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mixAK (version 5.4)

Multivariate Normal Mixture Models and Mixtures of Generalized Linear Mixed Models Including Model Based Clustering

Description

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

1,211

Version

5.4

License

GPL (>= 3)

Maintainer

Arnošt Komárek

Last Published

April 19th, 2022

Functions in mixAK (5.4)

Acidity

Acidity index of lakes in North-Central Wisconsin
BLA

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

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

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

Create MCMC chains derived from previously sampled values
MatSqrt

Square root of a matrix
NMixCluster

Clustering based on the MCMC output of the mixture model
GLMM_MCMCscale.b

Handle scale.b argument of GLMM_MCMC function
Faithful

Old Faithful Geyser Data
Enzyme

Enzymatic activity in the blood
GLMM_MCMCprior.eps

Handle prior.eps argument of GLMM_MCMC function
NMixChainComp

Chains for mixture parameters
GLMM_MCMCdata

Data manipulation for the GLMM_MCMC function
NMixRelabelAlgorithm

Argument manipulation for the NMixRelabel functions
GLMM_MCMC

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

Marginal (univariate) densities: plug-in estimate
NMixPredCDFMarg

Marginal (univariate) predictive cumulative distribution function
NMixMCMCinity

Initial values of censored observations for the NMixMCMC function
GLMM_MCMCprior.alpha

Handle prior.alpha argument of GLMM_MCMC function
GLMM_MCMCprior.b

Handle prior.eps argument of GLMM_MCMC function
NMixMCMCwrapper

Wrapper to the NMixMCMC main simulation.
NMixEM

EM algorithm for a homoscedastic normal mixture
BsBasis

B-spline basis
Dirichlet

Dirichlet distribution
SP2Rect

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

Univariate conditional predictive density
NMixSummComp

Summary for the mixture components
GLMM_MCMCwrapper

Wrapper to the GLMM_MCMC main simulation.
GLMM_MCMCifit

Initial (RE)ML fits for the GLMM_MCMC function
GLMM_MCMCinit.alpha

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

Velocities of distant galaxies
GLMM_longitDA2

Discriminant analysis for longitudinal profiles based on fitted GLMM's
SimData

Simulated dataset
MVN

Multivariate normal distribution
GLMM_longitDA

Discriminant analysis for longitudinal profiles based on fitted GLMM's
NMixPredDA

Discriminant analysis based on MCMC output from the mixture model
plot.NMixPlugCondDensMarg

Plot computed univariate conditional densities (plug-in estimate)
NMixPseudoGOF

Pseudo goodness-of-fit test for a normal mixture model
NMixPlugCondDensJoint2

Pairwise bivariate conditional densities: plug-in estimate
MVNmixture

Mixture of (multivariate) normal distributions
NMixPlugCondDensMarg

Univariate conditional densities: plug-in estimate
NMixMCMCinitr

Initial component allocations for the NMixMCMC function
NMixMCMCdata

Data manipulation for the NMixMCMC function
NMixPredDensJoint2

Pairwise bivariate predictive density
MVT

Multivariate Student t distribution
NMixMCMC

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

Fitted profiles in the GLMM model
plot.NMixPlugDensJoint2

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

Marginal (univariate) predictive density
rRotationMatrix

Random rotation matrix
rSamplePair

Sample a pair (with replacement)
NMixPredCondCDFMarg

Univariate conditional predictive cumulative distribution function
NMixPlugDA

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

Moore-Penrose pseudoinverse of a squared matrix
Tandmob

Signal Tandmobiel data
TandmobEmer

Signal Tandmobiel data - emergence times
TMVN

Truncated multivariate normal distribution
autolayout

Automatic layout for several plots in one figure
NMixPlugDensJoint2

Pairwise bivariate densities: plug-in estimate
generatePermutations

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

Individual longitudinal profiles of a given variable
TNorm

Truncated normal distribution
NMixPredCondDensJoint2

Pairwise bivariate conditional predictive densities
PBC910

Subset of Mayo Clinic Primary Biliary Cholangitis (Cirrhosis) data
PBCseq

Mayo Clinic Primary Biliary Cholangitis (Cirrhosis), sequential data
cbplot

Plot a function together with its confidence/credible bands
Wishart

Wishart distribution
NMixRelabel

Re-labeling the MCMC output of the mixture model
plotProfiles

Plot individual longitudinal profiles
plot.NMixPredDensMarg

Plot computed marginal predictive densities
plot.NMixPredCondCDFMarg

Plot computed univariate conditional predictive cumulative distribution functions
plot.NMixPlugCondDensJoint2

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

Plot computed marginal predictive densities
plot.NMixPredCondDensJoint2

Plot computed predictive pairwise bivariate conditional densities
Y2T

Transform fitted distribution of Y=trans(T) into distribution of T
plot.NMixPredCDFMarg

Plot computed marginal predictive cumulative distribution functions
plot.NMixPredCondDensMarg

Plot computed univariate conditional predictive densities
tracePlots

Traceplots for selected parameters
summaryDiff

Posterior summary statistics for a difference of two quantities
plot.NMixPredDensJoint2

Plot computed marginal pairwise bivariate predictive densities