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

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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.

Author
Wilson Toussile
Date of publication
2016-05-30 20:26:19
Maintainer
Wilson Toussile <wilson.toussile@gmail.com>
License
GPL (>= 2)
Version
1.0.4

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'.

Files in this package

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