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hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributionsand Diversity

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.

Version:	4.0.0
Depends:	R (≥ 3.4.0)
Imports:	data.table,ggplot2,pander, stats, utils
Suggests:	ape,dplyr,knitr,rmarkdown,roxyglobals,testthat,vdiffr,vegan
Published:	2025-07-26
DOI:	10.32614/CRAN.package.hagis
Author:	Austin G. McCoy [aut, ccp], Zachary Noel [aut, ccp], Adam H. Sparks [aut, cre], Martin Chilvers [aut, ths], Jari Oksanen [aut] (Contributed fix for the use of 'vegan' in betadiversity vignette.), Zhian N. Kamvar [ctb, rev], 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)), Michigan State University [fnd, cph] (MSU AgBioResearch and MSU Extension), University of Southern Queensland [fnd, cph], Curtin University [fnd, cph]
Maintainer:	Adam H. Sparks <adamhsparks at gmail.com>
BugReports:	https://github.com/openplantpathology/hagis/issues
License:	MIT + fileLICENSE
URL:	https://github.com/openplantpathology/hagis,https://openplantpathology.github.io/hagis/
NeedsCompilation:	no
Language:	en-US
Citation:	hagis citation info
Materials:	README,NEWS
In views:	Agriculture
CRAN checks:	hagis results

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