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  "Title": "Analysis of Plant Disease Epidemics",
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  "Authors@R": "c(\nperson(\"Christophe\", \"Gigot\", email = \"ch.gigot@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0002-1748-2902\")),\nperson(\"Adam H.\", \"Sparks\", role = \"ctb\"),\nperson(\"Katrin\", \"Leinweber\", role = \"ctb\")\n)",
  "Description": "A toolbox to make it easy to analyze plant disease\nepidemics. It provides a common framework for plant disease\nintensity data recorded over time and/or space. Implemented\nstatistical methods are currently mainly focused on spatial\npattern analysis (e.g., aggregation indices, Taylor and binary\npower laws, distribution fitting, SADIE and 'mapcomp' methods).\nSee Laurence V. Madden, Gareth Hughes, Franck van den Bosch\n(2007) <doi:10.1094/9780890545058> for further information on\nthese methods. Several data sets that were mainly published in\nplant disease epidemiology literature are also included in this\npackage.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/chgigot/epiphy,\nhttps://chgigot.github.io/epiphy/",
  "BugReports": "https://github.com/chgigot/epiphy/issues",
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  "Collate": "'RcppExports.R' 'betabinom.R' 'data.R' 'utils.R'\n'mle-factory.R' 'epiphy.R' 'intensity-classes.R'\n'distr-fitting.R' 'indices.R' 'mapcomp.R' 'power-law.R'\n'sadie.R' 'spatial-hier.R'",
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  "Repository": "https://chgigot.r-universe.dev",
  "Date/Publication": "2023-11-18 09:24:52 UTC",
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  "Packaged": {
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  "Author": "Christophe Gigot [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-1748-2902>),\nAdam H. Sparks [ctb],\nKatrin Leinweber [ctb]",
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    "count",
    "count_data",
    "dbetabinom",
    "fit_two_distr",
    "incidence",
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    "is.severity",
    "logit",
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    "mapped_var<-",
    "mapping",
    "mapping_",
    "pbetabinom",
    "power_law",
    "probit",
    "qbetabinom",
    "rbetabinom",
    "remap",
    "sadie",
    "severity",
    "severity_data",
    "smle",
    "smle_betabinom",
    "smle_binom",
    "smle_nbinom",
    "smle_pois",
    "spatial_hier",
    "sub2ind",
    "threshold",
    "z.test"
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      "title": "Counts of aphids.",
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        "y",
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        "ym",
        "i"
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      "table": true,
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        "i"
      ],
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      "table": true,
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    {
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      "title": "Incidence of citrus tristeza virus (CTV) disease in three fields.",
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      "class": [
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      ],
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Count of codling moth larvae.",
      "object": "codling_moths",
      "class": [
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      ],
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        "ym",
        "i"
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      "table": true,
      "tojson": true
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      ],
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        "i",
        "n"
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      "table": true,
      "tojson": true
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      "class": [
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      ],
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      "table": true,
      "tojson": true
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      "title": "Offspring survival of rats experiencing different diets.",
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        "n"
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      "table": true,
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      "title": "Easily switch between different power law formulations.",
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        "chisq.test.fisher"
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      "topics": [
        "citrus_ctv"
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    },
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      "title": "Regroup observational data into even clumps of individuals.",
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      "topics": [
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      "title": "Incidence of dogwood anthracnose.",
      "topics": [
        "dogwood_anthracnose"
      ]
    },
    {
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      "title": "Maximum likelihood fitting of two distributions and goodness-of-fit comparison.",
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        "fit_two_distr.count",
        "fit_two_distr.default",
        "fit_two_distr.incidence"
      ]
    },
    {
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      "title": "Incidence of three viruses in an Australian hop garden.",
      "topics": [
        "hop_viruses"
      ]
    },
    {
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      "title": "Construct count, incidence and severity objects.",
      "topics": [
        "count",
        "count_data",
        "incidence",
        "incidence_data",
        "intensity",
        "severity",
        "severity_data"
      ]
    },
    {
      "page": "is.intensity",
      "title": "Test if an object is of class 'intensity' or one of its subclasses.",
      "topics": [
        "is.count",
        "is.incidence",
        "is.intensity",
        "is.severity"
      ]
    },
    {
      "page": "link",
      "title": "Some link functions.",
      "topics": [
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        "link",
        "logit",
        "probit"
      ]
    },
    {
      "page": "mapcomp",
      "title": "Map Comparison procedure.",
      "topics": [
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        "mapcomp.count",
        "mapcomp.data.frame",
        "mapcomp.incidence",
        "mapcomp.matrix"
      ]
    },
    {
      "page": "mapped_var",
      "title": "Existing variable mappings.",
      "topics": [
        "mapped_var",
        "mapped_var<-"
      ]
    },
    {
      "page": "mapping",
      "title": "Construct data mappings.",
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        "mapping_",
        "remap"
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    {
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      "title": "Offspring survival of rats experiencing different diets.",
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      "title": "Taylor's and binary power laws.",
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      "topics": [
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    },
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      "title": "Spatial Analysis by Distance IndicEs (SADIE).",
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        "sadie.count",
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        "Conceptual framework",
        "Statistical methods",
        "Aggregation indices",
        "Distribution fitting",
        "Power law",
        "Spatial hierarchy",
        "Spatial Analysis by Distance IndicEs (SADIE)",
        "Map comparison (MAPCOMP)",
        "Conclusion",
        "Acknowledgments",
        "Annexes",
        "References"
      ],
      "created": "2018-05-12 06:47:32",
      "modified": "2018-05-20 08:05:16",
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      "filename": "defs-and-eqns.html",
      "title": "Definitions and relationships between parameters",
      "author": "Christophe Gigot",
      "engine": "knitr::rmarkdown",
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        "Variable definitions",
        "Parameters of the beta-binomial distribution",
        "Definitions",
        "Base relationships",
        "Parameters of the binary power law",
        "Two possible formulas for parametrization",
        "Relationship tables",
        "Relationship between beta-binomial and binary power law parameters",
        "References"
      ],
      "created": "2018-02-08 22:05:47",
      "modified": "2018-05-12 06:47:32",
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