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.

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

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

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