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  "Date": "2026-03-31",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/davidearn/epigrowthfit",
  "BugReports": "https://github.com/davidearn/epigrowthfit/issues",
  "Title": "Nonlinear Mixed Effects Models of Epidemic Growth",
  "Description": "Maximum likelihood estimation of nonlinear mixed effects\nmodels of epidemic growth using Template Model Builder ('TMB').\nEnables joint estimation for collections of disease incidence\ntime series, including time series that describe multiple\nepidemic waves. Supports a set of widely used phenomenological\nmodels: exponential, logistic, Richards (generalized logistic),\nsubexponential, and Gompertz.  Provides methods for\ninterrogating model objects and several auxiliary functions,\nincluding one for computing basic reproduction numbers from\nfitted values of the initial exponential growth rate.\nPreliminary versions of this software were applied in Ma et al.\n(2014) <doi:10.1007/s11538-013-9918-2> and in Earn et al.\n(2020) <doi:10.1073/pnas.2004904117>.",
  "Authors@R": "c(person(\"Mikael\", \"Jagan\", role = c(\"aut\", \"cre\"),\nemail = \"jaganmn@mcmaster.ca\",\ncomment = c(ORCID = \"0000-0002-3542-2938\")),\nperson(\"Ben\", \"Bolker\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-2127-0443\")),\nperson(\"Jonathan\", \"Dushoff\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0506-4794\")),\nperson(\"David\", \"Earn\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3597-617X\")),\nperson(\"Junling\", \"Ma\", role = \"ctb\"))",
  "LazyData": "true",
  "Repository": "https://davidearn.r-universe.dev",
  "Date/Publication": "2026-03-31 22:55:12 UTC",
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  "Packaged": {
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    "User": "root"
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  "Author": "Mikael Jagan [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3542-2938>),\nBen Bolker [aut] (ORCID: <https://orcid.org/0000-0002-2127-0443>),\nJonathan Dushoff [ctb] (ORCID: <https://orcid.org/0000-0003-0506-4794>),\nDavid Earn [ctb] (ORCID: <https://orcid.org/0000-0003-3597-617X>),\nJunling Ma [ctb]",
  "Maintainer": "Mikael Jagan <jaganmn@mcmaster.ca>",
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  "_created": "2026-05-11T10:13:23.000Z",
  "_published": "2026-05-22T11:20:13.959Z",
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      ],
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        "cases",
        "tests"
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      "table": true,
      "tojson": true
    }
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      "title": "R Package 'epigrowthfit'",
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        "epigrowthfit"
      ]
    },
    {
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      "title": "Extract Coefficients and Random Effect Covariance Parameters",
      "topics": [
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        "coef.egf",
        "coef.egf_no_fit",
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        "plot.confint.egf"
      ]
    },
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        "theta2cov"
      ]
    },
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      "title": "COVID-19 in Ontario, Canada",
      "topics": [
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    },
    {
      "page": "df.residual.egf",
      "title": "Extract the Residual Degrees of Freedom",
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        "df.residual.egf_no_fit"
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    },
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      "title": "Fit Nonlinear Mixed Effects Models of Epidemic Growth",
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        "egf.egf_model"
      ]
    },
    {
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      "title": "Define Control Parameters",
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    },
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    {
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      "title": "Define an Optimization Method",
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        "InverseWishart",
        "LKJ",
        "Normal",
        "Wishart"
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    },
    {
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      "title": "Top Level Nonlinear Model Parameter Names",
      "topics": [
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        "egf_top.egf",
        "egf_top.egf_model",
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      "title": "Fit Nonlinear Models of Epidemic Growth",
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        "egf1scan"
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      "title": "Not Yet Implemented Functions in Package 'epigrowthfit'",
      "topics": [
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    },
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      "topics": [
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      "topics": [
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        "fitted.egf",
        "fitted.egf_no_fit"
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      "title": "Extract Model Formulae",
      "topics": [
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    },
    {
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      "title": "Extract Model Calls",
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      "page": "plot.egf",
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      "topics": [
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        "predict.egf"
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      "title": "Univariate Likelihood Profiles",
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        "profile.egf"
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      "topics": [
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        "ranef.egf_no_fit"
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