Package: ClusTorus 0.2.4

Seungki Hong

ClusTorus: Prediction and Clustering on the Torus by Conformal Prediction

Provides various tools of for clustering multivariate angular data on the torus. The package provides angular adaptations of usual clustering methods such as the k-means clustering, pairwise angular distances, which can be used as an input for distance-based clustering algorithms, and implements clustering based on the conformal prediction framework. Options for the conformal scores include scores based on a kernel density estimate, multivariate von Mises mixtures, and naive k-means clusters. Moreover, the package provides some basic data handling tools for angular data.

Authors:Sungkyu Jung [aut, cph], Seungki Hong [aut, cre], Kiho Park [ctb], Byungwon Kim [ctb]

ClusTorus_0.2.4.tar.gz
ClusTorus_0.2.4.zip(r-4.5)ClusTorus_0.2.4.zip(r-4.4)ClusTorus_0.2.4.zip(r-4.3)
ClusTorus_0.2.4.tgz(r-4.4-any)ClusTorus_0.2.4.tgz(r-4.3-any)
ClusTorus_0.2.4.tar.gz(r-4.5-noble)ClusTorus_0.2.4.tar.gz(r-4.4-noble)
ClusTorus_0.2.4.tgz(r-4.4-emscripten)ClusTorus_0.2.4.tgz(r-4.3-emscripten)
ClusTorus.pdf |ClusTorus.html✨
ClusTorus/json (API)

# Install 'ClusTorus' in R:
install.packages('ClusTorus', repos = c('https://sungkyujung.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sungkyujung/clustorus/issues

Datasets:
  • ILE - ILE: Structure of the Isoleucine
  • SARS_CoV_2 - SARS-CoV-2: chain B of Structure of the SARS-CoV-2 spike glycoprotein
  • data_6VXX - 6VXX: Structure of the SARS-CoV-2 spike glycoprotein
  • toydata1 - Toydata1: Labelled Data for 5 Clusters
  • toydata2 - Toydata2: Labelled Data for 3 Clusters

On CRAN:

19 exports 3 stars 1.03 score 63 dependencies 7 scripts 294 downloads

Last updated 2 years agofrom:617d57a6b9. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 10 2024
R-4.5-winNOTESep 10 2024
R-4.5-linuxNOTESep 10 2024
R-4.4-winNOTESep 10 2024
R-4.4-macNOTESep 10 2024
R-4.3-winNOTESep 10 2024
R-4.3-macNOTESep 10 2024

Exports:ang.distang.minusang.pdistclus.toruscluster.assign.toruscp.torus.kdeellip.kmeans.torusEMsinvMmixgrid.torushyperparam.alphahyperparam.Jhyperparam.torusicp.torusicp.torus.evalkde.toruskmeans.toruson.torustor.minuswtd.stat.ang

Dependencies:abindbackportsBAMBIbridgesamplingBrobdingnagcheckmateclicodacodetoolscolorspacecombinatcowplotcpp11digestdistributionalfansifarverfuturefuture.applygenericsggplot2globalsgluegtablegtoolsigraphisobandlabel.switchinglabelinglatticelifecyclelistenvloolpSolvemagrittrMASSMatrixmatrixStatsmgcvmunsellmvtnormnlmenumDerivparallellypillarpkgconfigposteriorpurrrqrngR6RColorBrewerRcppRcppArmadillorlangscalesstringistringrtensorAtibbleutf8vctrsviridisLitewithr

Introduction to ClusTorus

Seungki Hong

Rendered fromClusTorus.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2021-12-16
Started: 2021-01-20

Readme and manuals

Help Manual

Help pageTopics
Angular distanceang.dist
Angular subtractionang.minus
Pairwise L2 angular distanceang.pdist
Clustering on the torus by conformal predictionclus.torus plot.clus.torus
Clustering by connected components of ellipsoidscluster.assign.torus plot.cluster.obj
Conformal prediction set indices with kernel density estimationcp.torus.kde plot.cp.torus.kde
6VXX: Structure of the SARS-CoV-2 spike glycoprotein(closed state)data_6VXX
K-Means Clustering to K-Spheres Clustering on Torusellip.kmeans.torus
Fitting mixtures of bivariate von Mises distributionEMsinvMmix
Grid on torusgrid.torus
Selecting optimal level based on the runs of the number of clustershyperparam.alpha plot.hyperparam.alpha
Selecting optimal number of mixture components based on various criteriahyperparam.J plot.hyperparam.J
Selecting optimal hyperparameters for the conformal prediction sethyperparam.torus plot.hyperparam.torus
Conformity score for inductive prediction setsicp.torus logLik.icp.torus plot.icp.torus predict.icp.torus
Inductive prediction sets for each levelicp.torus.eval
ILE: Structure of the IsoleucineILE
Kernel density estimation using circular von Mises distributionkde.torus
K-Means Clustering on Toruskmeans.torus predict.kmeans.torus
Transform the angular data to be on principal intervalon.torus
SARS-CoV-2: chain B of Structure of the SARS-CoV-2 spike glycoprotein(closed state)SARS_CoV_2
Toroidal subtractiontor.minus
toydata1: Labelled Data for 5 Clusterstoydata1
toydata2: Labelled Data for 3 Clusterstoydata2
Weighted extrinsic mean direction and mean resultant lengthwtd.stat.ang