ADPclust: Fast Clustering Using Adaptive Density Peak Detection

An implementation of ADPclust clustering procedures (Fast Clustering Using Adaptive Density Peak Detection). The work is built and improved upon the idea of Rodriguez and Laio (2014)<DOI:10.1126/science.1242072>. ADPclust clusters data by finding density peaks in a density-distance plot generated from local multivariate Gaussian density estimation. It includes an automatic centroids selection and parameter optimization algorithm, which finds the number of clusters and cluster centroids by comparing average silhouettes on a grid of testing clustering results; It also includes a user interactive algorithm that allows the user to manually selects cluster centroids from a two dimensional "density-distance plot". Here is the research article associated with this package: "Wang, Xiao-Feng, and Yifan Xu (2015)<DOI:10.1177/0962280215609948> Fast clustering using adaptive density peak detection." Statistical methods in medical research". url: http://smm.sagepub.com/content/early/2015/10/15/0962280215609948.abstract.

Install the latest version of this package by entering the following in R:
install.packages("ADPclust")
AuthorYifan (Ethan) Xu [aut, cre], Xiao-Feng Wang [aut]
Date of publication2016-10-15 11:37:01
MaintainerYifan (Ethan) Xu <ethan.yifanxu@gmail.com>
LicenseGPL (>= 2)
Version0.7
https://github.com/ethanyxu/ADPclust

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Files

inst
inst/CITATION
inst/doc
inst/doc/ADPclust.Rmd
inst/doc/ADPclust.html
inst/doc/ADPclust.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test_FindCentersAutoV.R
tests/testthat/Rplots.pdf
tests/testthat/test_FindCentersAutoD.R tests/testthat/test_FindClustersGivenCenters.R tests/testthat/test_FindSilhouette.R
tests/testthat/clust3_test.RData
tests/testthat/2clust.RData
tests/testthat/test_FindH.R
tests/testthat/data_fd.RData
tests/testthat/test_FindDistm.R tests/testthat/test_summary.adpclust.R tests/testthat/test_FindClustersAuto.R tests/testthat/manual_test_plot.R tests/testthat/test_ADPclust.R tests/testthat/test_FindFD.R tests/testthat/test_IsDup.R tests/testthat/manual_test_FindClusterManual.R
NAMESPACE
data
data/dat_gene.RData
data/clust3.RData
data/clust10.RData
data/clust5.RData
data/clust5.1.RData
R
R/FindCentersAutoD.R R/FindCentersAutoV.R R/clust5.R R/dat_gene.R R/clust10.R R/clust5.1.R R/FindH.R R/FindDistm.R R/PickCenters.R R/FindClustersAuto.R R/ADPclust.R R/summary.adpclust.R R/FindFD.R R/plot.adpclust.R R/IsDup.R R/AMISE.R R/FindClustersManual.R R/ROT.R R/FindClustersGivenCenters.R R/FindSilhouette.R R/clust3.R R/defCol.R
vignettes
vignettes/ADPclust.Rmd
vignettes/manual.png
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/clust10.Rd man/FindH.Rd man/clust5.1.Rd man/ROT.Rd man/FindCentersAutoD.Rd man/FindCentersAutoV.Rd man/clust5.Rd man/clust3.Rd man/FindClustersManual.Rd man/dat_gene.Rd man/FindClustersGivenCenters.Rd man/FindFD.Rd man/FindClustersAuto.Rd man/AMISE.Rd man/plot.adpclust.Rd man/FindDistm.Rd man/summary.adpclust.Rd man/adpclust.Rd man/defCol.Rd

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