Package: optpart 3.0-3

optpart: Optimal Partitioning of Similarity Relations

Contains a set of algorithms for creating partitions and coverings of objects largely based on operations on (dis)similarity relations (or matrices). There are several iterative re-assignment algorithms optimizing different goodness-of-clustering criteria. In addition, there are covering algorithms 'clique' which derives maximal cliques, and 'maxpact' which creates a covering of maximally compact sets. Graphical analyses and conversion routines are also included.

Authors:David W. Roberts <[email protected]>

optpart_3.0-3.tar.gz
optpart_3.0-3.zip(r-4.5)optpart_3.0-3.zip(r-4.4)optpart_3.0-3.zip(r-4.3)
optpart_3.0-3.tgz(r-4.4-x86_64)optpart_3.0-3.tgz(r-4.4-arm64)optpart_3.0-3.tgz(r-4.3-x86_64)optpart_3.0-3.tgz(r-4.3-arm64)
optpart_3.0-3.tar.gz(r-4.5-noble)optpart_3.0-3.tar.gz(r-4.4-noble)
optpart_3.0-3.tgz(r-4.4-emscripten)optpart_3.0-3.tgz(r-4.3-emscripten)
optpart.pdf |optpart.html✨
optpart/json (API)

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

Peer review:

Datasets:
  • shoshsite - Site Data for the Shoshone National Forest, Wyoming, USA
  • shoshveg - Vascular Plant Species Cover for the Shoshone National Forest, Wyoming, USA

On CRAN:

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

1.69 score 49 scripts 288 downloads 62 exports 10 dependencies

Last updated 5 years agofrom:31bff48200. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 31 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:archibestfitbestoptclassmatchcliqueclique.testclustifycompareconfusconsiderdisdiamdisdiam.defaultdisdiam.strideextractextract.strideflexbetagensilwidthgetsetsgetsets.msslambdamaxsimsetmergeclustmss.testmurdochneighboroptimclassoptindvaloptpartoptpart.defaultoptpart.strideoptsiloptsil.defaultoptsil.strideopttdevpartanapartana.defaultpartana.partitionpartana.stridepartitionphiplot.cliqueplot.murdochplot.partanaplot.strideprint.disdiamprint.murdochrefinereordclustsilhouette.clusteringsilhouette.partanasilhouette.strideslicestridesummary.cliquesummary.murdochsummary.partanasummary.tabdevtabdevtabdev.defaulttabdev.stridetestparttypal

Dependencies:clusterlabdsvlatticeMASSMatrixmgcvnlmeplotrixRcppRtsne

Readme and manuals

Help Manual

Help pageTopics
Archipelago Analysisarchi
Identify the Goodness-of-Fit of Cluster Membersbestfit
Best Of Set Optimal Partitions From Random Startsbestopt
Classification Matching and Differencingclassmatch
Maximal Clique Analysisclique plot.clique summary.clique
Clique Testclique.test
Clustering Objectclustering
Compare Species Constancy for Specified Clusterscompare
(Fuzzy) Confusion Matrixconfus fuzconfus
Recommendations for Possible Merging of Clustersconsider
Dissimilarity Diameters of a Partitiondisdiam disdiam.default disdiam.stride print.disdiam
Extract A Specific Cluster Solution From A Strideextract extract.stride
Calculate a Flexible-Beta Dendrogramflexbeta
Generalized Silhouette Widthgensilwidth
Goodman- Kruskal Lambda Index of Classification Associationlambda
Maximally Similar Sets Analysisgetsets getsets.mss maxpact maxsimset mss.test plot.mss
Merge Specified Clusters in a Classificationmergeclust
Indicator Species Analysis by Murdoch Preference Functionmurdoch plot.murdoch print.murdoch summary.murdoch
Neighbor Analysis of Partitionsneighbor
Optimum Classification by Counts of Indicator Speciesoptimclass
Optimizing Classification by Maximizing Dufrene and Legendre's Indicator Valueoptindval
Optimal Partitioning of Dissimilarity/Distance Matricesoptpart optpart.clustering optpart.default optpart.partana optpart.partition optpart.stride
Clustering by Optimizing Silhouette Widthsoptsil optsil.clustering optsil.default optsil.partana optsil.partition optsil.stride
Optimizing Classification by Minimizing Table Devianceopttdev
Partition Analysispartana partana.clustering partana.default partana.partition partana.stride plot.partana summary.partana
Convert Object to Partition Objectpartition partition.clustering partition.partana
Calculating the phi Statistic on Taxon Classificationsphi
Refining a Classification by Re-Assigning Membershipsrefine refine.default refine.dsvord refine.nmds refine.pco
Re-order Clusters in a Classificationreordclust
Site Data for the Shoshone National Forest, Wyoming, USAshoshsite
Vascular Plant Species Cover for the Shoshone National Forest, Wyoming, USAshoshveg
Produce a Silhouette Object From a Partana, Clustering, or Stride Objectsilhouette.clustering silhouette.partana silhouette.stride testsil
Slice a Hierarchical Clustering Dendrogram with a Mouseslice
Stride: Producing a Sequence of Clusteringsplot.stride stride
Classification Validity Assessment by Table Deviancesummary.tabdev tabdev tabdev.default tabdev.stride
Identify Misclassified Plots in a Partitiontestpart
Identification of Typal Samples in a Partitiontypal