Package: hagis
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
        and Diversity
Version: 4.0.0.9000
Authors@R: c(
    person("Austin G.", "McCoy", , "mccoyaus@msu.edu", role = c("aut", "ccp"),
           comment = c(ORCID = "0000-0003-2483-4184")),
    person("Zachary", "Noel", , "noelzach@msu.edu", role = c("aut", "ccp"),
           comment = c(ORCID = "0000-0001-6375-8300")),
    person("Adam H.", "Sparks", , "adamhsparks@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0061-8359")),
    person("Martin", "Chilvers", , "chilvers@msu.edu", role = c("aut", "ths"),
           comment = c(ORCID = "0000-0001-8832-1666")),
    person("Jari", "Oksanen", , "jhoksane@gmail.com", role = "aut",
           comment = "Contributed fix for the use of 'vegan' in betadiversity vignette."),
    person("Zhian N.", "Kamvar", role = c("ctb", "rev"),
           comment = c(ORCID = "0000-0003-1458-7108")),
    person("Michigan Soybean Promotion Committee", role = c("fnd", "cph")),
    person("Project GREEEN", role = c("fnd", "cph")),
    person("North Central Soybean Research Program", role = c("fnd", "cph")),
    person("Grains Research and Development Corporation", role = c("fnd", "cph"),
           comment = c("GRDC Project DAQ00186 and GRDC Project CUR2210-005OPX\n           (AAGI-CU)", ROR = "02xwr1996")),
    person("Michigan State University", role = c("fnd", "cph"),
           comment = c("MSU AgBioResearch and MSU Extension", ROR = "05hs6h993")),
    person("University of Southern Queensland", role = c("fnd", "cph"),
           comment = c(ROR = "04sjbnx57")),
    person("Curtin University", role = c("fnd", "cph"),
           comment = c(ROR = "02n415q13"))
  )
Description: Analysis of plant pathogen pathotype survey data.
        Functions provided calculate distribution of susceptibilities,
        distribution of complexities with statistics, pathotype
        frequency distribution, as well as diversity indices for
        pathotypes.  This package is meant to be a direct replacement
        for Herrmann, Löwer and Schachtel's (1999)
        <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour
        Spreadsheet, 'HaGiS', previously used for pathotype analysis.
License: MIT + file LICENSE
URL: https://github.com/openplantpathology/hagis,
        https://openplantpathology.github.io/hagis/
BugReports: https://github.com/openplantpathology/hagis/issues
Depends: R (>= 3.5.0)
Imports: data.table, ggplot2, pander, stats, utils
Suggests: ape, dplyr, knitr, rmarkdown, roxyglobals, testthat, vdiffr,
        vegan
VignetteBuilder: knitr
Config/Needs/build: moodymudskipper/devtag
Config/roxyglobals/filename: globals.R
Config/roxyglobals/unique: FALSE
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace",
        "rd", "roxyglobals::global_roclet", "devtag::dev_roclet"))
RoxygenNote: 7.3.3
X-schema.org-applicationCategory: Tools
X-schema.org-isPartOf: https://openplantpathology.org
X-schema.org-keywords: plant-pathology, pathotype, pathogen-survey,
        virulence analysis, differential set, assessment scale
Repository: https://openplantpathology.r-universe.dev
Date/Publication: 2026-06-02 09:04:56 UTC
RemoteUrl: https://github.com/openplantpathology/hagis
RemoteRef: HEAD
RemoteSha: a8ecfd647877cc21c40b58c6f69145b2d62c4464
NeedsCompilation: no
Packaged: 2026-07-02 09:34:55 UTC; root
Author: Austin G. McCoy [aut, ccp] (ORCID:
    <https://orcid.org/0000-0003-2483-4184>),
  Zachary Noel [aut, ccp] (ORCID:
    <https://orcid.org/0000-0001-6375-8300>),
  Adam H. Sparks [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0061-8359>),
  Martin Chilvers [aut, ths] (ORCID:
    <https://orcid.org/0000-0001-8832-1666>),
  Jari Oksanen [aut] (Contributed fix for the use of 'vegan' in
    betadiversity vignette.),
  Zhian N. Kamvar [ctb, rev] (ORCID:
    <https://orcid.org/0000-0003-1458-7108>),
  Michigan Soybean Promotion Committee [fnd, cph],
  Project GREEEN [fnd, cph],
  North Central Soybean Research Program [fnd, cph],
  Grains Research and Development Corporation [fnd, cph] (GRDC Project
    DAQ00186 and GRDC Project CUR2210-005OPX (AAGI-CU), ROR:
    <https://ror.org/02xwr1996>),
  Michigan State University [fnd, cph] (MSU AgBioResearch and MSU
    Extension, ROR: <https://ror.org/05hs6h993>),
  University of Southern Queensland [fnd, cph] (ROR:
    <https://ror.org/04sjbnx57>),
  Curtin University [fnd, cph] (ROR: <https://ror.org/02n415q13>)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>