Last data update: 2014.03.03

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mvSLOUCH-internal (Package: mvSLOUCH) : Internal mvSLOUCH objects

Internal mvSLOUCH objects.
● Data Source: CranContrib
● Keywords: internal
● Alias: .CalcVlq, .CalcVlq2, .CalcVlqStat, .EvaluatePoint, .GridEvaluatePointA, .Kappa.matrix, .Kappa.matrix.NA, .M.mult.givens, .MinusPhylLogLikFunc, .MinusPhylLogLikFuncMVslouch, .MinusPhylLogLikFuncouch, .beginEstimationParams, .bm.phyl.cov, .bm.phyl.mean, .calc.cov.ouch.mv, .calc.cov.slouch.mv, .calc.exptA, .calc.exptA.2dim, .calc.integral.evAStevA, .calc.integral.evAStevA.2dim, .calc.intercept, .calc.mean.ouch.mv, .calc.mean.slouch.mv, .calc.phyl.LogLik.traits, .calc.phyl.cov, .calc.phyl.halflife, .calc.phyl.mean, .calc.vec.dist, .calcAncestorTimes, .calcAprecalcMatrices, .calcCI, .calcLogLikParametrized, .calcTreeDist, .calculate.Tree.dists, .ci.HL.loglikfunc, .ci.listParams, .ci.loglikfunc, .ci.vectorizeParams, .cleanUpModelParams, .col.rot, .correct.names, .decompEigenA.S, .drawRandomNiches, .drawRandomRegimes, .dzeta.matrix.t, .dzeta.matrix.t1t2, .dzeta.matrix.t1t2v2, .dzeta.matrix.tv2, .dzetaIJ.matrix, .dzetaKappa.intercept, .dzetaKappa.matrix, .dzetaKappa.matrix.simp.t, .dzetaKappa.matrix2, .dzetaKappa.simp.intercept, .generate.model.description, .generate.model.se, .generategrid, .generatenames, .givens.mult.M, .givens.real, .interpret.intercept, .inv.rho.givens.real, .make.states.mvsl, .min.RSS.BmPsi, .min.mLogLik.BmPsi, .num.inv.transform.positive, .num.transform.positive, .ouch.GLS, .ouch.design.matrix, .ouch2slouch.mvsl, .par.inv.transform, .par.inv.transform.decomp.matrix, .par.inv.transform.decomp.neg.real.matrix, .par.inv.transform.decomp.pos.real.matrix, .par.inv.transform.decomp.real.matrix, .par.inv.transform.decomp.sym.matrix, .par.inv.transform.invert.matrix, .par.inv.transform.invert.qr.matrix, .par.inv.transform.invert.svd.matrix, .par.inv.transform.lowertri.matrix, .par.inv.transform.normal.matrix, .par.inv.transform.orth.matrix.cayley, .par.inv.transform.orth.matrix.givens, .par.inv.transform.symmetric.matrix, .par.inv.transform.twobytwo.matrix, .par.inv.transform.uppertri.matrix, .par.transform, .par.transform.decomp.matrix, .par.transform.decomp.neg.real.matrix, .par.transform.decomp.pos.real.matrix, .par.transform.decomp.real.matrix, .par.transform.decomp.sym.matrix, .par.transform.invert.matrix, .par.transform.invert.qr.matrix, .par.transform.invert.svd.matrix, .par.transform.lowertri.matrix, .par.transform.normal.matrix, .par.transform.orth.matrix.cayley, .par.transform.orth.matrix.givens, .par.transform.symmetric.matrix, .par.transform.twobytwo.matrix, .par.transform.uppertri.matrix, .params.summary.bm, .params.summary.mvslouch, .params.summary.ouch, .resizegrid, .row.rot, .set.estimparams, .set.maxiter, .set.paramatrizationnames, .set.tol, .slouch.mv.design.matrix.YcT, .slouch.mv.iGLS, .slouch.mv.residual.covar, .solve.reg
● 0 images

simulMVSLOUCHProcPhylTree (Package: mvSLOUCH) :

Simulate data on a phylogeny under a (multivariate) OUBM model
● Data Source: CranContrib
● Keywords: models
● Alias: simulMVSLOUCHProcPhylTree
● 0 images

fitch.mvsl (Package: mvSLOUCH) : Unordered Fitch parsimony reconstruction of discrete character states

Implements an unordered Fitch parsimony reconstruction of discrete niche variables for use in the OU models where optima are modeled on discrete, categorical niche encodings. Allows for delayed and accelerated transformations to deal with ambiguities. Function was originally the fitch function from the slouch package.
● Data Source: CranContrib
● Keywords: models
● Alias: fitch.mvsl
● 0 images

SummarizeMVSLOUCH (Package: mvSLOUCH) :

Compiles a summary (appropriate moments, conditional moments, information criteria) of parameters of a multivariate OUBM model at a given time point.
● Data Source: CranContrib
● Keywords: models
● Alias: SummarizeMVSLOUCH
● 0 images

estimate.evolutionary.model (Package: mvSLOUCH) :

The estimate.evolutionary.model function calls the BrownianMotionModel, ouchModel and mvslouchModel functions with different classes of evolutionary model parameters. It then compares the resulting estimates by the AICc and returns the best overall model.
● Data Source: CranContrib
● Keywords: models
● Alias: estimate.evolutionary.model
● 0 images

SummarizeBM (Package: mvSLOUCH) : Summarize parameters estimated under a Brownian motion model

Compiles a summary (appropriate moments, conditional moments, information criteria) of parameters of a Brownian motion model at a given time point.
● Data Source: CranContrib
● Keywords: models
● Alias: SummarizeBM
● 0 images

mvSLOUCH-package (Package: mvSLOUCH) : Multivariate Ornstein-Uhlenbeck type stochastic differential equation models

The package allows for maximum likelihood estimation, simulation and study of properties of multivariate Brownian motion
● Data Source: CranContrib
● Keywords: models
● Alias: mvSLOUCH, mvSLOUCH-package
● 0 images

simulBMProcPhylTree (Package: mvSLOUCH) :

Simulate data on a phylogeny under a (multivariate) Brownian motion model
● Data Source: CranContrib
● Keywords: models
● Alias: simulBMProcPhylTree
● 0 images

drawPhylProcess (Package: mvSLOUCH) : Plots the realization of a process evolving on a phylogenetic tree

The function takes the output of the simulation functions and based on it plots the realization of the process on the tree. Can handle multiple traits, in this case each trait is plotted separately. The function does draw anything else (like axes) but the realization of the process. Any additions are up to the user.
● Data Source: CranContrib
● Keywords: hplot, models
● Alias: drawPhylProcess
● 0 images

generate.model.setups (Package: mvSLOUCH) : Generate a list of model setups for the function

The function generates a list of models that will be used by the function
estimate.evolutionary.model. A minimum example list will be list(list(evolmodel="BM")).
● Data Source: CranContrib
● Keywords: models
● Alias: generate.model.setups
● 0 images

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO