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.

Author
Yifan (Ethan) Xu [aut, cre], Xiao-Feng Wang [aut]
Date of publication
2016-10-15 11:37:01
Maintainer
Yifan (Ethan) Xu <ethan.yifanxu@gmail.com>
License
GPL (>= 2)
Version
0.7
URLs

View on CRAN

Man pages

adpclust
Fast Clustering Using Adaptive Density Peak Detection
AMISE
AMISE bandwidth
clust10
1000 5-dimensional data points that form ten clusters
clust3
90 2-dimensional data points that form three clusters
clust5
500 5-dimensional data points that form five clusters
clust5.1
500 5-dimensional data points that form five clusters
dat_gene
243-dimensional gene expression data of 38 patients (243...
defCol
Default colors
FindCentersAutoD
Automatically finds centers with diagonal f(x) vs delta(x)...
FindCentersAutoV
Automatically find centers with vertical threshold
FindClustersAuto
Automatically find cluster assignment given f and delta.
FindClustersGivenCenters
Find cluster assignments given centers and distance matrix
FindClustersManual
User-interactive routine to find clusters
FindDistm
Find the distance matrix from data.
FindFD
Find f and delta from distance matrix.
FindH
Find bandwidth h.
plot.adpclust
Visualize the result of adpclust()
ROT
Calculate ROT bandwidth
summary.adpclust
Summary of adpclust

Files in this package

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