Package: rEMM 1.2.1

rEMM: Extensible Markov Model for Modelling Temporal Relationships Between Clusters

Implements TRACDS (Temporal Relationships between Clusters for Data Streams), a generalization of Extensible Markov Model (EMM). TRACDS adds a temporal or order model to data stream clustering by superimposing a dynamically adapting Markov Chain. 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>.

Authors:Michael Hahsler [aut, cre, cph], Margaret H. Dunham [ctb]

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

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

Peer review:

Bug tracker:https://github.com/mhahsler/remm/issues

Datasets:

On CRAN:

clusteringdata-streamsequence-analysis

4.49 score 1 stars 31 scripts 734 downloads 1 mentions 54 exports 34 dependencies

Last updated 3 months agofrom:a9c599d472. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winOKOct 26 2024
R-4.5-linuxOKOct 26 2024
R-4.4-winOKOct 26 2024
R-4.4-macOKOct 26 2024
R-4.3-winOKOct 26 2024
R-4.3-macOKOct 26 2024

Exports:as.graphas.graph.TRACDSas.igraphas.igraph.TRACDSbuildclustercluster_centerscluster_countsclusterscompactcopycurrent_stateDSC_EMMDSC_tNNEMMfadefind_clustersget_EMMinitial_transitionlast_clusteringmerge_clustersnclustersnstatesntransitionsobject.sizeplotpredictprunerare_clustersrare_transitionsrecluster_hclustrecluster_kmeansrecluster_pamrecluster_reachabilityrecluster_tNNrecluster_transitionsremove_clustersremove_selftransitionsremove_transitionsresetscoreset_EMMsizesmooth_transitionsstatessynthetic_streamtNNTRACTRACDStransitiontransition_matrixtransition_tabletransitionsupdate

Dependencies:BHclasscliclueclusterclusterGenerationcpp11dbscanDEoptimRdiptestflexmixfpcgenericsglueigraphkernlablatticelifecyclemagrittrMASSMatrixmclustmlbenchmodeltoolsnnetpkgconfigprabclusproxyRcpprlangrobustbaserpartstreamvctrs

Extensible Markov Model for data stream clustering

Rendered fromrEMM.Rnwusingutils::Sweaveon Oct 26 2024.

Last update: 2022-05-31
Started: 2021-10-26

Readme and manuals

Help Manual

Help pageTopics
Count Data for 16S rRNA Sequences16S Alphaproteobacteria16S Mollicutes16S
Building an EMM using New Databuild build,EMM,data.frame-method build,EMM,matrix-method build,EMM,numeric-method
Data stream clustering with tNNcluster cluster,tNN,data.frame-method cluster,tNN,matrix-method cluster,tNN,numeric-method
Combining EMM Objectsc c,EMM-method
Derwent Catchment DataDerwent
DSC Interface for EMM and tNN (package stream)DSC_EMM DSC_tNN get_EMM set_EMM
Creator for Class "EMM"EMM object.size,EMM-method
Class "EMM"copy copy,EMM-method EMM-class show,EMM-method size size,EMM-method
Synthetic Data to Demonstrate EMMsEMMsim EMMsim_sequence_test EMMsim_sequence_train EMMsim_test EMMsim_train
Hypothetical Traffic Data Set for EMMEMMTraffic
Fading Cluster Structure and EMM Layerfade fade,EMM,missing,missing-method fade,EMM,missing,numeric-method fade,EMM,numeric,missing-method fade,EMM,numeric,numeric-method
Find the EMM State/Cluster for an Observationfind_clusters find_clusters,tNN,data.frame-method find_clusters,tNN,matrix-method find_clusters,tNN,numeric-method
Merge States of an EMMmerge_clusters merge_clusters,EMM,character-method merge_clusters,EMM,integer-method
Visualize EMM Objectsplot plot,EMM,missing-method
Predict a Future Statepredict predict,TRACDS-method
Prune States and/or Transitionsprune prune,EMM-method rare_clusters rare_clusters,tNN-method rare_transitions rare_transitions,TRACDS-method
Reclustering EMM statesrecluster recluster_hclust recluster_hclust,EMM-method recluster_kmeans recluster_kmeans,EMM-method recluster_pam recluster_pam,EMM-method recluster_reachability recluster_reachability,EMM-method recluster_tNN recluster_tNN,EMM-method recluster_transitions recluster_transitions,EMM-method
Remove States/Clusters or Transitions from an EMMremove_clusters remove_clusters,EMM,character-method remove_selftransitions remove_selftransitions,EMM-method remove_transitions remove_transitions,EMM,character,character-method remove_transitions,EMM,matrix,missing-method
Score a New Sequence Given an EMMscore score,EMM,data.frame-method score,EMM,EMM-method score,EMM,matrix-method score,EMM,numeric-method
Smooths transition counts between neighboring states/clusterssmooth_transitions smooth_transitions,EMM-method
Create a Synthetic Data Streamsynthetic_stream
Class "tNN"clusters clusters,tNN-method cluster_centers cluster_centers,tNN-method cluster_counts cluster_counts,tNN-method copy,tNN-method last_clustering last_clustering,tNN-method nclusters nclusters,tNN-method object.size,tNN-method plot,tNN,missing-method StreamClustering-class tNN tNN-class
TRAC: Creating a Markov Model from a Regular ClusteringTRAC
Class "TRACDS"as.graph as.graph.TRACDS as.igraph as.igraph.TRACDS copy,TRACDS-method current_state current_state,TRACDS-method nstates nstates,TRACDS-method ntransitions ntransitions,TRACDS-method object.size,TRACDS-method plot,TRACDS,missing-method show,TRACDS-method states states,TRACDS-method TRACDS TRACDS-class transitions transitions,TRACDS-method
Access Transition Probabilities/Counts in an EMMinitial_transition initial_transition,TRACDS-method transition transition,TRACDS,character,character-method transition,TRACDS,data.frame,missing-method transition,TRACDS,matrix,missing-method transition_matrix transition_matrix,TRACDS-method
Extract a Transition Table for a New Sequence Given an EMMtransition_table transition_table,EMM,data.frame-method transition_table,EMM,matrix-method transition_table,EMM,numeric-method
Update a TRACDS temporal structure with new state assignementscompact compact,TRACDS-method reset reset,TRACDS-method update update,TRACDS-method