pmclust: Parallel Model-Based Clustering using Expectation-Gathering-Maximization Algorithm for Finite Mixture Gaussian Model
Version 0.1-9

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.

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AuthorWei-Chen Chen [aut, cre], George Ostrouchov [aut]
Date of publication2016-12-19 08:34:03
MaintainerWei-Chen Chen <wccsnow@gmail.com>
LicenseGPL (>= 2)
Version0.1-9
URL http://r-pbd.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pmclust")

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...

Functions

.PMC.CT Man page
.pmclustEnv Man page
CHECK Man page
CLASS.dmat Man page
CLASS.spmd Man page
COMM.RANK Man page
COMM.SIZE Man page
CONTROL Man page
ETA Man page
MU Man page
PARAM Man page
PARAM.org Man page
SAVE.iter Man page
SAVE.param Man page
SIGMA Man page
U.dmat Man page
U.spmd Man page
W.dmat Man page
W.dmat.rowSums Man page
W.plus.y Source code
W.plus.y.k Source code
W.spmd Man page
W.spmd.rowSums Man page
X.dmat Man page
X.gbd Man page
X.spmd Man page
Z.colSums Man page
Z.dmat Man page
Z.spmd Man page
aecm.onestep.spmd Source code
aecm.step Man page
aecm.step.spmd Source code
ape.step.spmd Source code
ape.step.spmd.k Source code
ape.update.expectation Source code
ape.update.expectation.k Source code
apea.step.spmd.k Source code
apecm.onestep.spmd Source code
apecm.step Man page
apecm.step.spmd Source code
apecma.onestep.spmd Source code
apecma.step Man page
apecma.step.spmd Source code
as.dmat Man page Source code
as.gbd Man page
as.spmd Man page Source code
assign.N.sample Man page Source code
balance.info Source code
check.em.convergence Source code
check.kmeans.convergence Source code
cm.step.spmd.ETA Source code
cm.step.spmd.ETA.MU.SIGMA.k Source code
cm.step.spmd.MU Source code
cm.step.spmd.MU.SIGMA.k Source code
cm.step.spmd.SIGMA Source code
convert.data Source code
decompsigma Source code
e.step Man page
e.step.dmat Man page Source code
e.step.spmd Source code
em.onestep Man page
em.onestep.dmat Man page Source code
em.onestep.spmd Source code
em.step Man page
em.step.dmat Man page Source code
em.step.spmd Source code
em.update.class Man page
em.update.class.dmat Man page Source code
em.update.class.spmd Source code
estimate.MU Source code
estimate.SIGMA Source code
generate.MixSim Man page
generate.MixSim.spmd Source code
generate.basic Man page
generate.basic.spmd Source code
get.CLASS Man page Source code
get.N.CLASS Man page Source code
get.N.CLASS.dmat Man page Source code
indep.logL Man page Source code
indep.logL.dmat Man page Source code
initial.RndEM Man page
initial.RndEM.dmat Man page Source code
initial.RndEM.spmd Source code
initial.center Man page
initial.center.dmat Man page Source code
initial.center.spmd Source code
initial.em Man page
initial.em.dmat Man page Source code
initial.em.spmd Source code
kmeans.e.step.dmat Source code
kmeans.e.step.spmd Source code
kmeans.logL.step.dmat Source code
kmeans.logL.step.spmd Source code
kmeans.m.step.dmat Source code
kmeans.m.step.spmd Source code
kmeans.onestep.dmat Source code
kmeans.onestep.spmd Source code
kmeans.step Man page
kmeans.step.dmat Man page Source code
kmeans.step.spmd Source code
kmeans.update.class Man page
kmeans.update.class.dmat Man page Source code
kmeans.update.class.spmd Source code
load.balance Source code
logL.step.dmat Source code
logL.step.spmd Source code
logdmvnorm Source code
logdmvnorm.dmat Source code
m.step Man page
m.step.dmat Man page Source code
m.step.spmd Source code
mb.print Man page Source code
onLoad Source code
onUnload Source code
p.times.logtwopi Man page
pkmeans Man page Source code
pmclust Man page Source code
pmclust-package Man page
pmclust.internal Source code
pmclust.internal.dmat Source code
print.pkmeans Man page Source code
print.pmclust Man page Source code
readme Man page Source code
readme.dmat Man page Source code
set.global Man page Source code
set.global.dmat Man page Source code
set.global.gbd Man page Source code
unload.balance Source code
update.expectation Source code
update.expectation.dmat Source code

Files

COPYING
inst
inst/CITATION
inst/tests
inst/tests/iris_em_dmat.r
inst/tests/dmat_em.r
inst/tests/iris_kmeans_dmat.r
inst/tests/dmat_kmeans.r
inst/tests/iris_em_spmd.r
inst/tests/iris_EMCluster.r
inst/tests/iris_kmeans_spmd.r
inst/doc
inst/doc/pmclust-guide.pdf
inst/doc/pmclust-guide.Rnw
src
src/my_c_em.c
src/my_c_apecm.c
NAMESPACE
demo
demo/gbd_kmeans.r
demo/ex_aecm.r
demo/iris_common.r
demo/gbd_em.r
demo/io_csv.r
demo/iris_dmat.r
demo/gbd_apecma.r
demo/ex_em.r
demo/ex_apecm.r
demo/ex_MixSim.r
demo/iris_single.r
demo/gbd_aecm.r
demo/iris_gbdr.r
demo/dmat_em.r
demo/ex_apecma.r
demo/00Index
demo/gbd_apecm.r
demo/dmat_kmeans.r
demo/ex_kmeans.r
data
data/control.r
data/envir.r
R
R/dmat_00_readme.r
R/pm_em_decompsigma.r
R/dmat_kmeans_initial.r
R/dmat_em_tools.r
R/dmat_em_initial.r
R/03_print_object.r
R/pm_my_c_tools.r
R/pm_indep_logL.r
R/00_pmclust_internal_dmat.r
R/000_globalVariables.r
R/pm_aecm_base.r
R/pm_kmeans_base.r
R/00_pmclust_internal.r
R/pm_apecm_base.r
R/pm_em_tools.r
R/02_convert_data.r
R/01_as_dmat.r
R/01_as_spmd.r
R/00_pmclust.r
R/gbd_my_tools.r
R/dmat_indep_logL.r
R/pm_my_tools.r
R/pm_em_initial.r
R/pm_kmeans_initial.r
R/pm_generate_basic.r
R/zzz.r
R/pm_em_logdmvnorm.r
R/dmat_em_logdmvnorm.r
R/dmat_em_base.r
R/dmat_my_tools.r
R/02_load_balance.r
R/04_mb_print.r
R/pm_generate_MixSim.r
R/yyy.r
R/pm_em_base.r
R/dmat_kmeans_base.r
R/pm_00_readme.r
R/pm_sampling.r
R/pm_apecma_base.r
vignettes
vignettes/pmclust-include
vignettes/pmclust-include/03-algorithm.tex
vignettes/pmclust-include/04-discussion.tex
vignettes/pmclust-include/pmclust.bib
vignettes/pmclust-include/00-preamble.tex
vignettes/pmclust-include/02-example.tex
vignettes/pmclust-include/01-acknowledgement.tex
vignettes/pmclust-include/01-introduction.tex
vignettes/pmclust-include/my_jss.cls
vignettes/pmclust-guide.Rnw
vignettes/build_pdf.sh
MD5
README
DESCRIPTION
ChangeLog
man
man/50-indep.logL.Rd
man/60-print.Rd
man/30-em.one.m.Rd
man/20-assign.N.sample.Rd
man/40-generate.MixSim.Rd
man/30-em.one.e.Rd
man/50-mb.print.Rd
man/30-em.one.Rd
man/13_d.control.Rd
man/41-get.N.CLASS.Rd
man/12_d.param.Rd
man/30-em_initial.Rd
man/50-update.class.Rd
man/11_d.set.global.Rd
man/40-generate.basic.Rd
man/50-as.dmat.spmd.Rd
man/00_pmclust-package.Rd
man/10_d.readme.Rd
man/30-em_like.Rd
man/01-pmclust_pkmeans.Rd
cleanup
pmclust documentation built on May 19, 2017, 3 p.m.