hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and 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 + file LICENSE |
| 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 |
Documentation:
| Reference manual: | hagis.html , hagis.pdf |
| Vignettes: |
Beta-diversity Analysis with hagis (source, R code) hagis: Tools for Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity (source, R code) |
Downloads:
| Package source: | hagis_4.0.0.tar.gz |
| Windows binaries: | r-devel: hagis_4.0.0.zip, r-release: hagis_4.0.0.zip, r-oldrel: hagis_4.0.0.zip |
| macOS binaries: | r-release (arm64): hagis_4.0.0.tgz, r-oldrel (arm64): hagis_4.0.0.tgz, r-release (x86_64): hagis_4.0.0.tgz, r-oldrel (x86_64): hagis_4.0.0.tgz |
| Old sources: | hagis archive |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=hagis to link to this page.