Package: hagis 4.0.0.9000

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, cph], Project GREEEN [fnd, cph], North Central Soybean Research Program [fnd, cph], Grains Research and Development Corporation [fnd, cph], Michigan State University [fnd, cph], University of Southern Queensland [fnd, cph], Curtin University [fnd, cph]

hagis_4.0.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hagis/json (API)

# 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/docs site:https://openplantpathology.github.io

Datasets:

On CRAN:

Conda:

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

5.23 score 1 stars 14 scripts 329 downloads 7 exports 21 dependencies

Last updated from:a8ecfd6478. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK167
source / vignettesOK281
linux-release-x86_64OK151
macos-release-arm64OK205
macos-oldrel-arm64OK185
windows-develOK86
windows-releaseOK97
windows-oldrelOK85
wasm-releaseOK153

Exports:autoplotcalculate_complexitiescalculate_diversitiescreate_binary_matrixdiversities_tableindividual_pathotypessummarize_gene

Dependencies:clicpp11data.tabledigestfarverggplot2gluegtableisobandlabelinglifecyclepanderR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr

hagis: Tools for Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity
Getting Started With | Function Arguments Used in | Determination of Effective Resistance Genes | Plotting Rps Summary Data | Pathotype Complexities | Plotting Complexities Data | Diversity Indices, Frequency of Unique Pathotypes and Individual Isolate Pathotypes | Table of Diversities | Table of Individual Pathotypes | Advanced Plotting | {hagis} autoplot() Objects | Changing the ggplot2 Theme | Changing the Font | Make a Horizontal Plot | Use Colors in Autoplot Objects | Sorting the x-axis
Rendered fromhagis.Rmdusingknitr::rmarkdown

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

Beta-diversity Analysis with hagis
Load Packages | Convert the Dataset to a Binary Data Matrix | Perform Principle Coordinates Analysis (PCOA) | Add Metadata to your PCOA Data | Statistical Tests for Beta Diversity | Permutation Based Analysis of Variance (PERMANOVA) and Beta-dispersion Analyses | Beta-Dispersion | Permutation Based Analysis of Variance (PERMANOVA) | Analysis of Similarity (ANOSIM)
Rendered frombetadiversity.Rmdusingknitr::rmarkdown

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