ClustMMDD: Variable Selection in Clustering by Mixture Models for Discrete Data

An implementation of a variable selection procedure in clustering by mixture models for discrete data (clustMMDD). Genotype data are examples of such data with two unordered observations (alleles) at each locus for diploid individual. The two-fold problem of variable selection and clustering is seen as a model selection problem where competing models are characterized by the number of clusters K, and the subset S of clustering variables. Competing models are compared by penalized maximum likelihood criteria. We considered asymptotic criteria such as Akaike and Bayesian Information criteria, and a family of penalized criteria with penalty function to be data driven calibrated.

Install the latest version of this package by entering the following in R:
install.packages("ClustMMDD")
AuthorWilson Toussile
Date of publication2016-05-30 20:26:19
MaintainerWilson Toussile <wilson.toussile@gmail.com>
LicenseGPL (>= 2)
Version1.0.4

View on CRAN

Man pages

backward.explorer: Gather a set of the most competitive models.

ClustMMDD-package: 'ClustMMDD' : Clustering by Mixture Models for Discrete Data.

cutEachCol: Retrieve data from strings in the dataset.

dataR2C: Transform a (normal) data frame to be compatible with...

dimJump.R: Data driven calibration of the penalty function

em.cluster.R: Compute estimates of the parameters by Expectation and...

EmOptions: Display the current Expectation and Maximization options.

exModelKS: An example of 'modelKS'.

genotype1: 'genotype1' is a data frame of genotype data with 'ploidy =...

genotype2: A genotype data frame compatible with 'ClustMMDD' main...

genotype2_ExploredModels: A data frame of competing models gathered by...

is.element-methods: Check if a 'modelKS' object is in a set of such objects.

isInFile.R: Find a model in a file.

is.modelKS-methods: Is an object from class 'modelKS'?

modelKS-class: 'modelKS' is a class of parameters of (K, S) model.

model-methods: Retrieve a list of model <=ft(K,S\right) from a 'modelKS'...

model.selection.R: Selection of both the number K of clusters and the subset S...

Rcpp_modules_examples: Functions and Objects created by Rcpp Modules Example

read.modelKS-methods: Read the parameters of a model <=ft(K,S\right) from a file.

read.or.compute: Read a given model from a file or compute the estimates of...

selectK.R: Selection of the number K of clusters.

setEmOptions: Set Expectation and Maximization options.

setModelKS-methods: Set an instance of class 'modelKS' from a list.

show-methods: 'show' method for an object of class 'modelKS'

simulData-methods: Simulate a dataset from a given set of parameters in an...

z==-methods: Methods for Function '=='

z[_--methods: Get or set a slot from 'modelKS'.

z[-methods: Get a slot from 'modelKS'.

Functions

== Man page
[ Man page
[<- Man page
backward.explorer Man page
bar Man page
bla Man page
bla1 Man page
bla2 Man page
ClustMMDD Man page
ClustMMDD-package Man page
C++Object-class Man page
cutEachCol Man page
dataR2C Man page
dimJump.R Man page
em.cluster.R Man page
EmOptions Man page
exModelKS Man page
foo Man page
genotype1 Man page
genotype2 Man page
genotype2_ExploredModels Man page
hello Man page
is.element Man page
is.element-methods Man page
is.element,modelKS,modelKS-method Man page
isInFile.R Man page
is.modelKS Man page
is.modelKS,ANY-method Man page
is.modelKS-methods Man page
==-methods Man page
[<--methods Man page
[-methods Man page
model Man page
==,modelKS,ANY-method Man page
modelKS-class Man page
[<-,modelKS-method Man page
[,modelKS-method Man page
model-methods Man page
model,modelKS-method Man page
model.selection.R Man page
Num Man page
Rcpp_Num-class Man page
Rcpp_vec-class Man page
Rcpp_World-class Man page
read.modelKS Man page
read.modelKS,character-method Man page
read.modelKS-methods Man page
read.or.compute Man page
selectK.R Man page
setEmOptions Man page
setModelKS,list-methods Man page
setModelKS-methods,list-methods Man page
show Man page
show-methods Man page
show,modelKS-method Man page
simulData Man page
simulData-methods Man page
simulData,modelKS,numeric,numeric-method Man page
vec Man page
World Man page

Files

inst
inst/CITATION
inst/exdata$data_ExploredModels.txt
inst/test
inst/test/stdVector.cpp
inst/test/rcpp_module.cpp
inst/test/genotype2_ExploredModels.txt
inst/test/exData$data_ExploredModels.txt
inst/test/par.txt
inst/test/tab$data_ExploredModels.txt
inst/test/test.R
inst/test/Num.cpp
inst/test/symbols.rds
inst/test/par
inst/test/Readme
src
src/ClustMMDD.cpp
src/macros.h
src/ClustMMDD.h
src/RcppExports.cpp
NAMESPACE
data
data/exModelKS.rda
data/genotype2.rda
data/genotype1.rda
data/genotype2_ExploredModels.rda
R
R/modelKS.R R/ClustMMDD.R R/RcppExports.R R/zzz.R
MD5
DESCRIPTION
man
man/is.element-methods.Rd man/dataR2C.Rd man/dimJump.R.Rd man/setModelKS-methods.Rd man/genotype2_ExploredModels.Rd man/read.modelKS-methods.Rd man/z[-methods.Rd man/is.modelKS-methods.Rd man/ClustMMDD-package.Rd man/exModelKS.Rd man/model.selection.R.Rd man/modelKS-class.Rd man/simulData-methods.Rd man/model-methods.Rd man/z[_--methods.Rd man/selectK.R.Rd man/z==-methods.Rd man/Rcpp_modules_examples.Rd man/genotype2.Rd man/em.cluster.R.Rd man/EmOptions.Rd man/setEmOptions.Rd man/read.or.compute.Rd man/cutEachCol.Rd man/backward.explorer.Rd man/genotype1.Rd man/isInFile.R.Rd man/show-methods.Rd

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