dbscan - Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms
A fast reimplementation of several density-based algorithms of the DBSCAN family. Includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering points to identify the clustering structure), shared nearest neighbor clustering, and the outlier detection algorithms LOF (local outlier factor) and GLOSH (global-local outlier score from hierarchies). The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided. Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.
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clusteringdbscandensity-based-clusteringhdbscanlofopticscpp
16.83 score 354 stars 126 dependents 3.2k scripts 40k downloads
seriation - Infrastructure for Ordering Objects Using Seriation
Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
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combinatorial-optimizationordinationseriation
15.11 score 87 stars 100 dependents 956 scripts 38k downloads
arules - Mining Association Rules and Frequent Itemsets
Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
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arulesassociation-rulesfrequent-itemsets
14.94 score 195 stars 33 dependents 4.4k scripts 16k downloads
TSP - Infrastructure for the Traveling Salesperson Problem
Basic infrastructure and some algorithms for the traveling salesperson problem (also traveling salesman problem; TSP). The package provides some simple algorithms and an interface to the Concorde TSP solver and its implementation of the Chained-Lin-Kernighan heuristic. The code for Concorde itself is not included in the package and has to be obtained separately. Hahsler and Hornik (2007) <doi:10.18637/jss.v023.i02>.
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concorde-tsp-solvertsp
13.33 score 70 stars 116 dependents 430 scripts 40k downloads
arulesViz - Visualizing Association Rules and Frequent Itemsets
Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration. Michael Hahsler (2017) <doi:10.32614/RJ-2017-047>.
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arulesassociation-rulesfrequent-itemsetsinteractive-visualizationsvisualization
11.26 score 56 stars 2 dependents 2.1k scripts 8.6k downloads
recommenderlab - Lab for Developing and Testing Recommender Algorithms
Provides a research infrastructure to develop and evaluate collaborative filtering recommender algorithms. This includes a sparse representation for user-item matrices, many popular algorithms, top-N recommendations, and cross-validation. Hahsler (2022) <doi:10.48550/arXiv.2205.12371>.
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collaborative-filteringrecommender-system
10.77 score 216 stars 3 dependents 1.1k scripts 895 downloads
stream - Infrastructure for Data Stream Mining
A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
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data-stream-clusteringdatastreamstream-miningcpp
9.97 score 41 stars 3 dependents 222 scripts 1.9k downloadsrBLAST - R Interface for the Basic Local Alignment Search Tool
Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
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geneticssequencingsequencematchingalignmentmultiplesequencealignmentdataimportbioconductorbioinformaticsblast-search
8.35 score 115 stars 1 dependents 143 scripts 469 downloadsrBLAST - R Interface for the Basic Local Alignment Search Tool
Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) running locally to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
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geneticssequencingsequencematchingalignmentmultiplesequencealignmentdataimportbioconductorbioinformaticsblast-search
8.35 score 115 stars 1 dependents 143 scripts
qap - Heuristics for the Quadratic Assignment Problem (QAP)
Implements a simulated annealing heuristic for the Quadratic Assignment Problem (QAP). Originally formulated as a facility location problem in operations research, the QAP also has applications in data analysis. The problem is NP-hard.
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combinatorial-optimizationheuristicqapquadratic-assignment-problem
7.89 score 6 stars 103 dependents 11 scripts 38k downloads
pomdp - Infrastructure for Partially Observable Markov Decision Processes (POMDP)
Provides the infrastructure to define and analyze solutions to Partially Observable Markov Decision Process (POMDP) models. Interfaces to various exact and approximate solution algorithms are available, including value iteration, point-based value iteration, and SARSOP. Hahsler and Cassandra <doi:10.32614/RJ-2024-021>.
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control-theorymarkov-decision-processesoptimizationcpp
7.09 score 22 stars 31 scripts 622 downloads
pmml - Generate PMML for Various Models
The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <https://dmg.org/>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products.
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interoperabilitymachine-learning-modelspmml
6.85 score 1 stars 602 scripts 1.3k downloads
streamMOA - Interface for MOA Stream Clustering Algorithms
Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework (Albert Bifet, Geoff Holmes, Richard Kirkby, Bernhard Pfahringer (2010). MOA: Massive Online Analysis, Journal of Machine Learning Research 11: 1601-1604).
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clusteringdataminingdatastreamopenjdk
6.61 score 13 stars 26 scripts 409 downloads
arulesCBA - Classification Based on Association Rules
Provides the infrastructure for association rule-based classification including the algorithms CBA, CMAR, CPAR, C4.5, FOIL, PART, PRM, RCAR, and RIPPER to build associative classifiers. Hahsler et al (2019) <doi:10.32614/RJ-2019-048>.
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association-rulesclassification
6.43 score 4 stars 1 dependents 56 scripts 1.3k downloads
rEMM - Extensible Markov Model for Modelling Temporal Relationships Between Clusters
Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of the Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. It also provides an implementation of EMM (TRACDS on top of tNN data stream clustering). Development of this package was supported in part by NSF IIS-0948893 and R21HG005912 from the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
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clusteringdata-streamsequence-analysis
5.52 score 2 stars 41 scripts 548 downloadsarulesSequences - Mining Frequent Sequences
Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
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4.91 score 10 stars 5 dependents 143 scripts 1.3k downloadscba - Clustering for Business Analytics
Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
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4.78 score 3 dependents 201 scripts 3.7k downloads
arulesNBMiner - Mining NB-Frequent Itemsets and NB-Precise Rules
NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets and NB-precise rules. Michael Hahsler (2006) <doi:10.1007/s10618-005-0026-2>.
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association-rulesopenjdk
4.78 score 6 stars 9 scripts 517 downloadsrRDP - Interface to the RDP Classifier
This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained.
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geneticssequencinginfrastructureclassificationmicrobiomeimmunooncologyalignmentsequencematchingdataimportbayesianbioconductorbioinformaticsopenjdk
4.24 score 3 stars 23 scripts
markovDP - Infrastructure for Discrete-Time Markov Decision Processes (MDP)
Provides the infrastructure to work with Markov Decision Processes (MDPs) in R. The focus is on convenience in formulating MDPs, the support of sparse representations (using sparse matrices, lists and data.frames) and visualization of results. Some key components are implemented in C++ to speed up computation. Several popular solvers are implemented.
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control-theorymarkov-decision-processoptimizationcpp
4.15 score 7 stars
pomdpSolve - Interface to 'pomdp-solve' for Partially Observable Markov Decision Processes
Installs an updated version of 'pomdp-solve' and provides a low-level interface. Pomdp-solve is a program to solve Partially Observable Markov Decision Processes (POMDPs) using a variety of exact and approximate value iteration algorithms. A convenient R infrastructure is provided in the separate package pomdp. Hahsler and Cassandra <doi:10.32614/RJ-2024-021>.
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control-theorymarkov-decision-processesoptimization
3.95 score 2 stars 1 dependents 2 scripts 591 downloadsrMSA - Interface for Popular Multiple Sequence Alignment Tools
Seamlessly interfaces the Multiple Sequence Alignment software packages ClustalW, MAFFT, MUSCLE and Kalign (downloaded separately) and provides support to calcualte distances between sequences. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
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geneticssequencinginfrastructurealignmentbioinformaticssequence-alignment
3.78 score 12 stars 8 scripts
streamConnect - Connecting Stream Mining Components Using Sockets and Web Services
Adds functionality to connect stream mining components from the stream package using sockets and Web services. The package can be used to create distributed workflows and plumber-based Web services that can be deployed on most common cloud services.
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3.30 score 4 stars 1 scripts 22 downloads
recommenderlabJester - Jester Dataset for 'recommenderlab'
Provides the Jester Dataset for package recommenderlab.
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recommender-systems
2.70 score 2 scripts 248 downloads
recommenderlabBX - Book-Crossing Dataset (BX) for 'recommenderlab'
Provides the Book-Crossing Dataset for the package recommenderlab.
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recommender-systems
2.70 score 1 scripts 261 downloads