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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: 3.1.12
Depends: R (≥ 3.4.0)
Imports: data.table, ggplot2, pander, stats, utils
Suggests: ape, dplyr, knitr, rmarkdown, roxyglobals, testthat, vdiffr, vegan
Published: 2024-05-16
DOI: 10.32614/CRAN.package.hagis
Author: Austin G. McCoy ORCID iD [aut, ccp], Zachary Noel ORCID iD [aut, ccp], Adam H. Sparks ORCID iD [aut, cre], Martin Chilvers ORCID iD [aut, ths], Jari Oksanen [aut] (Contributed fix for the use of 'vegan' in betadiversity vignette.), Zhian N. Kamvar ORCID iD [ctb, rev], Michigan Soybean Promotion Committee [fnd], Project GREEEN [fnd], North Central Soybean Research Program [fnd], GRDC Project DAQ00186 [fnd]
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.pdf
Vignettes: Beta-diversity Analysis with hagis
hagis: Tools for Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

Downloads:

Package source: hagis_3.1.12.tar.gz
Windows binaries: r-devel: hagis_3.1.12.zip, r-release: hagis_3.1.12.zip, r-oldrel: hagis_3.1.12.zip
macOS binaries: r-release (arm64): hagis_3.1.12.tgz, r-oldrel (arm64): hagis_3.1.12.tgz, r-release (x86_64): hagis_3.1.12.tgz, r-oldrel (x86_64): hagis_3.1.12.tgz
Old sources: hagis archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.