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.

AuthorE. Andres Houseman, Sc.D. and Devin C. Koestler, Ph.D.
Date of publication2014-09-14 07:22:44
MaintainerE. Andres Houseman <andres.houseman@oregonstate.edu>
LicenseGPL (>= 2)
Version1.20

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

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