Package: clValid 0.7

clValid: Validation of Clustering Results

Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) <doi:10.18637/jss.v025.i04>.

Authors:Guy Brock <[email protected]>, Vasyl Pihur <[email protected]>, Susmita Datta <[email protected]>, and Somnath Datta <[email protected]>

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clValid.pdf |clValid.html
clValid/json (API)

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

Peer review:

Datasets:
  • mouse - Mouse Mesenchymal Cells

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

21 exports 5 stars 5.61 score 3 dependencies 14 dependents 62 mentions 398 scripts 1.6k downloads

Last updated 4 years agofrom:92b8a8219f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-winOKAug 21 2024
R-4.5-linuxOKAug 21 2024
R-4.4-winOKAug 21 2024
R-4.4-macOKAug 21 2024
R-4.3-winOKAug 21 2024
R-4.3-macOKAug 21 2024

Exports:annotationListToMatrixBHIBSIclusterMethodsclustersclValidconnectivitydunngetRanksWeightsmatchGOmeasNamesmeasuresnClustersoptimalScoresplotprintreadAnnotationFileshowsotastabilitysummary

Dependencies:classclusterMASS

clValid Overview

Rendered fromclValid.Rnwusingutils::Sweaveon Aug 21 2024.

Last update: 2020-07-14
Started: 2014-03-24

Readme and manuals

Help Manual

Help pageTopics
Change annotation list to matrixannotationListToMatrix
Biological Homogeneity IndexBHI
Biological Stability IndexBSI
Validate Cluster ResultsclValid
Class "clValid"clusterMethods clusterMethods,clValid-method clusters clusters,clValid-method clValid-class clValidObj measNames measNames,clValid-method measures measures,clValid-method nClusters nClusters,clValid-method optimalScores optimalScores,clValid-method plot,clValid,missing-method print,clValid-method show,clValid-method summary,clValid-method
Connectivity Measureconnectivity
Dunn Indexdunn
Extract ranks and weights from clValid objectgetRanksWeights
Mouse Mesenchymal Cellsmouse
Plot Function for a SOTA Objectplot.sota
Print Function for a SOTA Objectprint.sota
Read in biological annotation files from external filereadAnnotationFile
Self-organizing Tree Algorithm (SOTA)sota
Stability MeasuresAD ADM APN FOM stability