R Observatory: Metrics for hagis version 4.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hagis

4.0.0

Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

0packages depend

3.4Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Adam H. SparksFirst published 2019-06-2412 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("hagis", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("openplantpathology/hagis")

Development version from openplantpathology/hagis. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hagis

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-hagis

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-hagis

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.43

100.0%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 506 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 86%
References docs: 0%

Downloads

3.4K

CRAN downloads in the past year

Rank #13,929 · ~9/day · ~281/mo

Releases R versions

Daily download trend is not available in this view yet.

15430 days

73390 days

3.4K1 year

Compare downloads with other packages →

Also on111 r2u21 autocran47 c2d4u

Repository

GitHub ↗ openplantpathology/hagis

1Stars

2Forks

0Open issues

0Open PRs

2Releases

762Commits

8Contributors

plant-diseaseplant-pathologypathotype-complexitiespopulation-diversities

762 commits · Last activity 2026-08-01

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/openplantpathology/hagis on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

Show all practices

Lint, format, editor (2)

AirRStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (5)

data.table ggplot2 panderstatsutils

LinkingTo (0)

none

Suggests (8)

ape dplyr knitr rmarkdown roxyglobals testthat vdiffr vegan

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (13)

Maintainer (1)

Adam H. Sparks

Author, Maintainer

Authors (5)

Adam H. Sparks

Author, Maintainer

Martin Chilvers

Author, Thesis advisor

Austin G. McCoy

Author, ccp

Zachary Noel

Author, ccp

Jari Oksanen

Author · added in 3.1.12

Contributors (1)

Zhian N. Kamvar

Contributor, Reviewer · added in 3.0.0

Copyright holders (7)

Curtin University