{
  "_id": "6a1effa0b401979e7341aa98",
  "Package": "HMMHSMM",
  "Type": "Package",
  "Title": "Inference and Estimation of Hidden Markov Models and Hidden\nSemi-Markov Models",
  "Version": "0.1.0",
  "Authors@R": "c(person(\"Aimee\", \"Cody\", email = \"codai942@student.otago.ac.nz\", role = c(\"aut\")), person(\"Ting\", \"Wang\",email = \"ting.wang@otago.ac.nz\", role = c(\"cre\", \"ctb\"), comment = \"Research Supervisor\"))",
  "Maintainer": "Ting Wang <ting.wang@otago.ac.nz>",
  "Description": "Provides flexible maximum likelihood estimation and\ninference for Hidden Markov Models (HMMs) and Hidden\nSemi-Markov Models (HSMMs), as well as the underlying systems\nin which they operate. The package supports a wide range of\nobservation and dwell-time distributions, offering a flexible\nmodelling framework suitable for diverse practical data.\nEfficient implementations of the forward-backward and Viterbi\nalgorithms are provided via 'Rcpp' for enhanced computational\nperformance. Additional functionality includes model\nsimulation, residual analysis, non-initialised estimation,\nlocal and global decoding, calculation of diverse information\ncriteria, computation of confidence intervals using parametric\nbootstrap methods, numerical covariance matrix estimation, and\ncomprehensive visualisation functions for interpreting the\ndata-generating processes inferred from the models. Methods\nfollow standard approaches described by Guédon (2003)\n<doi:10.1198/1061860032030>, Zucchini and MacDonald (2009,\nISBN:9781584885733), and O'Connell and Højsgaard (2011)\n<doi:10.18637/jss.v039.i04>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-18 09:12:56 UTC",
    "User": "root"
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  "Author": "Aimee Cody [aut], Ting Wang [cre, ctb] (Research Supervisor)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-12-18 14:20:10 UTC",
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    "conditionalreturnsHMMgev",
    "conditionalreturnsHSMMgev",
    "confintHMM",
    "confintHSMM",
    "exceedanceplotHMMgev",
    "exceedanceplotHSMMgev",
    "findmleHMM",
    "findmleHMMnostarting",
    "findmleHSMM",
    "findmleHSMMnostarting",
    "generateHMM",
    "generateHSMM",
    "globaldecodeHMM",
    "globaldecodeHSMM",
    "HMMVarianceMatrix",
    "HSMMVarianceMatrix",
    "IC",
    "localdecodeHMM",
    "localdecodeHSMM",
    "plotHMMParameters",
    "plotHSMMParameters",
    "residualsHMM",
    "residualsHSMM"
  ],
  "_datasets": [
    {
      "name": "daily_maxima",
      "title": "Daily maxima of geomagnetic rate-of-change data from Eskdalemuir Magnetic Observatory",
      "object": "daily_maxima",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "weekly_maxima",
      "title": "Weekly maxima of geomagnetic rate-of-change data from Eskdalemuir Magnetic Observatory",
      "object": "weekly_maxima",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "conditionalreturnsHMMgev",
      "title": "Plot Conditional Return Levels from GEV-HMM",
      "topics": [
        "conditionalreturnsHMMgev"
      ]
    },
    {
      "page": "conditionalreturnsHSMMgev",
      "title": "Plot Conditional Return Levels from GEV-HSMM",
      "topics": [
        "conditionalreturnsHSMMgev"
      ]
    },
    {
      "page": "confintHMM",
      "title": "Bootstrap Confidence Intervals for Hidden Markov Models",
      "topics": [
        "confintHMM"
      ]
    },
    {
      "page": "confintHSMM",
      "title": "Bootstrap Confidence Intervals for Hidden Semi-Markov Models",
      "topics": [
        "confintHSMM"
      ]
    },
    {
      "page": "daily_maxima",
      "title": "Daily maxima of geomagnetic rate-of-change data from Eskdalemuir Magnetic Observatory",
      "topics": [
        "daily_maxima"
      ]
    },
    {
      "page": "exceedanceplotHMMgev",
      "title": "Plot Exceedance Probabilities from GEV-HMM",
      "topics": [
        "exceedanceplotHMMgev"
      ]
    },
    {
      "page": "exceedanceplotHSMMgev",
      "title": "Plot Exceedance Probabilities from GEV-HSMM",
      "topics": [
        "exceedanceplotHSMMgev"
      ]
    },
    {
      "page": "findmleHMM",
      "title": "Maximum Likelihood Estimation for Hidden Markov Models",
      "topics": [
        "findmleHMM"
      ]
    },
    {
      "page": "findmleHMMnostarting",
      "title": "Multiple Initialization Maximum Likelihood Estimation for Hidden Markov Models",
      "topics": [
        "findmleHMMnostarting"
      ]
    },
    {
      "page": "findmleHSMM",
      "title": "Maximum Likelihood Estimation for Hidden Semi-Markov Models",
      "topics": [
        "findmleHSMM"
      ]
    },
    {
      "page": "findmleHSMMnostarting",
      "title": "Fit Hidden Semi-Markov Model (HSMM) Without User-Provided Starting Values",
      "topics": [
        "findmleHSMMnostarting"
      ]
    },
    {
      "page": "generateHMM",
      "title": "Generate Data from a Hidden Markov Model",
      "topics": [
        "generateHMM"
      ]
    },
    {
      "page": "generateHSMM",
      "title": "Generate Data from a Hidden Semi-Markov Model",
      "topics": [
        "generateHSMM"
      ]
    },
    {
      "page": "globaldecodeHMM",
      "title": "Global Decoding for Hidden Markov Models",
      "topics": [
        "globaldecodeHMM"
      ]
    },
    {
      "page": "globaldecodeHSMM",
      "title": "Global Decoding of Hidden Semi-Markov Models",
      "topics": [
        "globaldecodeHSMM"
      ]
    },
    {
      "page": "HMMVarianceMatrix",
      "title": "Variance-Covariance Matrix for Hidden Markov Models",
      "topics": [
        "HMMVarianceMatrix"
      ]
    },
    {
      "page": "HSMMVarianceMatrix",
      "title": "Variance-Covariance Matrix for Hidden Semi-Markov Models",
      "topics": [
        "HSMMVarianceMatrix"
      ]
    },
    {
      "page": "IC",
      "title": "Calculate Information Criteria for HMM/HSMM Models",
      "topics": [
        "IC"
      ]
    },
    {
      "page": "localdecodeHMM",
      "title": "Local Decoding for Hidden Markov Models",
      "topics": [
        "localdecodeHMM"
      ]
    },
    {
      "page": "localdecodeHSMM",
      "title": "Local Decoding for Hidden Semi-Markov Models",
      "topics": [
        "localdecodeHSMM"
      ]
    },
    {
      "page": "plotHMMParameters",
      "title": "Plot Hidden Markov Model Parameters Over Time",
      "topics": [
        "plotHMMParameters"
      ]
    },
    {
      "page": "plotHSMMParameters",
      "title": "Plot Hidden Semi-Markov Model Parameters Over Time",
      "topics": [
        "plotHSMMParameters"
      ]
    },
    {
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      "title": "Ordinary Residuals for Hidden Markov Models",
      "topics": [
        "residualsHMM"
      ]
    },
    {
      "page": "residualsHSMM",
      "title": "Ordinary Residuals for Hidden Semi-Markov Models",
      "topics": [
        "residualsHSMM"
      ]
    },
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      "page": "weekly_maxima",
      "title": "Weekly maxima of geomagnetic rate-of-change data from Eskdalemuir Magnetic Observatory",
      "topics": [
        "weekly_maxima"
      ]
    }
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