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.

Install the latest version of this package by entering the following in R:
install.packages("RPMM")
AuthorE. Andres Houseman, Sc.D. and Devin C. Koestler, Ph.D.
Date of publication2017-02-28 23:05:39
MaintainerE. Andres Houseman <eahouseman@gmail.com>
LicenseGPL (>= 2)
Version1.25

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

Functions

betaEst Man page
betaEstMultiple Man page
betaObjf Man page
blc Man page
blcInitializeSplitDichotomizeUsingMean Man page
blcInitializeSplitEigen Man page
blcInitializeSplitFanny Man page
blcInitializeSplitHClust Man page
blcSplit Man page
blcSplitCriterionBIC Man page
blcSplitCriterionBICICL Man page
blcSplitCriterionJustRecordEverything Man page
blcSplitCriterionLevelWtdBIC Man page
blcSplitCriterionLRT Man page
blcSubTree Man page
blcTree Man page
blcTreeApply Man page
blcTreeLeafClasses Man page
blcTreeLeafMatrix Man page
blcTreeOverallBIC Man page
ebayes Man page
gaussEstMultiple Man page
glc Man page
glcInitializeSplitEigen Man page
glcInitializeSplitFanny Man page
glcInitializeSplitHClust Man page
glcSplit Man page
glcSplitCriterionBIC Man page
glcSplitCriterionBICICL Man page
glcSplitCriterionJustRecordEverything Man page
glcSplitCriterionLevelWtdBIC Man page
glcSplitCriterionLRT Man page
glcSubTree Man page
glcTree Man page
glcTreeApply Man page
glcTreeLeafClasses Man page
glcTreeLeafMatrix Man page
glcTreeOverallBIC Man page
glmLC Man page
IllumBeta Man page
IlluminaMethylation Man page
llikeRPMMObject Man page
plot.blcTree Man page
plot.glcTree Man page
plotImage.blcTree Man page
plotImage.glcTree Man page
plotTree.blcTree Man page
plotTree.glcTree Man page
predict.blcTree Man page
predict.glcTree Man page
print.blcTree Man page
print.glcTree Man page
tissue Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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