pmclust: Parallel Model-Based Clustering using Expectation-Gathering-Maximization Algorithm for Finite Mixture Gaussian Model

Aims to utilize model-based clustering (unsupervised) for high dimensional and ultra large data, especially in a distributed manner. The code employs pbdMPI to perform a expectation-gathering-maximization algorithm for finite mixture Gaussian models. The unstructured dispersion matrices are assumed in the Gaussian models. The implementation is default in the single program multiple data programming model. The code can be executed through pbdMPI and independent to most MPI applications. See the High Performance Statistical Computing website for more information, documents and examples.

Author
Wei-Chen Chen [aut, cre], George Ostrouchov [aut]
Date of publication
2016-09-22 09:22:55
Maintainer
Wei-Chen Chen <wccsnow@gmail.com>
License
GPL (>= 2)
Version
0.1-8
URLs

View on CRAN

Man pages

00_pmclust-package
Parallel Model-Based Clustering
01-pmclust_pkmeans
Parallel Model-Based Clustering and Parallel K-means...
10_d.readme
Read Me First Function
11_d.set.global
Set Global Variables According to the global matrix X.gbd...
12_d.param
A Set of Parameters in Model-Based Clustering.
13_d.control
A Set of Controls in Model-Based Clustering.
20-assign.N.sample
Obtain a Set of Random Samples for X.spmd
30-em_initial
Initialization for EM-like Algorithms
30-em_like
EM-like Steps for GBD
30-em.one
One EM Step for GBD
30-em.one.e
Compute One E-step and Log Likelihood Based on Current...
30-em.one.m
Compute One M-Step Based on Current Posterior Probabilities
40-generate.basic
Generate Examples for Testing
40-generate.MixSim
Generate MixSim Examples for Testing
41-get.N.CLASS
Obtain Total Elements for Every Clusters
50-as.dmat.spmd
Convert between X.gbd (X.spmd) and X.dmat
50-indep.logL
Independent Function for Log Likelihood
50-mb.print
Print Results of Model-Based Clustering
50-update.class
Update CLASS.spmd Based on the Final Iteration
60-print
Functions for Printing or Summarizing Objects According to...

Files in this package

pmclust
pmclust/COPYING
pmclust/inst
pmclust/inst/CITATION
pmclust/inst/tests
pmclust/inst/tests/iris_em_dmat.r
pmclust/inst/tests/dmat_em.r
pmclust/inst/tests/iris_kmeans_dmat.r
pmclust/inst/tests/dmat_kmeans.r
pmclust/inst/tests/iris_em_spmd.r
pmclust/inst/tests/iris_EMCluster.r
pmclust/inst/tests/iris_kmeans_spmd.r
pmclust/inst/doc
pmclust/inst/doc/pmclust-guide.pdf
pmclust/inst/doc/pmclust-guide.Rnw
pmclust/src
pmclust/src/my_c_em.c
pmclust/src/my_c_apecm.c
pmclust/NAMESPACE
pmclust/demo
pmclust/demo/gbd_kmeans.r
pmclust/demo/ex_aecm.r
pmclust/demo/iris_common.r
pmclust/demo/gbd_em.r
pmclust/demo/io_csv.r
pmclust/demo/iris_dmat.r
pmclust/demo/gbd_apecma.r
pmclust/demo/ex_em.r
pmclust/demo/ex_apecm.r
pmclust/demo/ex_MixSim.r
pmclust/demo/iris_single.r
pmclust/demo/gbd_aecm.r
pmclust/demo/iris_gbdr.r
pmclust/demo/dmat_em.r
pmclust/demo/ex_apecma.r
pmclust/demo/00Index
pmclust/demo/gbd_apecm.r
pmclust/demo/dmat_kmeans.r
pmclust/demo/ex_kmeans.r
pmclust/data
pmclust/data/control.r
pmclust/data/envir.r
pmclust/R
pmclust/R/dmat_00_readme.r
pmclust/R/pm_em_decompsigma.r
pmclust/R/dmat_kmeans_initial.r
pmclust/R/dmat_em_tools.r
pmclust/R/dmat_em_initial.r
pmclust/R/03_print_object.r
pmclust/R/pm_my_c_tools.r
pmclust/R/pm_indep_logL.r
pmclust/R/00_pmclust_internal_dmat.r
pmclust/R/000_globalVariables.r
pmclust/R/pm_aecm_base.r
pmclust/R/pm_kmeans_base.r
pmclust/R/00_pmclust_internal.r
pmclust/R/pm_apecm_base.r
pmclust/R/pm_em_tools.r
pmclust/R/02_convert_data.r
pmclust/R/01_as_dmat.r
pmclust/R/01_as_spmd.r
pmclust/R/00_pmclust.r
pmclust/R/gbd_my_tools.r
pmclust/R/dmat_indep_logL.r
pmclust/R/pm_my_tools.r
pmclust/R/pm_em_initial.r
pmclust/R/pm_kmeans_initial.r
pmclust/R/pm_generate_basic.r
pmclust/R/zzz.r
pmclust/R/pm_em_logdmvnorm.r
pmclust/R/dmat_em_logdmvnorm.r
pmclust/R/dmat_em_base.r
pmclust/R/dmat_my_tools.r
pmclust/R/02_load_balance.r
pmclust/R/04_mb_print.r
pmclust/R/pm_generate_MixSim.r
pmclust/R/yyy.r
pmclust/R/pm_em_base.r
pmclust/R/dmat_kmeans_base.r
pmclust/R/pm_00_readme.r
pmclust/R/pm_sampling.r
pmclust/R/pm_apecma_base.r
pmclust/vignettes
pmclust/vignettes/pmclust-include
pmclust/vignettes/pmclust-include/03-algorithm.tex
pmclust/vignettes/pmclust-include/04-discussion.tex
pmclust/vignettes/pmclust-include/pmclust.bib
pmclust/vignettes/pmclust-include/00-preamble.tex
pmclust/vignettes/pmclust-include/02-example.tex
pmclust/vignettes/pmclust-include/01-acknowledgement.tex
pmclust/vignettes/pmclust-include/01-introduction.tex
pmclust/vignettes/pmclust-include/my_jss.cls
pmclust/vignettes/pmclust-guide.Rnw
pmclust/vignettes/build_pdf.sh
pmclust/MD5
pmclust/README
pmclust/DESCRIPTION
pmclust/ChangeLog
pmclust/man
pmclust/man/50-indep.logL.Rd
pmclust/man/60-print.Rd
pmclust/man/30-em.one.m.Rd
pmclust/man/20-assign.N.sample.Rd
pmclust/man/40-generate.MixSim.Rd
pmclust/man/30-em.one.e.Rd
pmclust/man/50-mb.print.Rd
pmclust/man/30-em.one.Rd
pmclust/man/13_d.control.Rd
pmclust/man/41-get.N.CLASS.Rd
pmclust/man/12_d.param.Rd
pmclust/man/30-em_initial.Rd
pmclust/man/50-update.class.Rd
pmclust/man/11_d.set.global.Rd
pmclust/man/40-generate.basic.Rd
pmclust/man/50-as.dmat.spmd.Rd
pmclust/man/00_pmclust-package.Rd
pmclust/man/10_d.readme.Rd
pmclust/man/30-em_like.Rd
pmclust/man/01-pmclust_pkmeans.Rd
pmclust/cleanup