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'))

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.

7.31 score 5 stars 14 packages 364 scripts 2.7k downloads 62 mentions 21 exports 3 dependencies

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

Target	Result	Date
Doc / Vignettes	OK	Nov 21 2024
R-4.5-win	OK	Nov 21 2024
R-4.5-linux	OK	Nov 21 2024
R-4.4-win	OK	Nov 21 2024
R-4.4-mac	OK	Nov 21 2024
R-4.3-win	OK	Nov 21 2024
R-4.3-mac	OK	Nov 21 2024

Exports:annotationListToMatrix BHI BSI clusterMethods clusters clValid connectivity dunn getRanksWeights matchGO measNames measures nClusters optimalScores plot print readAnnotationFile show sota stability summary

Dependencies:class cluster MASS

clValid Overview

Rendered fromclValid.Rnwusingutils::Sweaveon Nov 21 2024.

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

Citation

Readme and manuals

Help Manual

Help page	Topics
Change annotation list to matrix	annotationListToMatrix
Biological Homogeneity Index	BHI
Biological Stability Index	BSI
Validate Cluster Results	clValid
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 Measure	connectivity
Dunn Index	dunn
Extract ranks and weights from clValid object	getRanksWeights
Mouse Mesenchymal Cells	mouse
Plot Function for a SOTA Object	plot.sota
Print Function for a SOTA Object	print.sota
Read in biological annotation files from external file	readAnnotationFile
Self-organizing Tree Algorithm (SOTA)	sota
Stability Measures	AD ADM APN FOM stability