{
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  "Package": "mhsmm",
  "Type": "Package",
  "Title": "Inference for Hidden Markov and Semi-Markov Models",
  "Version": "0.4.21",
  "Date": "2023-08-21",
  "Author": "Jared O'Connell <jaredoconnell@gmail.com>, Søren Højsgaard\n<sorenh@math.aau.dk>",
  "Maintainer": "Jared O'Connell <jaredoconnell@gmail.com>",
  "Description": "Parameter estimation and prediction for hidden Markov and\nsemi-Markov models for data with multiple observation\nsequences.  Suitable for equidistant time series data, with\nmultivariate and/or missing data. Allows user defined emission\ndistributions.",
  "License": "GPL (>= 2)",
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  "Date/Publication": "2023-08-23 04:30:55 UTC",
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  "_rbuild": "4.6.0",
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    "extra/citation.html",
    "extra/citation.json",
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    "manual.pdf"
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      "date": "2009-03-02"
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      "date": "2017-01-15"
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    "addStates",
    "createTransition",
    "dmvnorm.hsmm",
    "dnorm.hsmm",
    "dpois.hsmm",
    "gammafit",
    "hmmfit",
    "hmmspec",
    "hsmmfit",
    "hsmmspec",
    "mstep.mvnorm",
    "mstep.norm",
    "mstep.pois",
    "plot.hsmm",
    "plot.hsmm.data",
    "predict.hmm",
    "predict.hmmspec",
    "predict.hsmm",
    "predict.hsmmspec",
    "predict.smoothDiscrete",
    "print.hmm",
    "print.hmmspec",
    "print.hsmmspec",
    "print.smoothDiscrete",
    "rmvnorm.hsmm",
    "rnorm.hsmm",
    "rpois.hsmm",
    "sim.mc",
    "simulate.hmmspec",
    "simulate.hsmmspec",
    "smooth.discrete",
    "summary.hmm",
    "summary.hsmm",
    "summary.smoothDiscrete"
  ],
  "_datasets": [
    {
      "name": "reproai",
      "title": "Artificial insemination times for seven cows",
      "object": "reproai",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "days.from.calving"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "reprocows",
      "title": "Reproductive data from seven dairy cows",
      "object": "reprocows",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "days.from.calving",
        "activity",
        "progesterone"
      ],
      "rows": 13040,
      "table": true,
      "tojson": true
    },
    {
      "name": "reproppa",
      "title": "Observed lengths of post-partum anoestrus for 73 dairy cows",
      "object": "reproppa",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addStates",
      "title": "Adds a bar representing state sequence.",
      "topics": [
        "addStates"
      ]
    },
    {
      "page": "dmvnorm.hsmm",
      "title": "Emission ensity function for a multivariate normal emission distribution",
      "topics": [
        "dmvnorm.hsmm"
      ]
    },
    {
      "page": "dnorm.hsmm",
      "title": "Emission density function for normal emission distribution",
      "topics": [
        "dnorm.hsmm"
      ]
    },
    {
      "page": "dpois.hsmm",
      "title": "Emission density function for Poisson emission distribution",
      "topics": [
        "dpois.hsmm"
      ]
    },
    {
      "page": "gammafit",
      "title": "Parameter estimation for the Gamma distribution",
      "topics": [
        "gammafit"
      ]
    },
    {
      "page": "hmmfit",
      "title": "fit a hidden Markov model",
      "topics": [
        "hmmfit"
      ]
    },
    {
      "page": "hmmspec",
      "title": "Specificatin of HMMs",
      "topics": [
        "hmmspec"
      ]
    },
    {
      "page": "hsmmfit",
      "title": "fit a hidden semi-Markov model",
      "topics": [
        "hsmmfit"
      ]
    },
    {
      "page": "hsmmspec",
      "title": "Hidden semi-Markov model specification",
      "topics": [
        "hsmmspec"
      ]
    },
    {
      "page": "mstep.mvnorm",
      "title": "Performs re-estimation (the M-step) for a multivariate normal emission distribution",
      "topics": [
        "mstep.mvnorm"
      ]
    },
    {
      "page": "mstep.norm",
      "title": "Performs re-estimation (the M-step) for a normal emission distribution",
      "topics": [
        "mstep.norm"
      ]
    },
    {
      "page": "mstep.pois",
      "title": "Performs re-estimation (the M-step) for a Poisson emission distribution",
      "topics": [
        "mstep.pois"
      ]
    },
    {
      "page": "plot.hsmm",
      "title": "Plot function for hsmms",
      "topics": [
        "plot.hsmm"
      ]
    },
    {
      "page": "plot.hsmm.data",
      "title": "Plot function for hsmm data",
      "topics": [
        "plot.hsmm.data"
      ]
    },
    {
      "page": "predict.hmm",
      "title": "Prediction function for hmm",
      "topics": [
        "predict.hmm"
      ]
    },
    {
      "page": "predict.hmmspec",
      "title": "Prediction function for hmmspec",
      "topics": [
        "predict.hmmspec"
      ]
    },
    {
      "page": "predict.hsmm",
      "title": "Prediction for hsmms",
      "topics": [
        "predict.hsmm"
      ]
    },
    {
      "page": "predict.hsmmspec",
      "title": "Prediction for hsmmspec",
      "topics": [
        "predict.hsmmspec"
      ]
    },
    {
      "page": "print.hmm",
      "title": "Print method for hmm objects",
      "topics": [
        "print.hmm"
      ]
    },
    {
      "page": "print.hmmspec",
      "title": "Print function for hmmspec",
      "topics": [
        "print.hmmspec"
      ]
    },
    {
      "page": "print.hsmmspec",
      "title": "Print function for hsmmspec",
      "topics": [
        "print.hsmmspec"
      ]
    },
    {
      "page": "reproai",
      "title": "Artificial insemination times for seven cows",
      "topics": [
        "reproai"
      ]
    },
    {
      "page": "reprocows",
      "title": "Reproductive data from seven dairy cows",
      "topics": [
        "reprocows"
      ]
    },
    {
      "page": "reproppa",
      "title": "Observed lengths of post-partum anoestrus for 73 dairy cows",
      "topics": [
        "reproppa"
      ]
    },
    {
      "page": "rmvnorm.hsmm",
      "title": "Random number generation from a multivariate normal distributed emission distribution",
      "topics": [
        "rmvnorm.hsmm"
      ]
    },
    {
      "page": "rnorm.hsmm",
      "title": "Random number generation from a normally distributed emission distribution",
      "topics": [
        "rnorm.hsmm"
      ]
    },
    {
      "page": "rpois.hsmm",
      "title": "Random number generation from a Poisson distributed emission distribution",
      "topics": [
        "rpois.hsmm"
      ]
    },
    {
      "page": "sim.mc",
      "title": "Markov chain simulation",
      "topics": [
        "sim.mc"
      ]
    },
    {
      "page": "simulate.hmmspec",
      "title": "Simulation of hidden Markov models",
      "topics": [
        "simulate.hmmspec"
      ]
    },
    {
      "page": "simulate.hsmmspec",
      "title": "Simulation for HSMMs",
      "topics": [
        "simulate.hsmmspec"
      ]
    },
    {
      "page": "smooth.discrete",
      "title": "Smoothing a discrete time series.",
      "topics": [
        "createTransition",
        "predict.smoothDiscrete",
        "print.smoothDiscrete",
        "smooth.discrete",
        "summary.smoothDiscrete"
      ]
    },
    {
      "page": "summary.hmm",
      "title": "Summary method for hmm objects",
      "topics": [
        "summary.hmm"
      ]
    },
    {
      "page": "summary.hsmm",
      "title": "Summary function for hsmm",
      "topics": [
        "summary.hsmm"
      ]
    }
  ],
  "_rundeps": [
    "mvtnorm"
  ],
  "_vignettes": [
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      "source": "DHMM1.Rnw",
      "filename": "DHMM1.pdf",
      "title": "Smoothing discrete data (I) - smooth.discrete()",
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      "created": "2012-09-03",
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      "headings": [],
      "created": "2012-09-03",
      "modified": "2023-08-23 04:30:55",
      "commits": 4
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  "_indexed": true,
  "_nocasepkg": "mhsmm",
  "_universes": [
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