hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("hopach")
AuthorKatherine S. Pollard, with Mark J. van der Laan <laan@stat.berkeley.edu> and Greg Wall
Bioconductor views Clustering
Date of publicationNone
MaintainerKatherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
LicenseGPL (>= 2)
Version2.34.0
http://www.stat.berkeley.edu/~laan/
http://docpollard.org/

View on Bioconductor

Functions

as.hdist Man page
as.hdist,matrix-method Man page
as.matrix,hdist-method Man page
as.vector,hdist-method Man page
as.vector,hdist,missing-method Man page
boot2fuzzy Man page
boothopach Man page
bootmedoids Man page
bootplot Man page
coerce,hdist,matrix-method Man page
coerce,matrix,hdist-method Man page
collap Man page
correlationordering Man page
cutdigits Man page
cutzeros Man page
digits Man page
dim,hdist-method Man page
dissabscor Man page
dissabscosangle Man page
disscor Man page
disscosangle Man page
disseuclid Man page
dissmatrix Man page
dissvector Man page
distancematrix Man page
distancevector Man page
dplot Man page
generic,as.vector,hdist-method Man page
golub Man page
golub.cl Man page
golub.gnames Man page
hdist Man page
hdist-class Man page
[,hdist-method Man page
hopach Man page
hopach2tree Man page
improveordering Man page
is.hdist Man page
labels,hdist-method Man page
labelstomss Man page
length,hdist-method Man page
makeoutput Man page
makeTree Man page
msscheck Man page
msscollap Man page
msscomplete Man page
mssinitlevel Man page
mssmulticollap Man page
mssnextlevel Man page
mssrundown Man page
msssplitcluster Man page
newnextlevel Man page
newsplitcluster Man page
nonzeros Man page
orderelements Man page
paircoll Man page
prune Man page
show,hdist-method Man page
silcheck Man page
vdissabscor Man page
vdissabscosangle Man page
vdissabseuclid Man page
vdisscor Man page
vdisscosangle Man page
vdisseuclid Man page
vectmatrix Man page

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