Package: mixAK 5.8

Arnošt Komárek

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

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. The package is primarily related to the publications Komárek (2009, Comp. Stat. and Data Anal.) <doi:10.1016/j.csda.2009.05.006> and Komárek and Komárková (2014, J. of Stat. Soft.) <doi:10.18637/jss.v059.i12>. It also implements methods published in Komárek and Komárková (2013, Ann. of Appl. Stat.) <doi:10.1214/12-AOAS580>, Hughes, Komárek, Bonnett, Czanner, García-Fiñana (2017, Stat. in Med.) <doi:10.1002/sim.7397>, Jaspers, Komárek, Aerts (2018, Biom. J.) <doi:10.1002/bimj.201600253> and Hughes, Komárek, Czanner, García-Fiñana (2018, Stat. Meth. in Med. Res) <doi:10.1177/0962280216674496>.

Authors:Arnošt Komárek [aut, cre]

mixAK_5.8.tar.gz
mixAK_5.8.tar.gz(r-4.5-noble)mixAK_5.8.tar.gz(r-4.4-noble)
mixAK_5.8.tgz(r-4.4-emscripten)mixAK_5.8.tgz(r-4.3-emscripten)
mixAK.pdf |mixAK.html
mixAK/json (API)
NEWS

# Install 'mixAK' in R:
install.packages('mixAK', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
Datasets:
  • Acidity - Acidity index of lakes in North-Central Wisconsin
  • Enzyme - Enzymatic activity in the blood
  • Faithful - Old Faithful Geyser Data
  • Galaxy - Velocities of distant galaxies
  • PBC910 - Subset of Mayo Clinic Primary Biliary Cholangitis (Cirrhosis) data
  • PBCseq - Mayo Clinic Primary Biliary Cholangitis (Cirrhosis), sequential data
  • SimData - Simulated dataset
  • Tandmob - Signal Tandmobiel data
  • TandmobEmer - Signal Tandmobiel data - emergence times

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.84 score 4 stars 3 packages 108 scripts 891 downloads 9 mentions 154 exports 14 dependencies

Last updated 2 months agofrom:a50c3065b9. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-linux-x86_64OKNov 16 2024

Exports:autolayoutBLABsBasisC_GLMM_MCMCC_GLMM_NMixRelabelC_NMix_ChainsDerivedC_NMix_MCMCC_NMix_NMixRelabelC_NMix_PEDC_NMix_PredCDFMargC_NMix_PredCondDensCDFMargC_NMix_PredCondDensJoint2C_NMix_PredDAC_NMix_PredDensJoint2C_NMix_PredDensMargcbplotdMVNdMVNmixturedMVNmixture2dMVTdWISHARTfitted.GLMM_MCMCgeneratePermutationsgetProfilesGLMM_longitDAGLMM_longitDA2GLMM_MCMCGLMM_MCMCdataGLMM_MCMCifitGLMM_MCMCinit.alphaGLMM_MCMCinit.bGLMM_MCMCinit.epsGLMM_MCMCprior.alphaGLMM_MCMCprior.bGLMM_MCMCprior.epsGLMM_MCMCscale.bGLMM_MCMCwrapperMatMPpinvMatSqrtNMixChainCompNMixChainComp.defaultNMixChainComp.GLMM_MCMCNMixChainComp.NMixMCMCNMixChainsDerivedNMixClusterNMixCluster.defaultNMixCluster.GLMM_MCMCNMixEMNMixMCMCNMixMCMCdataNMixMCMCinitrNMixMCMCinityNMixMCMCwrapperNMixPlugCondDensJoint2NMixPlugCondDensJoint2.defaultNMixPlugCondDensJoint2.GLMM_MCMCNMixPlugCondDensJoint2.NMixMCMCNMixPlugCondDensMargNMixPlugCondDensMarg.defaultNMixPlugCondDensMarg.GLMM_MCMCNMixPlugCondDensMarg.NMixMCMCNMixPlugDANMixPlugDensJoint2NMixPlugDensJoint2.defaultNMixPlugDensJoint2.GLMM_MCMCNMixPlugDensJoint2.NMixMCMCNMixPlugDensMargNMixPlugDensMarg.defaultNMixPlugDensMarg.GLMM_MCMCNMixPlugDensMarg.NMixMCMCNMixPredCDFMargNMixPredCDFMarg.defaultNMixPredCDFMarg.GLMM_MCMCNMixPredCDFMarg.NMixMCMCNMixPredCondCDFMargNMixPredCondCDFMarg.defaultNMixPredCondCDFMarg.GLMM_MCMCNMixPredCondCDFMarg.NMixMCMCNMixPredCondDensJoint2NMixPredCondDensJoint2.defaultNMixPredCondDensJoint2.GLMM_MCMCNMixPredCondDensJoint2.NMixMCMCNMixPredCondDensMargNMixPredCondDensMarg.defaultNMixPredCondDensMarg.GLMM_MCMCNMixPredCondDensMarg.NMixMCMCNMixPredDANMixPredDensJoint2NMixPredDensJoint2.defaultNMixPredDensJoint2.GLMM_MCMCNMixPredDensJoint2.NMixMCMCNMixPredDensMargNMixPredDensMarg.defaultNMixPredDensMarg.GLMM_MCMCNMixPredDensMarg.NMixMCMCNMixPseudoGOFNMixPseudoGOF.defaultNMixPseudoGOF.NMixMCMCNMixRelabelNMixRelabel.defaultNMixRelabel.GLMM_MCMCNMixRelabel.GLMM_MCMClistNMixRelabel.NMixMCMCNMixRelabel.NMixMCMClistNMixRelabelAlgorithmNMixSummCompNMixSummComp.defaultNMixSummComp.GLMM_MCMCNMixSummComp.NMixMCMCplot.NMixPlugCondDensJoint2plot.NMixPlugCondDensMargplot.NMixPlugDensJoint2plot.NMixPlugDensMargplot.NMixPredCDFMargplot.NMixPredCondCDFMargplot.NMixPredCondDensJoint2plot.NMixPredCondDensMargplot.NMixPredDensJoint2plot.NMixPredDensMargplotProfilesprint.GLMM_MCMCprint.GLMM_MCMClistprint.NMixEMprint.NMixMCMCprint.NMixMCMClistrcMVNrDirichletrMVNrMVNmixturerMVNmixture2rMVTrRotationMatrixrSamplePairrTMVNrTNormrWISHARTSP2RectsummaryDifftracePlotstracePlots.GLMM_MCMCtracePlots.GLMM_MCMClisttracePlots.NMixMCMCtracePlots.NMixMCMClistY2TY2T.NMixPlugCondDensJoint2Y2T.NMixPlugCondDensMargY2T.NMixPlugDensJoint2Y2T.NMixPlugDensMargY2T.NMixPredCDFMargY2T.NMixPredCondCDFMargY2T.NMixPredCondDensJoint2Y2T.NMixPredCondDensMargY2T.NMixPredDensJoint2Y2T.NMixPredDensMarg

Dependencies:bootcodacolorspacefastGHQuadlatticelme4MASSMatrixminqamnormtnlmenloptrRcppRcppEigen

Readme and manuals

Help Manual

Help pageTopics
Acidity index of lakes in North-Central WisconsinAcidity
Automatic layout for several plots in one figureautolayout
Best linear approximation with respect to the mean square error (theoretical linear regression).BLA C_BLA
B-spline basisBsBasis
Plot a function together with its confidence/credible bandscbplot
Dirichlet distributionC_rDirichlet_R Dirichlet rDirichlet
Enzymatic activity in the bloodEnzyme
Old Faithful Geyser DataFaithful
Fitted profiles in the GLMM modelfitted.GLMM_MCMC
Velocities of distant galaxiesGalaxy
Generate all permutations of (1, ..., K)C_generatePermutations generatePermutations
Individual longitudinal profiles of a given variablegetProfiles
Discriminant analysis for longitudinal profiles based on fitted GLMM'sC_GLMM_longitDA GLMM_longitDA
Discriminant analysis for longitudinal profiles based on fitted GLMM'sC_GLMM_longitDA2 GLMM_longitDA2
MCMC estimation of a (multivariate) generalized linear mixed model with a normal mixture in the distribution of random effectsC_GLMM_MCMC C_GLMM_PED GLMM_MCMC print.GLMM_MCMC print.GLMM_MCMClist
Moore-Penrose pseudoinverse of a squared matrixC_MPpinvSP MatMPpinv
Square root of a matrixC_sqrtGE MatSqrt
Multivariate normal distributionC_dMVN1_R C_rMVN1_R C_rMVN2_R dMVN MVN rcMVN rMVN
Mixture of (multivariate) normal distributionsC_dmixMVN_R C_dmixNorm_R C_rmixMVN_R C_rmixNorm_R dMVNmixture dMVNmixture2 MVNmixture rMVNmixture rMVNmixture2
Multivariate Student t distributionC_deriv_ldMVT_x C_dMVT1_R C_rMVT1_R dMVT MVT rMVT
Chains for mixture parametersNMixChainComp NMixChainComp.default NMixChainComp.GLMM_MCMC NMixChainComp.NMixMCMC
Create MCMC chains derived from previously sampled valuesC_NMix_ChainsDerived NMixChainsDerived
Clustering based on the MCMC output of the mixture modelNMixCluster NMixCluster.default NMixCluster.GLMM_MCMC
EM algorithm for a homoscedastic normal mixtureNMixEM print.NMixEM
MCMC estimation of (multivariate) normal mixtures with possibly censored data.C_NMix_MCMC C_NMix_PED NMixMCMC print.NMixMCMC print.NMixMCMClist
Pairwise bivariate conditional densities: plug-in estimateNMixPlugCondDensJoint2 NMixPlugCondDensJoint2.default NMixPlugCondDensJoint2.GLMM_MCMC NMixPlugCondDensJoint2.NMixMCMC
Univariate conditional densities: plug-in estimateNMixPlugCondDensMarg NMixPlugCondDensMarg.default NMixPlugCondDensMarg.GLMM_MCMC NMixPlugCondDensMarg.NMixMCMC
Discriminant analysis based on plug-in estimates from the mixture modelNMixPlugDA
Pairwise bivariate densities: plug-in estimateNMixPlugDensJoint2 NMixPlugDensJoint2.default NMixPlugDensJoint2.GLMM_MCMC NMixPlugDensJoint2.NMixMCMC
Marginal (univariate) densities: plug-in estimateNMixPlugDensMarg NMixPlugDensMarg.default NMixPlugDensMarg.GLMM_MCMC NMixPlugDensMarg.NMixMCMC
Marginal (univariate) predictive cumulative distribution functionC_NMix_PredCDFMarg NMixPredCDFMarg NMixPredCDFMarg.default NMixPredCDFMarg.GLMM_MCMC NMixPredCDFMarg.NMixMCMC
Univariate conditional predictive cumulative distribution functionNMixPredCondCDFMarg NMixPredCondCDFMarg.default NMixPredCondCDFMarg.GLMM_MCMC NMixPredCondCDFMarg.NMixMCMC
Pairwise bivariate conditional predictive densitiesC_NMix_PredCondDensJoint2 NMixPredCondDensJoint2 NMixPredCondDensJoint2.default NMixPredCondDensJoint2.GLMM_MCMC NMixPredCondDensJoint2.NMixMCMC
Univariate conditional predictive densityC_NMix_PredCondDensCDFMarg NMixPredCondDensMarg NMixPredCondDensMarg.default NMixPredCondDensMarg.GLMM_MCMC NMixPredCondDensMarg.NMixMCMC
Discriminant analysis based on MCMC output from the mixture modelC_NMix_PredDA NMixPredDA
Pairwise bivariate predictive densityC_NMix_PredDensJoint2 NMixPredDensJoint2 NMixPredDensJoint2.default NMixPredDensJoint2.GLMM_MCMC NMixPredDensJoint2.NMixMCMC
Marginal (univariate) predictive densityC_NMix_PredDensMarg NMixPredDensMarg NMixPredDensMarg.default NMixPredDensMarg.GLMM_MCMC NMixPredDensMarg.NMixMCMC
Pseudo goodness-of-fit test for a normal mixture modelNMixPseudoGOF NMixPseudoGOF.default NMixPseudoGOF.NMixMCMC
Re-labeling the MCMC output of the mixture modelC_GLMM_NMixRelabel C_NMix_NMixRelabel NMixRelabel NMixRelabel.default NMixRelabel.GLMM_MCMC NMixRelabel.GLMM_MCMClist NMixRelabel.NMixMCMC NMixRelabel.NMixMCMClist
Summary for the mixture componentsNMixSummComp NMixSummComp.default NMixSummComp.GLMM_MCMC NMixSummComp.NMixMCMC
Subset of Mayo Clinic Primary Biliary Cholangitis (Cirrhosis) dataPBC910
Mayo Clinic Primary Biliary Cholangitis (Cirrhosis), sequential dataPBCseq
Plot computed pairwise bivariate conditional densities (plug-in estimate)plot.NMixPlugCondDensJoint2
Plot computed univariate conditional densities (plug-in estimate)plot.NMixPlugCondDensMarg
Plot computed marginal pairwise bivariate densities (plug-in estimate)plot.NMixPlugDensJoint2
Plot computed marginal predictive densitiesplot.NMixPlugDensMarg
Plot computed marginal predictive cumulative distribution functionsplot.NMixPredCDFMarg
Plot computed univariate conditional predictive cumulative distribution functionsplot.NMixPredCondCDFMarg
Plot computed predictive pairwise bivariate conditional densitiesplot.NMixPredCondDensJoint2
Plot computed univariate conditional predictive densitiesplot.NMixPredCondDensMarg
Plot computed marginal pairwise bivariate predictive densitiesplot.NMixPredDensJoint2
Plot computed marginal predictive densitiesplot.NMixPredDensMarg
Plot individual longitudinal profilesplotProfiles
Random rotation matrixC_RotationMatrix_R rRotationMatrix
Sample a pair (with replacement)C_SamplePair_R rSamplePair
Simulated datasetSimData
Conversion of a symmetric matrix stored in a packed format (lower triangle only) into a matrixSP2Rect
Posterior summary statistics for a difference of two quantitiessummaryDiff
Signal Tandmobiel dataTandmob
Signal Tandmobiel data - emergence timesTandmobEmer
Truncated multivariate normal distributionC_rTMVN1_R rTMVN TMVN
Truncated normal distributionC_rTNorm1_R rTNorm TNorm
Traceplots for selected parameterstracePlots tracePlots.default tracePlots.GLMM_MCMC tracePlots.GLMM_MCMClist tracePlots.NMixMCMC tracePlots.NMixMCMClist
Wishart distributionC_ldWishart_R C_rWishart_R dWISHART rWISHART Wishart
Transform fitted distribution of Y=trans(T) into distribution of TY2T Y2T.NMixPlugCondDensJoint2 Y2T.NMixPlugCondDensMarg Y2T.NMixPlugDensJoint2 Y2T.NMixPlugDensMarg Y2T.NMixPredCDFMarg Y2T.NMixPredCondCDFMarg Y2T.NMixPredCondDensJoint2 Y2T.NMixPredCondDensMarg Y2T.NMixPredDensJoint2 Y2T.NMixPredDensMarg