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-4.7-arm64)HDclust_1.0.4.tar.gz(r-4.7-x86_64)HDclust_1.0.4.tar.gz(r-4.6-arm64)HDclust_1.0.4.tar.gz(r-4.6-x86_64)
HDclust_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HDclust/json (API)

# Install 'HDclust' in R:

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

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

On CRAN:

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

cpp openmp

2.30 score 20 scripts 237 downloads 27 exports 3 dependencies

Last updated from:224847c430. Checks:4 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	147
linux-devel-x86_64	NOTE	141
source / vignettes	OK	246
linux-release-arm64	NOTE	146
linux-release-x86_64	NOTE	169
wasm-release	OK	176

Exports:clustControl clustModes getBdim getBIC getClsid getClustParam getDiagCov getDim getHmmChain getHmmParam getLoglikehd getNb getNumst getOptHMMVB getPrenumst getSize getVarorder getVb hmmvbBIC hmmvbClust hmmvbFindModes hmmvbTrain plot show trainControl vb vbSearchControl

Dependencies:Rcpp RcppProgress Rtsne

A quick tour of HDclust

Rendered fromHDclust.Rmdusingknitr::rmarkdown

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

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Readme and manuals

Help Manual

Help page	Topics
Clustering high dimensional data with Hidden Markov Model on Variable Blocks	HDclust-package HDclust
Parameters for MBM clustering algorithm.	clustControl
Hierarchical clustering of density modes	clustModes
Accessor for 'bdim' slot	getBdim 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' slot	getDim getDim,HMM-method getDim,HMMVB-method getDim,VB-method
Accessor for 'HmmChain' slot.	getHmmChain
Accessor for parameters of HMM	getHmmParam
Accessor for 'Loglikehd' slot.	getLoglikehd getLoglikehd,HMMVB-method getLoglikehd,HMMVBBIC-method getLoglikehd,HMMVBclust-method
Accessor for 'nb' slot	getNb getNb,HMMVB-method getNb,VB-method
Accessor for 'numst' slot	getNumst getNumst,HMM-method getNumst,HMMVB-method getNumst,VB-method
Accessor for 'optHMMVB' slot.	getOptHMMVB
Accessor for 'prenumst' slot	getPrenumst
Accessor for 'size' slot.	getSize
Accessor for 'varorder' slot	getVarorder getVarorder,HMMVB-method getVarorder,VB-method
Accessor for 'VbStructure' slot.	getVb
Class "HMM" to represent parameters associated with a variable block in the HMM-VB	getHmmParam,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-VB	hmmvbBIC
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-VB	hmmvbClust
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-VB	hmmvbFindModes
Train HMM-VB	hmmvbTrain
Synthetic dataset used in section 5.1.2 of the reference paper.	sim2
Synthetic dataset used in section 5.1.3 of the reference paper	sim3
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

Package: HDclust 1.0.4

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

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)