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

Documentation for package ‘mixAK’ version 5.7

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-- 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 Cholangitis (Cirrhosis) data
PBCseq	Mayo Clinic Primary Biliary Cholangitis (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