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mixAK (version 3.5)

Multivariate normal mixture models and mixtures of generalized linear mixed models including model based clustering

Description

This package contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.

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Version

Install

install.packages('mixAK')

Monthly Downloads

326

Version

3.5

License

GPL (>= 3)

Maintainer

Arnošt Komárek

Last Published

September 23rd, 2013

Functions in mixAK (3.5)

Moore-Penrose pseudoinverse of a squared matrix

MCMC estimation of (multivariate) normal mixtures with possibly censored data.

GLMM_MCMCprior.eps

Handle prior.eps argument of GLMM_MCMC function

Discriminant analysis for longitudinal profiles based on fitted GLMM's

NMixPlugDensJoint2

Pairwise bivariate densities: plug-in estimate

Signal Tandmobiel data - emergence times

NMixChainsDerived

Create MCMC chains derived from previously sampled values

GLMM_MCMCprior.b

Handle prior.eps argument of GLMM_MCMC function

Mixture of (multivariate) normal distributions

NMixPlugCondDensJoint2

Pairwise bivariate conditional densities: plug-in estimate

Discriminant analysis based on MCMC output from the mixture model

Subset of Mayo Clinic Primary Biliary Cirrhosis data

GLMM_MCMCinit.alpha

Handle init.alpha or init2.alpha argument of GLMM_MCMC function

Initial values of censored observations for the NMixMCMC function

Dirichlet distribution

GLMM_MCMCprior.alpha

Handle prior.alpha argument of GLMM_MCMC function

Initial component allocations for the NMixMCMC function

Best linear approximation with respect to the mean square error (theoretical linear regression).

Simulated dataset

Transform fitted distribution of Y=trans(T) into distribution of T

Initial (RE)ML fits for the GLMM_MCMC function

NMixRelabelAlgorithm

Argument manipulation for the NMixRelabel functions

NMixPlugCondDensMarg

Univariate conditional densities: plug-in estimate

NMixPredDensMarg

Marginal (univariate) predictive density

Conversion of a symmetric matrix stored in a packed format (lower triangle only) into a matrix

Chains for mixture parameters

Square root of a matrix

NMixPredDensJoint2

Pairwise bivariate predictive density

plot.NMixPlugDensJoint2

Plot computed marginal pairwise bivariate densities (plug-in estimate)

MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effects

NMixPredCondCDFMarg

Univariate conditional predictive cumulative distribution function

Posterior summary statistics for a difference of two quantities

Enzymatic activity in the blood

NMixMCMCwrapper

Wrapper to the NMixMCMC main simulation.

NMixPredCondDensJoint2

Pairwise bivariate conditional predictive densities

plot.NMixPredCDFMarg

Plot computed marginal predictive cumulative distribution functions

plot.NMixPredCondDensMarg

Plot computed univariate conditional predictive densities

Pseudo goodness-of-fit test for a normal mixture model

Velocities of distant galaxies

plot.NMixPredCondDensJoint2

Plot computed predictive pairwise bivariate conditional densities

plot.NMixPredDensMarg

Plot computed marginal predictive densities

plot.NMixPlugCondDensJoint2

Plot computed pairwise bivariate conditional densities (plug-in estimate)

Plot individual longitudinal profiles

NMixPredCondDensMarg

Univariate conditional predictive density

Plot a function together with its confidence/credible bands

Discriminant analysis based on plug-in estimates from the mixture model

NMixPredCDFMarg

Marginal (univariate) predictive cumulative distribution function

Truncated normal distribution

Wishart distribution

plot.NMixPredCondCDFMarg

Plot computed univariate conditional predictive cumulative distribution functions

plot.NMixPredDensJoint2

Plot computed marginal pairwise bivariate predictive densities

Re-labeling the MCMC output of the mixture model

NMixPlugDensMarg

Marginal (univariate) densities: plug-in estimate

Data manipulation for the NMixMCMC function

Truncated multivariate normal distribution

Mayo Clinic Primary Biliary Cirrhosis, sequential data

Individual longitudinal profiles of a given variable

Traceplots for selected parameters

rRotationMatrix

Random rotation matrix

GLMM_MCMCinit.eps

Handle init.eps or init2.eps argument of GLMM_MCMC function

GLMM_MCMCinit.b

Handle init.b or init2.b argument of GLMM_MCMC function

Multivariate normal distribution

Summary for the mixture components

GLMM_MCMCwrapper

Wrapper to the GLMM_MCMC main simulation.

plot.NMixPlugDensMarg

Plot computed marginal predictive densities

Signal Tandmobiel data

GLMM_MCMCscale.b

Handle scale.b argument of GLMM_MCMC function

Multivariate Student t distribution

EM algorithm for a homoscedastic normal mixture

Old Faithful Geyser Data

Automatic layout for several plots in one figure

Acidity index of lakes in North-Central Wisconsin

plot.NMixPlugCondDensMarg

Plot computed univariate conditional densities (plug-in estimate)

Data manipulation for the GLMM_MCMC function

fitted.GLMM_MCMC

Fitted profiles in the GLMM model

generatePermutations

Generate all permutations of (1, ..., K)

Sample a pair (with replacement)