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

## Documentation for package ‘mixAK’ version 5.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G M N P R S T W Y

## -- A --

Acidity | Acidity index of lakes in North-Central Wisconsin
autolayout | Automatic layout for several plots in one figure

## -- B --

BLA | Best linear approximation with respect to the mean square error (theoretical linear regression).
BsBasis | B-spline basis

## -- C --

cbplot | Plot a function together with its confidence/credible bands
C_BLA | Best linear approximation with respect to the mean square error (theoretical linear regression).
C_deriv_ldMVT_x | Multivariate Student t distribution
C_dmixMVN_R | Mixture of (multivariate) normal distributions
C_dmixNorm_R | Mixture of (multivariate) normal distributions
C_dMVN1_R | Multivariate normal distribution
C_dMVT1_R | Multivariate Student t distribution
C_generatePermutations | Generate all permutations of (1, ..., K)
C_GLMM_longitDA | Discriminant analysis for longitudinal profiles based on fitted GLMM's
C_GLMM_longitDA2 | Discriminant analysis for longitudinal profiles based on fitted GLMM's
C_GLMM_MCMC | MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effects
C_GLMM_NMixRelabel | Re-labeling the MCMC output of the mixture model
C_GLMM_PED | MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effects
C_ldWishart_R | Wishart distribution
C_MPpinvSP | Moore-Penrose pseudoinverse of a squared matrix
C_NMix_ChainsDerived | Create MCMC chains derived from previously sampled values
C_NMix_MCMC | MCMC estimation of (multivariate) normal mixtures with possibly censored data.
C_NMix_NMixRelabel | Re-labeling the MCMC output of the mixture model
C_NMix_PED | MCMC estimation of (multivariate) normal mixtures with possibly censored data.
C_NMix_PredCDFMarg | Marginal (univariate) predictive cumulative distribution function
C_NMix_PredCondDensCDFMarg | Univariate conditional predictive density
C_NMix_PredCondDensJoint2 | Pairwise bivariate conditional predictive densities
C_NMix_PredDA | Discriminant analysis based on MCMC output from the mixture model
C_NMix_PredDensJoint2 | Pairwise bivariate predictive density
C_NMix_PredDensMarg | Marginal (univariate) predictive density
C_rDirichlet_R | Dirichlet distribution
C_rmixMVN_R | Mixture of (multivariate) normal distributions
C_rmixNorm_R | Mixture of (multivariate) normal distributions
C_rMVN1_R | Multivariate normal distribution
C_rMVN2_R | Multivariate normal distribution
C_rMVT1_R | Multivariate Student t distribution
C_RotationMatrix_R | Random rotation matrix
C_rTMVN1_R | Truncated multivariate normal distribution
C_rTNorm1_R | Truncated normal distribution
C_rWishart_R | Wishart distribution
C_SamplePair_R | Sample a pair (with replacement)
C_sqrtGE | Square root of a matrix

## -- D --

Dirichlet | Dirichlet distribution
dMVN | Multivariate normal distribution
dMVNmixture | Mixture of (multivariate) normal distributions
dMVNmixture2 | Mixture of (multivariate) normal distributions
dMVT | Multivariate Student t distribution
dWISHART | Wishart distribution

## -- E --

Enzyme | Enzymatic activity in the blood

## -- F --

Faithful | Old Faithful Geyser Data
fitted.GLMM_MCMC | Fitted profiles in the GLMM model

## -- G --

Galaxy | Velocities of distant galaxies
generatePermutations | Generate all permutations of (1, ..., K)
getProfiles | Individual longitudinal profiles of a given variable
GLMM_longitDA | Discriminant analysis for longitudinal profiles based on fitted GLMM's
GLMM_longitDA2 | Discriminant analysis for longitudinal profiles based on fitted GLMM's
GLMM_MCMC | MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effects

## -- M --

MatMPpinv | Moore-Penrose pseudoinverse of a squared matrix
MatSqrt | Square root of a matrix
MVN | Multivariate normal distribution
MVNmixture | Mixture of (multivariate) normal distributions
MVT | Multivariate Student t distribution

## -- N --

NMixChainComp | Chains for mixture parameters
NMixChainComp.default | Chains for mixture parameters
NMixChainComp.GLMM_MCMC | Chains for mixture parameters
NMixChainComp.NMixMCMC | Chains for mixture parameters
NMixChainsDerived | Create MCMC chains derived from previously sampled values
NMixCluster | Clustering based on the MCMC output of the mixture model
NMixCluster.default | Clustering based on the MCMC output of the mixture model
NMixCluster.GLMM_MCMC | Clustering based on the MCMC output of the mixture model
NMixEM | EM algorithm for a homoscedastic normal mixture
NMixMCMC | MCMC estimation of (multivariate) normal mixtures with possibly censored data.
NMixPlugCondDensJoint2 | Pairwise bivariate conditional densities: plug-in estimate
NMixPlugCondDensJoint2.default | Pairwise bivariate conditional densities: plug-in estimate
NMixPlugCondDensJoint2.GLMM_MCMC | Pairwise bivariate conditional densities: plug-in estimate
NMixPlugCondDensJoint2.NMixMCMC | Pairwise bivariate conditional densities: plug-in estimate
NMixPlugCondDensMarg | Univariate conditional densities: plug-in estimate
NMixPlugCondDensMarg.default | Univariate conditional densities: plug-in estimate
NMixPlugCondDensMarg.GLMM_MCMC | Univariate conditional densities: plug-in estimate
NMixPlugCondDensMarg.NMixMCMC | Univariate conditional densities: plug-in estimate
NMixPlugDA | Discriminant analysis based on plug-in estimates from the mixture model
NMixPlugDensJoint2 | Pairwise bivariate densities: plug-in estimate
NMixPlugDensJoint2.default | Pairwise bivariate densities: plug-in estimate
NMixPlugDensJoint2.GLMM_MCMC | Pairwise bivariate densities: plug-in estimate
NMixPlugDensJoint2.NMixMCMC | Pairwise bivariate densities: plug-in estimate
NMixPlugDensMarg | Marginal (univariate) densities: plug-in estimate
NMixPlugDensMarg.default | Marginal (univariate) densities: plug-in estimate
NMixPlugDensMarg.GLMM_MCMC | Marginal (univariate) densities: plug-in estimate
NMixPlugDensMarg.NMixMCMC | Marginal (univariate) densities: plug-in estimate
NMixPredCDFMarg | Marginal (univariate) predictive cumulative distribution function
NMixPredCDFMarg.default | Marginal (univariate) predictive cumulative distribution function
NMixPredCDFMarg.GLMM_MCMC | Marginal (univariate) predictive cumulative distribution function
NMixPredCDFMarg.NMixMCMC | Marginal (univariate) predictive cumulative distribution function
NMixPredCondCDFMarg | Univariate conditional predictive cumulative distribution function
NMixPredCondCDFMarg.default | Univariate conditional predictive cumulative distribution function
NMixPredCondCDFMarg.GLMM_MCMC | Univariate conditional predictive cumulative distribution function
NMixPredCondCDFMarg.NMixMCMC | Univariate conditional predictive cumulative distribution function
NMixPredCondDensJoint2 | Pairwise bivariate conditional predictive densities
NMixPredCondDensJoint2.default | Pairwise bivariate conditional predictive densities
NMixPredCondDensJoint2.GLMM_MCMC | Pairwise bivariate conditional predictive densities
NMixPredCondDensJoint2.NMixMCMC | Pairwise bivariate conditional predictive densities
NMixPredCondDensMarg | Univariate conditional predictive density
NMixPredCondDensMarg.default | Univariate conditional predictive density
NMixPredCondDensMarg.GLMM_MCMC | Univariate conditional predictive density
NMixPredCondDensMarg.NMixMCMC | Univariate conditional predictive density
NMixPredDA | Discriminant analysis based on MCMC output from the mixture model
NMixPredDensJoint2 | Pairwise bivariate predictive density
NMixPredDensJoint2.default | Pairwise bivariate predictive density
NMixPredDensJoint2.GLMM_MCMC | Pairwise bivariate predictive density
NMixPredDensJoint2.NMixMCMC | Pairwise bivariate predictive density
NMixPredDensMarg | Marginal (univariate) predictive density
NMixPredDensMarg.default | Marginal (univariate) predictive density
NMixPredDensMarg.GLMM_MCMC | Marginal (univariate) predictive density
NMixPredDensMarg.NMixMCMC | Marginal (univariate) predictive density
NMixPseudoGOF | Pseudo goodness-of-fit test for a normal mixture model
NMixPseudoGOF.default | Pseudo goodness-of-fit test for a normal mixture model
NMixPseudoGOF.NMixMCMC | Pseudo goodness-of-fit test for a normal mixture model
NMixRelabel | Re-labeling the MCMC output of the mixture model
NMixRelabel.default | Re-labeling the MCMC output of the mixture model
NMixRelabel.GLMM_MCMC | Re-labeling the MCMC output of the mixture model
NMixRelabel.GLMM_MCMClist | Re-labeling the MCMC output of the mixture model
NMixRelabel.NMixMCMC | Re-labeling the MCMC output of the mixture model
NMixRelabel.NMixMCMClist | Re-labeling the MCMC output of the mixture model
NMixSummComp | Summary for the mixture components
NMixSummComp.default | Summary for the mixture components
NMixSummComp.GLMM_MCMC | Summary for the mixture components
NMixSummComp.NMixMCMC | Summary for the mixture components

## -- P --

PBC910 | Subset of Mayo Clinic Primary Biliary Cirrhosis data
PBCseq | Mayo Clinic Primary Biliary Cirrhosis, sequential data
plot.NMixPlugCondDensJoint2 | Plot computed pairwise bivariate conditional densities (plug-in estimate)
plot.NMixPlugCondDensMarg | Plot computed univariate conditional densities (plug-in estimate)
plot.NMixPlugDensJoint2 | Plot computed marginal pairwise bivariate densities (plug-in estimate)
plot.NMixPlugDensMarg | Plot computed marginal predictive densities
plot.NMixPredCDFMarg | Plot computed marginal predictive cumulative distribution functions
plot.NMixPredCondCDFMarg | Plot computed univariate conditional predictive cumulative distribution functions
plot.NMixPredCondDensJoint2 | Plot computed predictive pairwise bivariate conditional densities
plot.NMixPredCondDensMarg | Plot computed univariate conditional predictive densities
plot.NMixPredDensJoint2 | Plot computed marginal pairwise bivariate predictive densities
plot.NMixPredDensMarg | Plot computed marginal predictive densities
plotProfiles | Plot individual longitudinal profiles
print.GLMM_MCMC | MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effects
print.GLMM_MCMClist | MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effects
print.NMixEM | EM algorithm for a homoscedastic normal mixture
print.NMixMCMC | MCMC estimation of (multivariate) normal mixtures with possibly censored data.
print.NMixMCMClist | MCMC estimation of (multivariate) normal mixtures with possibly censored data.

## -- R --

rcMVN | Multivariate normal distribution
rDirichlet | Dirichlet distribution
rMVN | Multivariate normal distribution
rMVNmixture | Mixture of (multivariate) normal distributions
rMVNmixture2 | Mixture of (multivariate) normal distributions
rMVT | Multivariate Student t distribution
rRotationMatrix | Random rotation matrix
rSamplePair | Sample a pair (with replacement)
rTMVN | Truncated multivariate normal distribution
rTNorm | Truncated normal distribution
rWISHART | Wishart distribution

## -- S --

SimData | Simulated dataset
SP2Rect | Conversion of a symmetric matrix stored in a packed format (lower triangle only) into a matrix
summaryDiff | Posterior summary statistics for a difference of two quantities

## -- T --

Tandmob | Signal Tandmobiel data
TandmobEmer | Signal Tandmobiel data - emergence times
TMVN | Truncated multivariate normal distribution
TNorm | Truncated normal distribution
tracePlots | Traceplots for selected parameters
tracePlots.default | Traceplots for selected parameters
tracePlots.GLMM_MCMC | Traceplots for selected parameters
tracePlots.GLMM_MCMClist | Traceplots for selected parameters
tracePlots.NMixMCMC | Traceplots for selected parameters
tracePlots.NMixMCMClist | Traceplots for selected parameters

## -- W --

Wishart | Wishart distribution

## -- Y --

Y2T | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPlugCondDensJoint2 | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPlugCondDensMarg | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPlugDensJoint2 | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPlugDensMarg | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPredCDFMarg | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPredCondCDFMarg | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPredCondDensJoint2 | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPredCondDensMarg | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPredDensJoint2 | Transform fitted distribution of Y=trans(T) into distribution of T
Y2T.NMixPredDensMarg | Transform fitted distribution of Y=trans(T) into distribution of T