{
  "_id": "6a36cdd13efcd9bda4411235",
  "Package": "epifitter",
  "Type": "Package",
  "Title": "Analysis and Simulation of Plant Disease Progress Curves",
  "Version": "1.0.1",
  "Description": "Tools for analysis, visualization, and simulation of plant\ndisease progress curves. Includes functions to calculate\narea-under-the-curve summaries, fit and compare exponential,\nmonomolecular, logistic, and Gompertz models using linear or\nnonlinear regression, work with single or multiple epidemics,\nand produce 'ggplot2'-based visualizations. Also includes an\nexperimental powdery mildew dataset for reproducible teaching\nand research workflows. See Madden, Hughes, and van den Bosch\n(2007) <doi:10.1094/9780890545058> for background on the\nepidemiological methods.",
  "Authors@R": "c(\nperson(given = \"Kaique dos S.\",\nfamily = \"Alves\",\nrole = c(\"aut\", \"cre\"),\nemail = \"kaiquedsalves@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9187-0252\")),\nperson(given = \"Emerson M.\",\nfamily = \"Del Ponte\",\nrole = \"aut\",\nemail = \"delponte@ufv.br\",\ncomment = c(ORCID = \"0000-0003-4398-409X\")),\nperson(given = \"Adam H.\",\nfamily = \"Sparks\",\nrole = \"aut\",\nemail = \"adamhsparks@gmail.com\",\ncomment = c(\"ORCID\" = \"0000-0002-0061-8359\"))\n)",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Date": "2026-06-20",
  "URL": "https://github.com/AlvesKS/epifitter,\nhttps://alvesks.github.io/epifitter/",
  "BugReports": "https://github.com/AlvesKS/epifitter/issues",
  "Config/testthat/edition": "3",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev",
  "Repository": "https://alvesks.r-universe.dev",
  "Date/Publication": "2026-06-20 16:06:43 UTC",
  "RemoteUrl": "https://github.com/alvesks/epifitter",
  "RemoteRef": "HEAD",
  "RemoteSha": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-20 17:25:49 UTC",
    "User": "root"
  },
  "Author": "Kaique dos S. Alves [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9187-0252>),\nEmerson M. Del Ponte [aut] (ORCID:\n<https://orcid.org/0000-0003-4398-409X>),\nAdam H. Sparks [aut] (ORCID: <https://orcid.org/0000-0002-0061-8359>)",
  "Maintainer": "Kaique dos S. Alves <kaiquedsalves@gmail.com>",
  "MD5sum": "382b3eb904ae73456c9e50c8e2cf5fe3",
  "_user": "alvesks",
  "_type": "src",
  "_file": "epifitter_1.0.1.tar.gz",
  "_fileid": "131fae139806fa392bae6009116f75c183703b6262c8fcd44a63a3e98a55695b",
  "_filesize": 1266100,
  "_sha256": "131fae139806fa392bae6009116f75c183703b6262c8fcd44a63a3e98a55695b",
  "_created": "2026-06-20T17:25:49.000Z",
  "_published": "2026-06-20T17:28:49.703Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 82501956338,
      "time": 145,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7767362131"
    },
    {
      "job": 82501956360,
      "time": 148,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7767362369"
    },
    {
      "job": 82501956346,
      "time": 83,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7767355679"
    },
    {
      "job": 82501956332,
      "time": 78,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7767355123"
    },
    {
      "job": 82501677001,
      "time": 283,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7767346528"
    },
    {
      "job": 82501956359,
      "time": 121,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7767359694"
    },
    {
      "job": 82501956356,
      "time": 92,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7767356582"
    },
    {
      "job": 82501956354,
      "time": 86,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7767355971"
    },
    {
      "job": 82501956353,
      "time": 79,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7767355237"
    }
  ],
  "_buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/alvesks/epifitter",
  "_commit": {
    "id": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
    "author": "Kaique dos S. Alves <kai-quealves@hotmail.com>",
    "committer": "Kaique dos S. Alves <kai-quealves@hotmail.com>",
    "message": "Clarify confidence band interpretation\n",
    "time": 1781971603
  },
  "_maintainer": {
    "name": "Kaique dos S. Alves",
    "email": "kaiquedsalves@gmail.com",
    "orcid": "0000-0001-9187-0252"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "DescTools",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "minpack.lm",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "lemon",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "alvesks",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-11",
      "n": 2
    },
    {
      "week": "2026-15",
      "n": 2
    },
    {
      "week": "2026-25",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "alvesks",
      "count": 34,
      "uuid": 37162024
    },
    {
      "user": "adamhsparks",
      "count": 20,
      "uuid": 3195906
    }
  ],
  "_userbio": {
    "uuid": 37162024,
    "type": "user",
    "name": "Kaique S. Alves",
    "followers": 21,
    "description": "D.Sc in Plant Pathology"
  },
  "_downloads": {
    "count": 678,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epifitter"
  },
  "_devurl": "https://github.com/alvesks/epifitter",
  "_pkgdown": "https://alvesks.github.io/epifitter/",
  "_searchresults": 112,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/epifitter.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/alvesks/epifitter",
  "_realowner": "alvesks",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-10-29"
    },
    {
      "version": "0.2.0",
      "date": "2020-11-26"
    },
    {
      "version": "0.3.0",
      "date": "2021-06-14"
    },
    {
      "version": "1.0.0",
      "date": "2026-04-12"
    }
  ],
  "_exports": [
    "AUDPC",
    "AUDPC_2_points",
    "AUDPS",
    "expo_fun",
    "fit_lin",
    "fit_multi",
    "fit_nlin",
    "fit_nlin2",
    "gompi_fun",
    "logi_fun",
    "mono_fun",
    "plot_fit",
    "sim_exponential",
    "sim_gompertz",
    "sim_logistic",
    "sim_monomolecular"
  ],
  "_datasets": [
    {
      "name": "PowderyMildew",
      "title": "Powdery mildew disease progress curves in organic tomato",
      "object": "PowderyMildew",
      "class": [
        "data.frame"
      ],
      "fields": [
        "irrigation_type",
        "moisture",
        "block",
        "time",
        "sev"
      ],
      "rows": 240,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AUDPC",
      "title": "Area under the disease progress curve",
      "topics": [
        "AUDPC"
      ]
    },
    {
      "page": "AUDPC_2_points",
      "title": "Estimate AUDPC from two observations",
      "topics": [
        "AUDPC_2_points"
      ]
    },
    {
      "page": "AUDPS",
      "title": "Area under the disease progress stairs",
      "topics": [
        "AUDPS"
      ]
    },
    {
      "page": "expo_fun",
      "title": "Exponential model differential equation",
      "topics": [
        "expo_fun"
      ]
    },
    {
      "page": "fit_lin",
      "title": "Fit epidemic models using linearization",
      "topics": [
        "fit_lin"
      ]
    },
    {
      "page": "fit_multi",
      "title": "Fit models to multiple disease progress curves",
      "topics": [
        "fit_multi"
      ]
    },
    {
      "page": "fit_nlin",
      "title": "Fit epidemic models using nonlinear regression",
      "topics": [
        "fit_nlin"
      ]
    },
    {
      "page": "fit_nlin2",
      "title": "Fit epidemic models and estimate the asymptote",
      "topics": [
        "fit_nlin2"
      ]
    },
    {
      "page": "gompi_fun",
      "title": "Gompertz model differential equation",
      "topics": [
        "gompi_fun"
      ]
    },
    {
      "page": "logi_fun",
      "title": "Logistic model differential equation",
      "topics": [
        "logi_fun"
      ]
    },
    {
      "page": "mono_fun",
      "title": "Monomolecular model differential equation",
      "topics": [
        "mono_fun"
      ]
    },
    {
      "page": "plot_fit",
      "title": "Plot fitted epidemic models",
      "topics": [
        "plot_fit"
      ]
    },
    {
      "page": "PowderyMildew",
      "title": "Powdery mildew disease progress curves in organic tomato",
      "topics": [
        "PowderyMildew"
      ]
    },
    {
      "page": "print.fit_lin",
      "title": "Print fitted model summaries",
      "topics": [
        "print.fit_lin"
      ]
    },
    {
      "page": "print.fit_nlin2",
      "title": "Print fitted model summaries with asymptote estimates",
      "topics": [
        "print.fit_nlin2"
      ]
    },
    {
      "page": "sim_exponential",
      "title": "Simulate an exponential disease progress curve",
      "topics": [
        "sim_exponential"
      ]
    },
    {
      "page": "sim_gompertz",
      "title": "Simulate a Gompertz disease progress curve",
      "topics": [
        "sim_gompertz"
      ]
    },
    {
      "page": "sim_logistic",
      "title": "Simulate a logistic disease progress curve",
      "topics": [
        "sim_logistic"
      ]
    },
    {
      "page": "sim_monomolecular",
      "title": "Simulate a monomolecular disease progress curve",
      "topics": [
        "sim_monomolecular"
      ]
    }
  ],
  "_pkglogo": "https://github.com/alvesks/epifitter/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/alvesks/epifitter/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "bit",
    "bit64",
    "boot",
    "cellranger",
    "class",
    "cli",
    "clipr",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DescTools",
    "deSolve",
    "dplyr",
    "e1071",
    "Exact",
    "expm",
    "farver",
    "forcats",
    "fs",
    "generics",
    "ggplot2",
    "gld",
    "glue",
    "gtable",
    "haven",
    "hms",
    "httr",
    "isoband",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "lmom",
    "magrittr",
    "MASS",
    "Matrix",
    "mime",
    "minpack.lm",
    "mvtnorm",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "proxy",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "readxl",
    "rematch",
    "rlang",
    "rootSolve",
    "rstudioapi",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "model-fitting.Rmd",
      "filename": "model-fitting.html",
      "title": "Choosing and fitting disease progress models",
      "author": "Kaique S. Alves",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Compare models quickly with fit_lin()",
        "Nonlinear fitting with starting values",
        "Weighted nonlinear fitting",
        "Estimate K when the epidemic plateaus below 1",
        "Grouped fitting with fit_multi()",
        "Practical reporting"
      ],
      "created": "2026-04-11 21:42:11",
      "modified": "2026-06-20 15:35:04",
      "commits": 2
    },
    {
      "source": "powdery-mildew-data.Rmd",
      "filename": "powdery-mildew-data.html",
      "title": "Real-data workflow: powdery mildew in organic tomato",
      "author": "Kaique S. Alves",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Load the data",
        "Inspect the experimental structure",
        "Visualize treatment means over time",
        "Calculate AUDPC and AUDPS per experimental unit",
        "Fit a model to one observed curve",
        "Fit models to many observed curves at once",
        "Practical guidance",
        "Data source"
      ],
      "created": "2026-04-11 21:42:11",
      "modified": "2026-06-20 15:35:04",
      "commits": 2
    },
    {
      "source": "simulation-workflows.Rmd",
      "filename": "simulation-workflows.html",
      "title": "Simulation workflows for disease progress curves",
      "author": "Kaique S. Alves",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Simulate four canonical curve shapes",
        "Send simulated data into the fitting pipeline"
      ],
      "created": "2026-04-11 21:42:11",
      "modified": "2026-06-20 15:35:04",
      "commits": 2
    },
    {
      "source": "getting-started.Rmd",
      "filename": "getting-started.html",
      "title": "Start here: your first disease progress workflow",
      "author": "Kaique S. Alves",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What epifitter does",
        "A first epidemic",
        "Fit candidate models",
        "Visualize predictions",
        "Work with multiple epidemics",
        "Next steps"
      ],
      "created": "2026-04-11 21:42:11",
      "modified": "2026-06-20 15:35:04",
      "commits": 2
    },
    {
      "source": "area-under-curve.Rmd",
      "filename": "area-under-curve.html",
      "title": "Summarizing epidemics with AUDPC and AUDPS",
      "author": "Kaique S. Alves",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Build an example curve",
        "Compute AUDPC",
        "Multiple observations at the same time",
        "One summary curve versus one value per replicate",
        "Compute AUDPS",
        "Estimate AUDPC from two observations",
        "Absolute versus relative measures",
        "Practical guidance"
      ],
      "created": "2026-04-11 21:42:11",
      "modified": "2026-06-20 15:35:04",
      "commits": 2
    },
    {
      "source": "confidence-intervals.Rmd",
      "filename": "confidence-intervals.html",
      "title": "Uncertainty bands for fitted disease progress curves",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why add intervals?",
        "Example data",
        "Residual bootstrap confidence bands",
        "Wild bootstrap confidence bands",
        "Compare multiple models",
        "Nonlinear fits",
        "Choosing a method"
      ],
      "created": "2026-06-20 15:35:04",
      "modified": "2026-06-20 16:06:43",
      "commits": 2
    }
  ],
  "_score": 6.78161178249315,
  "_indexed": true,
  "_nocasepkg": "epifitter",
  "_universes": [
    "alvesks"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-20T17:28:12.000Z",
      "distro": "noble",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "7b60ebdf2491c1c5443b37f1f442d8cdbdfc263bdf74200f1314a4a48470579e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-20T17:28:14.000Z",
      "distro": "noble",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "9ef7328371cc0ad0c2bb4cbdec3ce883313d5963be9f8f16910e02acf0daac79",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-20T17:27:17.000Z",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "2edd44c08e114c0fec73a5a4f1cf95c24ba7e200b3ccb22a0b8c89240de3eba6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-20T17:27:12.000Z",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "091ef630006deaed838cd557547ec65ac3d26d694b3e2f53aa782384a4d898d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-06-20T17:28:10.000Z",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "b4eddbfe7a2d40dc5387f846e237e51ac4c853fc73021f7f4d9cee85ed34e971",
      "status": "success",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-20T17:27:11.000Z",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "29f0422f7002fabc8a125294180ea7276ed808a1cf1325953dc92404e37d4422",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-20T17:27:03.000Z",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "ed84cec75b049613ef78c42c19642cf127500fb9cc0dd93a8e537be8cc8190f6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-20T17:26:59.000Z",
      "commit": "597ca59e2cbce0c6ceccc9b31b8f57b586e11997",
      "fileid": "534a71b3ea65332901241baa991abc69055c2025b8919d5675e4a6cca282e18f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alvesks/actions/runs/27878397298"
    }
  ]
}