Package: hagis 4.0.0

Adam H. Sparks

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.

Authors:Austin G. McCoy [aut, ccp], Zachary Noel [aut, ccp], Adam H. Sparks [aut, cre], Martin Chilvers [aut, ths], Jari Oksanen [aut], Zhian N. Kamvar [ctb, rev], Michigan Soybean Promotion Committee [fnd], Project GREEEN [fnd], North Central Soybean Research Program [fnd], Grains Research and Development Corporation [fnd], Grains Research and Development Corporation [fnd, cph]

hagis_4.0.0.tar.gz
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hagis.pdf |hagis.html✨
hagis/json (API)
NEWS

# Install 'hagis' in R:
install.packages('hagis', repos = c('https://openplantpathology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/openplantpathology/hagis/issues

Pkgdown site:https://openplantpathology.github.io

Datasets:

On CRAN:

Conda:

plant-pathologypathotypepathogen-surveyvirulence analysisdifferential setassessment scalepathotype-complexitiesplant-diseasepopulation-diversities

5.26 score 1 stars 8 scripts 483 downloads 7 exports 32 dependencies

Last updated 25 days agofrom:a515edcccd. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 06 2025
R-4.5-winNOTEMar 06 2025
R-4.5-macNOTEMar 06 2025
R-4.5-linuxNOTEMar 06 2025
R-4.4-winOKMar 06 2025
R-4.4-macOKMar 06 2025
R-4.4-linuxOKMar 06 2025
R-4.3-winOKMar 06 2025
R-4.3-macOKMar 06 2025

Exports:autoplotcalculate_complexitiescalculate_diversitiescreate_binary_matrixdiversities_tableindividual_pathotypessummarize_gene

Dependencies:clicolorspacedata.tabledigestfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepanderpillarpkgconfigR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr

Beta-diversity Analysis with hagis

Austin McCoy

Rendered frombetadiversity.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2024-05-16
Started: 2020-10-06

hagis: Tools for Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

Austin McCoy and Zachary Noel

Rendered fromhagis.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-05
Started: 2019-01-09