par.transform.decomp.pos.real.matrix Man page
.par.transform.decomp.real.matrix Man page
.par.transform.decomp.sym.matrix Man page
.par.transform.invert.matrix Man page
.par.transform.invert.qr.matrix Man page
.par.transform.invert.svd.matrix Man page
.par.transform.lowertri.matrix Man page
.par.transform.orth.matrix.cayley Man page
.par.transform.orth.matrix.givens Man page
.par.transform.symmetric.matrix Man page
.par.transform.twobytwo.matrix Man page
.par.transform.uppertri.matrix Man page
.par_transform_withPCMBase Man page
.params.summary.bm Man page
.params.summary.mvslouch Man page
.params.summary.ouch Man page
.pcmbaseDphylGaussian_RSS Man page
.pcmbaseDphylOU_GLS Man page
.phyltree_remove_path_fields Man page
.row.rot Man page
.set.estimparams Man page
.set.maxiter Man page
.set.paramatrizationnames Man page
.set.tol Man page
.set_mean0_pcmbase_model_box Man page
.set_sing_bl_threshold Man page
.simulVasicekProcPhylTree Man page
.sym.par Man page
.sym.unpar Man page
.update_pcmbase_box_params Man page
.update_pcmbase_box_params_bm Man page
.update_pcmbase_box_params_mvslouch Man page
.update_pcmbase_box_params_ouch Man page
BrownianMotionModel Man page Source code
CalcVlq Source code
CalcVlq2 Source code
CalcVlqStat Source code
CheckSanityRegimes Source code
EvaluatePoint Source code
InitialRegimeSetup Source code
Kappa.matrix Source code
Kappa.matrix.NA Source code
M.mult.givens Source code
MinusPhylLogLikFunc Source code
MinusPhylLogLikFuncMVslouch Source code
MinusPhylLogLikFuncouch Source code
ModelSetupPCMBase Source code
OUtoBM_pcmbase_model_box Source code
Params.summary Source code
PhyloSDEestim Source code
SummarizeBM Man page Source code
SummarizeFullPoint Source code
SummarizeMVSLOUCH Man page Source code
SummarizeOUCH Man page Source code
beginEstimationParams Source code
bm.estim Source code
bm.phyl.cov Source code
bm.sim.est Source code
bm.simulate Source code
boot.cleanup Source code
boot.extract Source code
boot.extract.model.components Source code
boot.getval Source code
calc.cov.bm.mv Source code
calc.cov.ouch.mv Source code
calc.cov.slouch.mv Source code
calc.exptA Source code
calc.exptA.2dim Source code
calc.integral.evAStevA Source code
calc.integral.evAStevA.2dim Source code
calc.mean.bm.mv Source code
calc.mean.ouch.mv Source code
calc.mean.slouch.mv Source code
calc.phyl.LogLik.traits Source code
calc.phyl.cov Source code
calc.phyl.halflife Source code
calc.vec.dist Source code
calcCI Source code
calcESSanalytical Source code
calc_species_covariance Source code
calc_species_mean Source code
calculate_Tree_dists_forCovariance Source code
callPCMBase_mvlik Source code
changeSigmatoSyy Source code
check_input_trait_data Source code
check_is_better Source code
cleanUpModelParams Source code
col.rot Source code
correct.names Source code
correct_for_diagonalSigns_parscale Source code
correct_npar0 Source code
correct_phylGLS_response_by_intercept Source code
createMeasurementError Source code
createRegimes Source code
createStartPointsASyyB Source code
decompEigenA.S Source code
describe.best.model Source code
design_matrix_bm Source code
design_matrix_construction Source code
design_matrix_mvslouch Source code
design_matrix_ouch Source code
detV Source code
do_phylGLSestimation Source code
draw.bm Source code
draw.mvslouch Source code
draw.ouch Source code
drawOneLineage Source code
drawPhylProcess Man page Source code
dzeta.matrix.t Source code
dzeta.matrix.t1t2 Source code
dzeta.matrix.t1t2v2 Source code
dzeta.matrix.tv2 Source code
dzetaIJ.matrix Source code
dzetaKappa.intercept Source code
dzetaKappa.matrix Source code
dzetaKappa.matrix.simp.t Source code
dzetaKappa.matrix2 Source code
dzetaKappa.simp.intercept Source code
estimate.evolutionary.model Man page Source code
extract.model.key.properties Source code
extract_GLS_results Source code
extract_GLS_results_bm Source code
extract_GLS_results_mvslouch Source code
extract_GLS_results_ouch Source code
extract_from_signs Source code
fitch.mvsl Man page
generate.all.model.setups Source code
generate.basic.model.setups Source code
generate.ext.model.setups Source code
generate.fund.model.setups Source code
generate.list.of.model.setups Source code
generate.model.description Source code
generate.model.se Source code
generate.model.setups Man page Source code
generate.univ.model.setups Source code
generatenames Source code
getESScriteria Source code
getMVSLphylCovMatrix Source code
getMVSLproc_size Source code
get_fullGLSintercept Source code
get_fullGLSintercept_mvslouch Source code
givens.mult.M Source code
givens.real Source code
glsgc.estim Source code
maxlik.estim Source code
mvSLOUCH Man page
mvSLOUCH-package Man page
mvslouch.phyl.cov Source code
mvslouch.simulate Source code
mvslouchModel Man page Source code
mvslouch_to_ouch_model Source code
my_cov2cor Source code
my_message Source code
my_stop Source code
my_warning Source code
norm.max Source code
nternal_BrownianMotionModel Source code
nternal_mvslouchModel Source code
nternal_ouchModel Source code
nternal_phyltree_paths_BL Source code
num.inv.transform.positive Source code
num.transform.positive Source code
nv.rho.givens.real Source code
oubm.sim.est Source code
ouch.phyl.cov Source code
ouch.simulate Source code
ouchModel Man page Source code
ouou.sim.est Source code
par.inv.transform Source code
par.inv.transform.decomp.matrix Source code
par.inv.transform.decomp.neg.real.matrix Source code
par.inv.transform.decomp.pos.real.matrix Source code
par.inv.transform.decomp.real.matrix Source code
par.inv.transform.decomp.sym.matrix Source code
par.inv.transform.invert.matrix Source code
par.inv.transform.invert.qr.matrix Source code
par.inv.transform.invert.svd.matrix Source code
par.inv.transform.lowertri.matrix 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 Source code
par.inv.transform.twobytwo.matrix Source code
par.inv.transform.uppertri.matrix Source code
par.transform Source code
par.transform.decomp.matrix Source code
par.transform.decomp.neg.real.matrix Source code
par.transform.decomp.pos.real.matrix Source code
par.transform.decomp.real.matrix Source code
par.transform.decomp.sym.matrix Source code
par.transform.invert.matrix Source code
par.transform.invert.qr.matrix Source code
par.transform.invert.svd.matrix Source code
par.transform.lowertri.matrix Source code
par.transform.orth.matrix.cayley Source code
par.transform.orth.matrix.givens Source code
par.transform.symmetric.matrix Source code
par.transform.twobytwo.matrix Source code
par.transform.uppertri.matrix Source code
par_transform_withPCMBase Source code
parametric.bootstrap Man page Source code
params.summary.bm Source code
params.summary.mvslouch Source code
params.summary.ouch Source code
pcmbaseDphylGaussian_RSS Source code
pcmbaseDphylOU_GLS Source code
phyltree_paths Man page Source code
phyltree_remove_path_fields Source code
phyltree_remove_tips Source code
postproc_estres Source code
return_best_model Source code
row.rot Source code
s0_Merror Source code
s_det0 Source code
set.estimparams Source code
set.maxiter Source code
set.paramatrizationnames Source code
set.tol Source code
set_1var_pcmbase_model_box Source code
set_mean0_pcmbase_model_box Source code
set_parscale Source code
set_sing_bl_threshold Source code
simulBMProcPhylTree Man page Source code
simulMVSLOUCHProcPhylTree Man page Source code
simulOUCHProcPhylTree Man page Source code
simulVasicekProcPhylTree Source code
sym.par Source code
sym.unpar Source code
update_pcmbase_box_params Source code
update_pcmbase_box_params_bm Source code
update_pcmbase_box_params_mvslouch Source code
update_pcmbase_box_params_ouch Source code
mvSLOUCH documentation built on April 12, 2019, 1:08 a.m.