Package: HDclust 1.0.4

Jia Li

HDclust: Clustering High Dimensional Data with Hidden Markov Model on Variable Blocks

Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <https://jmlr.org/papers/v18/16-342.html>.

Authors:Yevhen Tupikov [aut], Lin Lin [aut], Lixiang Zhang [aut], Jia Li [aut, cre]

HDclust_1.0.4.tar.gz
HDclust_1.0.4.tar.gz(r-4.5-noble)HDclust_1.0.4.tar.gz(r-4.4-noble)
HDclust_1.0.4.tgz(r-4.4-emscripten)HDclust_1.0.4.tgz(r-4.3-emscripten)
HDclust.pdf |HDclust.html✨
HDclust/json (API)
NEWS

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • sim2 - Synthetic dataset used in section 5.1.2 of the reference paper.
  • sim3 - Synthetic dataset used in section 5.1.3 of the reference paper

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

2.26 score 18 scripts 200 downloads 27 exports 3 dependencies

Last updated 3 months agofrom:224847c430. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-linux-x86_64OKNov 20 2024

Exports:clustControlclustModesgetBdimgetBICgetClsidgetClustParamgetDiagCovgetDimgetHmmChaingetHmmParamgetLoglikehdgetNbgetNumstgetOptHMMVBgetPrenumstgetSizegetVarordergetVbhmmvbBIChmmvbClusthmmvbFindModeshmmvbTrainplotshowtrainControlvbvbSearchControl

Dependencies:RcppRcppProgressRtsne

A quick tour of HDclust

Yevhen Tupikov, Lixiang Zhang

Rendered fromHDclust.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-09-21
Started: 2018-07-29

Readme and manuals

Help Manual

Help pageTopics
Clustering high dimensional data with Hidden Markov Model on Variable BlocksHDclust-package HDclust
Parameters for MBM clustering algorithm.clustControl
Hierarchical clustering of density modesclustModes
Accessor for 'bdim' slotgetBdim getBdim,HMMVB-method getBdim,VB-method
Accessor for 'BIC' slot.getBIC getBIC,HMMVB-method getBIC,HMMVBBIC-method
Accessor for 'clsid' slot.getClsid
Accessor for 'clustParam' slot.getClustParam
Accessor for 'diagCov' slot.getDiagCov
Accessor for 'dim' slotgetDim getDim,HMM-method getDim,HMMVB-method getDim,VB-method
Accessor for 'HmmChain' slot.getHmmChain
Accessor for parameters of HMMgetHmmParam
Accessor for 'Loglikehd' slot.getLoglikehd getLoglikehd,HMMVB-method getLoglikehd,HMMVBBIC-method getLoglikehd,HMMVBclust-method
Accessor for 'nb' slotgetNb getNb,HMMVB-method getNb,VB-method
Accessor for 'numst' slotgetNumst getNumst,HMM-method getNumst,HMMVB-method getNumst,VB-method
Accessor for 'optHMMVB' slot.getOptHMMVB
Accessor for 'prenumst' slotgetPrenumst
Accessor for 'size' slot.getSize
Accessor for 'varorder' slotgetVarorder getVarorder,HMMVB-method getVarorder,VB-method
Accessor for 'VbStructure' slot.getVb
Class "HMM" to represent parameters associated with a variable block in the HMM-VBgetHmmParam,HMM-method getPrenumst,HMM-method HMM HMM-class show,HMM-method
Class "HMMVB" to represent a Hidden Markov Model on Variable Blocks (HMM-VB).getDiagCov,HMMVB-method getHmmChain,HMMVB-method getVb,HMMVB-method HMMVB HMMVB-class show,HMMVB-method
BIC for HMM-VBhmmvbBIC
Class "HMMVBBIC" to represent results of HMM-VB model selection.getOptHMMVB,HMMVBBIC-method HMMVBBIC HMMVBBIC-class plot,HMMVBBIC,missing-method show,HMMVBBIC-method
Cluster data with HMM-VBhmmvbClust
Class "HMMVBclust" to represent clustering results with Hidden Markov Model on variable block structure.getClsid,HMMVBclust-method getClustParam,HMMVBclust-method getSize,HMMVBclust-method HMMVBclust HMMVBclust-class plot,HMMVBclust,missing-method show,HMMVBclust-method
Find density modes with HMM-VBhmmvbFindModes
Train HMM-VBhmmvbTrain
Synthetic dataset used in section 5.1.2 of the reference paper.sim2
Synthetic dataset used in section 5.1.3 of the reference papersim3
Parameters for HMM-VB training.trainControl
Make an instance of class "VB"vb
Class "VB" to represent a variable block structure.show,VB-method VB VB-class
Parameters for variable block structure search.vbSearchControl