Type: Package
Package: epicrop
Title: SEIR Simulation Modelling of Crop Diseases
Version: 1.0.0
Authors@R: c(
    person("Adam H.", "Sparks", , "adamhsparks@gmail.com", role = c("cre", "aut"),
           comment = c(ORCID = "0000-0002-0061-8359")),
    person("Robert", "Hijmans", , "robert.hijmans@gmail.com", role = c("aut", "trl", "cph"),
           comment = c("Original R implementation", ORCID = "0000-0001-5872-2872")),
    person("Serge", "Savary", , "ssavary01@gmail.com", role = c("aut", "ccp", "cph"),
           comment = c("Model conception and development in Stella", ORCID = "0000-0002-6867-180X")),
    person("Ireno", "Pangga", , "ibpangga@yahoo.com", role = c("aut", "trl", "cph"),
           comment = "Model conception, development in Stella and original R\n           implementation"),
    person("Jorrel", "Aunario", , "j.aunario@cgiar.org", role = c("aut", "trl", "cph"),
           comment = "Original R implementation"),
    person("Kwang-Hyung", "Kim", , "sospicy77@gmail.com", role = c("aut", "cph"),
           comment = "Contributed code for modified Kim leaf blast and sheath blight functions and feedback on the implementation."),
    person("Aji", "Sukarta", , "aji.ixb@gmail.com", role = "ctb",
           comment = "Helped fix bug related to SEIR model and establishment\n           date"),
    person("Emerson", "Del Ponte", , "delponte@ufv.br", role = "aut",
           comment = c("Provided code for fetching era5 code via the 'r4pde' package and suggested fixes for several typos in the documentation", ORCID = "0000-0003-4398-409X"))
  )
Description: Generic simulation modelling of crop diseases using a
        Susceptible-Exposed-Infectious-Removed ('SEIR') model.  This
        type of model was first described in botanical epidemiology by
        Zadoks (1971) <doi:10.1094/Phyto-61-600> and implemented in the
        'EPIRICE' model by Savary et al. (2012)
        <doi:10.1016/j.cropro.2011.11.009> detailing the model's
        development, use and results from modelling global unmanaged
        epidemics of rice diseases for five major rice diseases,
        bacterial blight, brown spot, leaf blast, sheath blight and
        tungro.  Specific functions are provided to simulate all of
        these diseases with a generic 'SEIR' model function that is
        suitable for parameterising for use with other pathosystems as
        demonstrated in Savary et al. 2012 and Kim et al. 2015
        <doi:10.1016/j.agrformet.2015.01.011> along with two wheat
        diseases, brown (leaf) rust and Septoria tritici blotch as
        published in Savary et al. 2015
        <doi:10.1007/s10658-015-0650-7>. Based on a fork of the
        `cropsim` package that only provided the EPIRICE model;
        enhanced functions for fetching and formatting weather data
        from the NASA POWER and ERA5 databases are also provided to
        simplify the process of running simulations.
License: GPL (>= 3)
URL: https://codeberg.org/adamhsparks/epicrop,
        https://adamhsparks.codeberg.page/epicrop
BugReports: https://codeberg.org/adamhsparks/epicrop/issues
Depends: R (>= 4.4.0)
Imports: cli, data.table, digest, httr2, memoise, nasapower (>= 4.0),
        rlang, yyjsonr
Suggests: chirps, cropgrowdays, ggplot2, ggrepel, ggspatial, knitr,
        rmarkdown, roxyglobals, spelling, stats, testthat, vcr (>=
        0.6.0), withr
VignetteBuilder: knitr
ByteCompile: TRUE
Config/Needs/build: moodymudskipper/devtag
Config/roxygen2/version: 8.1.0
Config/roxyglobals/filename: globals.R
Config/roxyglobals/unique: FALSE
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace",
        "rd", "roxyglobals::global_roclet", "devtag::dev_roclet"))
X-schema.org-applicationCategory: Tools
X-schema.org-keywords: rice, wheat, botanical-epidemiology, disease,
        model, seir, agricultural-modelling, agricultural-modeling,
        crop-protection, agricultural-research, model, modelling,
        modeling, seir-model, plant-disease
Config/pak/sysreqs: libssl-dev libx11-dev
Repository: https://adamhsparks.r-universe.dev
Date/Publication: 2026-10-05 09:34:31 UTC
RemoteUrl: https://codeberg.org/adamhsparks/epicrop
RemoteRef: HEAD
RemoteSha: e519920314fd41cf34e3fbd1cc6fc13639f40894
NeedsCompilation: no
Packaged: 2026-10-05 16:21:31 UTC; root
Author: Adam H. Sparks [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-0061-8359>),
  Robert Hijmans [aut, trl, cph] (Original R implementation, ORCID:
    <https://orcid.org/0000-0001-5872-2872>),
  Serge Savary [aut, ccp, cph] (Model conception and development in
    Stella, ORCID: <https://orcid.org/0000-0002-6867-180X>),
  Ireno Pangga [aut, trl, cph] (Model conception, development in Stella
    and original R implementation),
  Jorrel Aunario [aut, trl, cph] (Original R implementation),
  Kwang-Hyung Kim [aut, cph] (Contributed code for modified Kim leaf
    blast and sheath blight functions and feedback on the
    implementation.),
  Aji Sukarta [ctb] (Helped fix bug related to SEIR model and
    establishment date),
  Emerson Del Ponte [aut] (Provided code for fetching era5 code via the
    'r4pde' package and suggested fixes for several typos in the
    documentation, ORCID: <https://orcid.org/0000-0003-4398-409X>)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>