RPMM: Recursively Partitioned Mixture Model

Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models.

Author
E. Andres Houseman, Sc.D. and Devin C. Koestler, Ph.D.
Date of publication
2014-09-14 07:22:44
Maintainer
E. Andres Houseman <andres.houseman@oregonstate.edu>
License
GPL (>= 2)
Version
1.20

View on CRAN

Man pages

betaEst
Beta Distribution Maximum Likelihood Estimator
betaEstMultiple
Beta Maximum Likelihood on a Matrix
betaObjf
Beta Maximum Likelihood Objective Function
blc
Beta Latent Class Model
blcInitializeSplitDichotomizeUsingMean
Initialize Gaussian Latent Class via Mean Dichotomization
blcInitializeSplitEigen
Initialize Gaussian Latent Class via Eigendecomposition
blcInitializeSplitFanny
Initialize Beta Latent Class via Fanny
blcInitializeSplitHClust
Initialize Beta Latent Class via Hierarchical Clustering
blcSplit
Beta Latent Class Splitter
blcSplitCriterionBIC
Beta RPMM Split Criterion: Use BIC
blcSplitCriterionBICICL
Beta RPMM Split Criterion: Use ICL-BIC
blcSplitCriterionJustRecordEverything
Beta RPMM Split Criterion: Always Split and Record Everything
blcSplitCriterionLevelWtdBIC
Beta RPMM Split Criterion: Level-Weighted BIC
blcSplitCriterionLRT
Beta RPMM Split Criterion: use likelihood ratio test p value
blcSubTree
Beta Subtree
blcTree
Beta RPMM Tree
blcTreeApply
Recursive Apply Function for Beta RPMM Objects
blcTreeLeafClasses
Posterior Class Assignments for Beta RPMM
blcTreeLeafMatrix
Posterior Weight Matrix for Beta RPMM
blcTreeOverallBIC
Overall BIC for Entire RPMM Tree (Beta version)
ebayes
Empirical Bayes predictions for a specific RPMM model
gaussEstMultiple
Gaussian Maximum Likelihood on a Matrix
glc
Gaussian Finite Mixture Model
glcInitializeSplitEigen
Initialize Gaussian Latent Class via Eigendecomposition
glcInitializeSplitFanny
Initialize Gaussian Latent Class via Fanny
glcInitializeSplitHClust
Initialize Gaussian Latent Class via Hierarchical Clustering
glcSplit
Gaussian Latent Class Splitter
glcSplitCriterionBIC
Gaussian RPMM Split Criterion: Use BIC
glcSplitCriterionBICICL
Gaussian RPMM Split Criterion: Use ICL-BIC
glcSplitCriterionJustRecordEverything
Gaussian RPMM Split Criterion: Always Split and Record...
glcSplitCriterionLevelWtdBIC
Gaussian RPMM Split Criterion: Level-Weighted BIC
glcSplitCriterionLRT
Gaussian RPMM Split Criterion: Use likelihood ratio test p...
glcSubTree
Gaussian Subtree
glcTree
Gaussian RPMM Tree
glcTreeApply
Recursive Apply Function for Gaussian RPMM Objects
glcTreeLeafClasses
Posterior Class Assignments for Gaussian RPMM
glcTreeLeafMatrix
Posterior Weight Matrix for Gaussian RPMM
glcTreeOverallBIC
Overall BIC for Entire RPMM Tree (Gaussian version)
glmLC
Weighted GLM for latent class covariates
IlluminaMethylation
DNA Methylation Data for Normal Tissue Types
llikeRPMMObject
Data log-likelihood implied by a specific RPMM model
plot.blcTree
Plot a Beta RPMM Tree Profile
plot.glcTree
Plot a Gaussian RPMM Tree Profile
plotImage.blcTree
Plot a Beta RPMM Tree Profile
plotImage.glcTree
Plot a Gaussian RPMM Tree Profile
plotTree.blcTree
Plot a Beta RPMM Tree Dendrogram
plotTree.glcTree
Plot a Gaussian RPMM Tree Dendrogram
predict.blcTree
Predict using a Beta RPMM object
predict.glcTree
Predict using a Gaussian RPMM object
print.blcTree
Print a Beta RPMM object
print.glcTree
Print a Gaussian RPMM object

Files in this package

RPMM
RPMM/NAMESPACE
RPMM/data
RPMM/data/IlluminaMethylation.RData
RPMM/R
RPMM/R/betaRPMM.R
RPMM/R/gaussRPMM.R
RPMM/R/rpmmPredict.R
RPMM/MD5
RPMM/DESCRIPTION
RPMM/man
RPMM/man/plotTree.glcTree.Rd
RPMM/man/glcSplit.Rd
RPMM/man/plotTree.blcTree.Rd
RPMM/man/betaEstMultiple.Rd
RPMM/man/print.glcTree.Rd
RPMM/man/blcSplit.Rd
RPMM/man/glcTreeLeafClasses.Rd
RPMM/man/glcInitializeSplitHClust.Rd
RPMM/man/glcTree.Rd
RPMM/man/blcSplitCriterionBICICL.Rd
RPMM/man/blcInitializeSplitFanny.Rd
RPMM/man/plotImage.blcTree.Rd
RPMM/man/glcTreeLeafMatrix.Rd
RPMM/man/plot.glcTree.Rd
RPMM/man/blcTree.Rd
RPMM/man/glmLC.Rd
RPMM/man/glcInitializeSplitEigen.Rd
RPMM/man/blcTreeApply.Rd
RPMM/man/blcSplitCriterionBIC.Rd
RPMM/man/glc.Rd
RPMM/man/ebayes.Rd
RPMM/man/gaussEstMultiple.Rd
RPMM/man/betaEst.Rd
RPMM/man/blcInitializeSplitHClust.Rd
RPMM/man/blcTreeOverallBIC.Rd
RPMM/man/glcInitializeSplitFanny.Rd
RPMM/man/glcSplitCriterionJustRecordEverything.Rd
RPMM/man/blcSubTree.Rd
RPMM/man/predict.glcTree.Rd
RPMM/man/blcTreeLeafClasses.Rd
RPMM/man/glcSplitCriterionLevelWtdBIC.Rd
RPMM/man/blc.Rd
RPMM/man/glcSplitCriterionBIC.Rd
RPMM/man/IlluminaMethylation.Rd
RPMM/man/blcInitializeSplitDichotomizeUsingMean.Rd
RPMM/man/glcSubTree.Rd
RPMM/man/llikeRPMMObject.Rd
RPMM/man/glcSplitCriterionBICICL.Rd
RPMM/man/glcTreeApply.Rd
RPMM/man/blcInitializeSplitEigen.Rd
RPMM/man/betaObjf.Rd
RPMM/man/blcTreeLeafMatrix.Rd
RPMM/man/glcSplitCriterionLRT.Rd
RPMM/man/plot.blcTree.Rd
RPMM/man/plotImage.glcTree.Rd
RPMM/man/blcSplitCriterionJustRecordEverything.Rd
RPMM/man/blcSplitCriterionLRT.Rd
RPMM/man/blcSplitCriterionLevelWtdBIC.Rd
RPMM/man/glcTreeOverallBIC.Rd
RPMM/man/predict.blcTree.Rd
RPMM/man/print.blcTree.Rd