{
  "_id": "6ad3d24d712795fb4dcafa21",
  "Package": "rEMM",
  "Version": "1.2.3",
  "Date": "2026-10-13",
  "Title": "Extensible Markov Model for Modelling Temporal Relationships\nBetween Clusters",
  "Authors@R": "c(person(\"Michael\", \"Hahsler\", role = c(\"aut\", \"cre\", \"cph\"),\nemail = \"mhahsler@lyle.smu.edu\",\ncomment = c(ORCID = \"0000-0003-2716-1405\")),\nperson(\"Margaret H.\", \"Dunham\", role = c(\"ctb\")))",
  "Description": "Implements TRACDS (Temporal Relationships between Clusters\nfor Data Streams), a generalization of the Extensible Markov\nModel (EMM). TRACDS adds a temporal or order model to data\nstream clustering by superimposing a dynamically adapting\nMarkov Chain. It also provides an implementation of EMM (TRACDS\non top of tNN data stream clustering). Development of this\npackage was supported in part by NSF IIS-0948893 and\nR21HG005912 from the National Human Genome Research Institute.\nHahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.",
  "Classification/ACM": "G.4, H.2.8, I.5.1",
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  "Repository": "https://mhahsler.r-universe.dev",
  "Date/Publication": "2026-10-17 17:42:47 UTC",
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  "Author": "Michael Hahsler [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-2716-1405>),\nMargaret H. Dunham [ctb]",
  "Maintainer": "Michael Hahsler <mhahsler@lyle.smu.edu>",
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  "_created": "2026-10-17T19:50:03.000Z",
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    "sequence-analysis"
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    "as.graph.TRACDS",
    "as.igraph",
    "as.igraph.TRACDS",
    "build",
    "cluster",
    "cluster_centers",
    "cluster_counts",
    "clusters",
    "compact",
    "copy",
    "current_state",
    "DSC_EMM",
    "DSC_tNN",
    "EMM",
    "fade",
    "find_clusters",
    "get_EMM",
    "initial_transition",
    "last_clustering",
    "merge_clusters",
    "nclusters",
    "nstates",
    "ntransitions",
    "object.size",
    "plot",
    "predict",
    "prune",
    "rare_clusters",
    "rare_transitions",
    "recluster_hclust",
    "recluster_kmeans",
    "recluster_pam",
    "recluster_reachability",
    "recluster_tNN",
    "recluster_transitions",
    "remove_clusters",
    "remove_selftransitions",
    "remove_transitions",
    "reset",
    "score",
    "set_EMM",
    "size",
    "smooth_transitions",
    "states",
    "synthetic_stream",
    "tNN",
    "TRAC",
    "TRACDS",
    "transition",
    "transition_matrix",
    "transition_table",
    "transitions",
    "update"
  ],
  "_datasets": [
    {
      "name": "Alphaproteobacteria16S",
      "title": "Count Data for 16S rRNA Sequences",
      "object": "16S",
      "file": "16S.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "aaa",
        "aac",
        "aag",
        "aat",
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        "caa",
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        "cat",
        "cca",
        "ccc",
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        "cgg",
        "cgt",
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        "ctc",
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        "ctt",
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        "tgt",
        "tta",
        "ttc",
        "ttg",
        "ttt"
      ],
      "rows": 456,
      "table": true,
      "tojson": true
    },
    {
      "name": "Derwent",
      "title": "Derwent Catchment Data",
      "object": "Derwent",
      "file": "Derwent.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Long Bridge",
        "Matlock Bath",
        "Chat Sworth",
        "What Stand Well",
        "Wye@Ashford",
        "Amber@Wind Field Park"
      ],
      "rows": 1918,
      "table": true,
      "tojson": true
    },
    {
      "name": "EMMsim_sequence_test",
      "title": "Synthetic Data to Demonstrate EMMs",
      "object": "EMMsim",
      "file": "EMMsim.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "EMMsim_sequence_train",
      "title": "Synthetic Data to Demonstrate EMMs",
      "object": "EMMsim",
      "file": "EMMsim.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "EMMsim_test",
      "title": "Synthetic Data to Demonstrate EMMs",
      "object": "EMMsim",
      "file": "EMMsim.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "x",
        "y"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "EMMsim_train",
      "title": "Synthetic Data to Demonstrate EMMs",
      "object": "EMMsim",
      "file": "EMMsim.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "x",
        "y"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "EMMTraffic",
      "title": "Hypothetical Traffic Data Set for EMM",
      "object": "EMMTraffic",
      "file": "EMMTraffic.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Loc_1",
        "Loc_2",
        "Loc_3",
        "Loc_4",
        "Loc_5",
        "Loc_6",
        "Loc_7"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "Mollicutes16S",
      "title": "Count Data for 16S rRNA Sequences",
      "object": "16S",
      "file": "16S.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "aaa",
        "aac",
        "aag",
        "aat",
        "aca",
        "acc",
        "acg",
        "act",
        "aga",
        "agc",
        "agg",
        "agt",
        "ata",
        "atc",
        "atg",
        "att",
        "caa",
        "cac",
        "cag",
        "cat",
        "cca",
        "ccc",
        "ccg",
        "cct",
        "cga",
        "cgc",
        "cgg",
        "cgt",
        "cta",
        "ctc",
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        "gac",
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        "gcc",
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        "ggc",
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        "tac",
        "tag",
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        "tca",
        "tcc",
        "tcg",
        "tct",
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        "tgt",
        "tta",
        "ttc",
        "ttg",
        "ttt"
      ],
      "rows": 479,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "rRNA16S",
      "title": "Count Data for 16S rRNA Sequences",
      "topics": [
        "16S",
        "Alphaproteobacteria16S",
        "Mollicutes16S",
        "rRNA16S"
      ]
    },
    {
      "page": "build",
      "title": "Building an EMM using New Data",
      "topics": [
        "build",
        "build,EMM,data.frame-method",
        "build,EMM,matrix-method",
        "build,EMM,numeric-method"
      ]
    },
    {
      "page": "cluster",
      "title": "Data stream clustering with tNN",
      "topics": [
        "cluster",
        "cluster,tNN,data.frame-method",
        "cluster,tNN,matrix-method",
        "cluster,tNN,numeric-method"
      ]
    },
    {
      "page": "combine",
      "title": "Combining EMM Objects",
      "topics": [
        "c",
        "c,EMM-method",
        "combine"
      ]
    },
    {
      "page": "Derwent",
      "title": "Derwent Catchment Data",
      "topics": [
        "Derwent"
      ]
    },
    {
      "page": "DSC_EMM",
      "title": "DSC Interface for EMM and tNN (package stream)",
      "topics": [
        "DSC_EMM",
        "DSC_tNN",
        "get_EMM",
        "set_EMM"
      ]
    },
    {
      "page": "EMM-class",
      "title": "Class \"EMM\"",
      "topics": [
        "copy",
        "copy,EMM-method",
        "EMM",
        "EMM-class",
        "object.size,EMM-method",
        "show,EMM-method",
        "size",
        "size,EMM-method"
      ]
    },
    {
      "page": "EMMsim",
      "title": "Synthetic Data to Demonstrate EMMs",
      "topics": [
        "EMMsim",
        "EMMsim_sequence_test",
        "EMMsim_sequence_train",
        "EMMsim_test",
        "EMMsim_train"
      ]
    },
    {
      "page": "EMMTraffic",
      "title": "Hypothetical Traffic Data Set for EMM",
      "topics": [
        "EMMTraffic"
      ]
    },
    {
      "page": "fade",
      "title": "Fading Cluster Structure and EMM Layer",
      "topics": [
        "fade",
        "fade,EMM,missing,missing-method",
        "fade,EMM,missing,numeric-method",
        "fade,EMM,numeric,missing-method",
        "fade,EMM,numeric,numeric-method"
      ]
    },
    {
      "page": "find_clusters",
      "title": "Find the EMM State/Cluster for an Observation",
      "topics": [
        "find_clusters",
        "find_clusters,tNN,data.frame-method",
        "find_clusters,tNN,matrix-method",
        "find_clusters,tNN,numeric-method"
      ]
    },
    {
      "page": "merge",
      "title": "Merge States of an EMM",
      "topics": [
        "merge_clusters",
        "merge_clusters,EMM,character-method",
        "merge_clusters,EMM,integer-method"
      ]
    },
    {
      "page": "plot.EMM",
      "title": "Visualize EMM Objects",
      "topics": [
        "plot",
        "plot,EMM,missing-method"
      ]
    },
    {
      "page": "predict",
      "title": "Predict a Future State",
      "topics": [
        "predict",
        "predict,TRACDS-method"
      ]
    },
    {
      "page": "prune",
      "title": "Prune States and/or Transitions",
      "topics": [
        "prune",
        "prune,EMM-method",
        "rare_clusters",
        "rare_clusters,tNN-method",
        "rare_transitions",
        "rare_transitions,TRACDS-method"
      ]
    },
    {
      "page": "recluster",
      "title": "Reclustering EMM states",
      "topics": [
        "recluster",
        "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"
      ]
    },
    {
      "page": "remove",
      "title": "Remove States/Clusters or Transitions from an EMM",
      "topics": [
        "remove",
        "remove_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"
      ]
    },
    {
      "page": "score",
      "title": "Score a New Sequence Given an EMM",
      "topics": [
        "score",
        "score,EMM,data.frame-method",
        "score,EMM,EMM-method",
        "score,EMM,matrix-method",
        "score,EMM,numeric-method"
      ]
    },
    {
      "page": "smooth_transitions",
      "title": "Smooths transition counts between neighboring states/clusters",
      "topics": [
        "smooth_transitions",
        "smooth_transitions,EMM-method"
      ]
    },
    {
      "page": "synthetic_stream",
      "title": "Create a Synthetic Data Stream",
      "topics": [
        "synthetic_stream"
      ]
    },
    {
      "page": "tNN-class",
      "title": "Class \"tNN\"",
      "topics": [
        "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"
      ]
    },
    {
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