Package: apcluster 1.4.13

apcluster: Affinity Propagation Clustering

Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <doi:10.1126/science.1136800>. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.

Authors:Ulrich Bodenhofer [aut, cre], Johannes Palme [ctb], Chrats Melkonian [ctb], Andreas Kothmeier [aut], Nikola Kostic [ctb]

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apcluster.pdf |apcluster.html✨
apcluster/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ubod/apcluster/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

9.74 score 9 stars 27 packages 284 scripts 2.7k downloads 20 mentions 21 exports 3 dependencies

Last updated 6 months agofrom:096bede013. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 23 2024
R-4.5-win-x86_64NOTEOct 23 2024
R-4.5-linux-x86_64NOTEOct 23 2024
R-4.4-win-x86_64OKOct 23 2024
R-4.4-mac-x86_64OKOct 23 2024
R-4.4-mac-aarch64OKOct 23 2024
R-4.3-win-x86_64OKOct 23 2024
R-4.3-mac-x86_64OKOct 23 2024
R-4.3-mac-aarch64OKOct 23 2024

Exports:aggExClusterapclusterapclusterDemoapclusterKapclusterLas.dendrogramas.DenseSimilarityMatrixas.hclustas.SparseSimilarityMatrixcorSimMatcutreeexpSimMatheatmaplabelslinKernellinSimMatnegDistMatplotpreferenceRangeshowsimilarity

Dependencies:latticeMatrixRcpp

An R Package for Affinity Propagation Clustering

Rendered fromapcluster.Rnwusingknitr::knitron Oct 23 2024.

Last update: 2024-04-26
Started: 2018-05-15

Readme and manuals

Help Manual

Help pageTopics
APCluster Packageapcluster-package
Exemplar-based Agglomerative ClusteringaggExCluster aggexcluster aggExCluster,character,ANY-method aggExCluster,function,ANY-method aggExCluster,Matrix,ExClust-method aggExCluster,matrix,ExClust-method aggExCluster,Matrix,missing-method aggExCluster,matrix,missing-method aggExCluster,missing,ExClust-method aggExCluster-methods
Class "AggExResult"AggExResult aggexresult AggExResult-class length,AggExResult-method similarity,AggExResult-method [,AggExResult,index,missing,missing-method [[,AggExResult,index,missing-method
Affinity Propagationapcluster apcluster,character,ANY-method apcluster,dgTMatrix,missing-method apcluster,function,ANY-method apcluster,Matrix,missing-method apcluster,matrix,missing-method apcluster,sparseMatrix,missing-method apcluster-methods
Affinity Propagation DemoapclusterDemo
Affinity Propagation for Pre-defined Number of ClustersapclusterK apclusterK,character,ANY-method apclusterK,dgTMatrix,missing-method apclusterK,function,ANY-method apclusterK,Matrix,missing-method apclusterK,matrix,missing-method apclusterK,sparseMatrix,missing-method apclusterK-methods
Leveraged Affinity PropagationapclusterL apclusterL,character,ANY-method apclusterL,function,ANY-method apclusterL,matrix,missing-method apclusterL-methods
Class "APResult"APResult apresult APResult-class length,APResult-method similarity similarity,APResult-method [,APResult,index,missing,missing-method [[,APResult,index,missing-method
Coercion of cluster hierarchiesas.dendrogram as.dendrogram,AggExResult-method as.dendrogram,ExClust-method as.hclust as.hclust,AggExResult-method as.hclust,ExClust-method
Conversions Between Dense and Sparse Similarity Matricesas.DenseSimilarityMatrix as.DenseSimilarityMatrix,Matrix-method as.DenseSimilarityMatrix,matrix-method as.DenseSimilarityMatrix,sparseMatrix-method as.DenseSimilarityMatrix-method as.SparseSimilarityMatrix as.SparseSimilarityMatrix,Matrix-method as.SparseSimilarityMatrix,matrix-method as.SparseSimilarityMatrix,sparseMatrix-method as.SparseSimilarityMatrix-methods conversions
Cut Out Clustering Level from Cluster Hierarchycutree cutree,AggExResult-method cutree,APResult-method cutree-methods
Class "ExClust"ExClust exclust ExClust-class length,ExClust-method similarity,ExClust-method [,ExClust,index,missing,missing-method [[,ExClust,index,missing-method
Plot Heatmapheatmap heatmap,AggExResult,matrix-method heatmap,AggExResult,missing-method heatmap,ExClust,Matrix-method heatmap,ExClust,matrix-method heatmap,ExClust,missing-method heatmap,ExClust,sparseMatrix-method heatmap,matrix,missing-method heatmap,missing,matrix-method heatmap-methods
Generate label vector from clustering resultlabels labels,APResult-method labels,ExClust-method labels-methods
Plot Clustering Resultsplot plot,AggExResult,data.frame-method plot,AggExResult,matrix-method plot,AggExResult,missing-method plot,APResult,missing-method plot,ExClust,data.frame-method plot,ExClust,matrix-method plot,ExClust,missing-method plot-methods
Determine Meaningful Ranges for Input PreferencespreferenceRange preferenceRange,dgTMatrix-method preferenceRange,Matrix-method preferenceRange,matrix-method preferenceRange,sparseMatrix-method preferenceRange-methods
Display Clustering Result Objectsshow show,AggExResult-method show,APResult-method show,ExClust-method show-methods
Methods for Computing Similarity MatricescorSimMat expSimMat linKernel linSimMat negDistMat similarities
Sort clusterssort sort,APResult-method sort,ExClust-method sort-methods