Package: hagis
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
        and Diversity
Version: 4.0.0
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 (>= 3.4.0)
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
RoxygenNote: 7.3.2.9000
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
NeedsCompilation: no
Packaged: 2025-07-26 03:58:08 UTC; adamsparks
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>
Repository: CRAN
Date/Publication: 2025-07-26 04:20:02 UTC
Built: R 4.6.0; ; 2026-04-26 07:59:01 UTC; unix
