Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity R package hagis version 4.0.0 CRAN Task View: Agriculture (https://CRAN.R-project.org/view=Agriculture) 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. Software Depends: R (>= 3.4.0) Imports: data.table, ggplot2, pander, stats, utils Suggests: ape, dplyr, knitr, rmarkdown, roxyglobals, testthat, vdiffr, vegan Adam H. Sparks <adamhsparks@gmail.com> Comprehensive R Archive Network (CRAN) 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>) MIT + file LICENSE (https://CRAN.R-project.org/package=hagis/LICENSE) 2025-07-26 application/tgz https://CRAN.R-project.org/package=hagis doi:10.32614/CRAN.package.hagis en-US