BHC: Bayesian Hierarchical Clustering

The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.

Author
Rich Savage, Emma Cooke, Robert Darkins, Yang Xu
Date of publication
None
Maintainer
Rich Savage <r.s.savage@warwick.ac.uk>
License
GPL-3
Version
1.26.0

View on Bioconductor

Man pages

BHC
Function to perform Bayesian Hierarchical Clustering on a 2D...

Files in this package

BHC/DESCRIPTION
BHC/NAMESPACE
BHC/R
BHC/R/ConstructDendrogramObject.R
BHC/R/DiscretiseData.R
BHC/R/FindOptimalBinning.R
BHC/R/FindOptimalHyperparameter.R
BHC/R/RunBhcWrapper.R
BHC/R/WriteOutClusterLabels.R
BHC/R/bhc.R
BHC/build
BHC/build/vignette.rds
BHC/configure
BHC/configure.ac
BHC/inst
BHC/inst/doc
BHC/inst/doc/bhc.R
BHC/inst/doc/bhc.Rnw
BHC/inst/doc/bhc.pdf
BHC/man
BHC/man/BHC.Rd
BHC/src
BHC/src/BlockCovarianceMatrix.cpp
BHC/src/BlockCovarianceMatrix.h
BHC/src/CubicSplineTimecourseDataSet.cpp
BHC/src/CubicSplineTimecourseDataSet.h
BHC/src/DataSet.cpp
BHC/src/DataSet.h
BHC/src/DirichletProcessMixture.cpp
BHC/src/DirichletProcessMixture.h
BHC/src/Makevars
BHC/src/Makevars.in
BHC/src/MultinomialDataSet.cpp
BHC/src/MultinomialDataSet.h
BHC/src/Node.cpp
BHC/src/Node.h
BHC/src/RobustCubicSplineTimecourseDataSet.cpp
BHC/src/RobustCubicSplineTimecourseDataSet.h
BHC/src/RobustSquaredExponentialTimecourseDataSet.cpp
BHC/src/RobustSquaredExponentialTimecourseDataSet.h
BHC/src/SquaredExponentialTimecourseDataSet.cpp
BHC/src/SquaredExponentialTimecourseDataSet.h
BHC/src/TimecourseDataSet.cpp
BHC/src/TimecourseDataSet.h
BHC/src/bhc.cpp
BHC/src/gammaln.cpp
BHC/src/gammaln.h
BHC/src/header.cpp
BHC/src/header.h
BHC/src/multinomial_CalculateHyperparameters.cpp
BHC/src/multinomial_OutputDendrogramInformation.cpp
BHC/src/multinomial_ReadInData.cpp
BHC/src/multinomial_bayeslink_binf.cpp
BHC/src/multinomial_binevidence.cpp
BHC/src/multinomial_header.h
BHC/vignettes
BHC/vignettes/bhc.Rnw