R Observatory: Metrics for hagis version 4.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hagis

4.0.0Package record

Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

0packages depend

3.4Kdownloads / year

100.0%test coverage

13/13flavors OK

Overview

About

Maintained by Adam H. SparksCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Curtin University, Grains Research and Development Corporation and 5 more

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.

Changes in 4.0.0

Major changes

Fixes spelling of "individual" in hagis.complexities objects

Bug fixes

Corrects cross-references in documentation to fix CRAN NOTEs as requested by CRAN maintainers on 2025-07-23.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.0.0

READMEYes · 506 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 4.0.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 12 (2 internal)includes a package overview page
Examples that run: 100%10 run in a plain check (10 of them under a condition)
Exported functions with examples: 86%
Documented parameters: 100%
Return-value docs: 86%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #12,638 · ~9/day · ~287/mo

Releases R versions

Daily download trend is not available in this view yet.

35430 days

89490 days

3.4K1 year

Compare downloads with other packages →

Also on82 r2u6 autocran89 c2d4u

How downloads are counted

Repository

openplantpathology/hagis ↗Organization: openplantpathology

1Stars

2Forks

0Open issues

0Open PRs

2Releases

763Commits

9Commit identities

plant-diseaseplant-pathologypathotype-complexitiespopulation-diversities

763 commits · Last activity 2026-10-08 · Default branch at 4.0.0.9000, ahead of CRAN 4.0.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Commits over time

2026-07-19 · 7622026-10-11 · 763

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/openplantpathology/hagis on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conductContributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-08 · The repository has a site deploy workflow

pkgdown site last built 2026-10-08

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdrevdep/

Research and citation (1)

codemeta.json

Lint, format, editor (1)

Air

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing hagis adds 21 packages (11 with compiled code, 22 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (13)

Adam H. Sparks

Author, Maintainer since 2.0.0 (2019)

Martin Chilvers

Author, Thesis advisor

Austin G. McCoy

Author, ccp

Zachary Noel

Author, ccp

Jari Oksanen

Author · added in 3.1.12

Contributed fix for the use of 'vegan' in betadiversity vignette.

Zhian N. Kamvar

Contributor, Reviewer · added in 3.0.0

Curtin University

Funder, Copyright holder · added in 4.0.0

Grains Research and Development Corporation

Funder, Copyright holder · added in 4.0.0

GRDC Project DAQ00186 and GRDC Project CUR2210-005OPX (AAGI-CU)

Michigan Soybean Promotion Committee

Funder, Copyright holder · added in 3.0.0

Michigan State University

Funder, Copyright holder · added in 4.0.0

MSU AgBioResearch and MSU Extension

North Central Soybean Research Program

Funder, Copyright holder · added in 3.0.0

Project GREEEN

Funder, Copyright holder · added in 3.0.0

University of Southern Queensland

Funder, Copyright holder · added in 4.0.0

Listed in earlier versions (1)

GRDC Project DAQ00186

no longer listed · 3.0.0 to 3.1.12

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
4.0.0Latest
record
2025-07-26 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
3.1.12
record
2024-05-16 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.1.11
record
2023-09-06 · diff ↗
3.1.6
record
2023-04-25 · diff ↗ ·
removed 1 export
.create_summary_isolate
R
R 4.3.0 released · 2023-04-21
3.1.4
record
2022-08-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
3.1.3
record
2021-10-14 · diff ↗
3.1.2
record
2021-09-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
3.1.1
record
2020-12-09 · diff ↗
3.1.0
record
2020-10-07 · diff ↗ ·
added 1 export
create_binary_matrix
R
R 4.0.0 released · 2020-04-24

Show 4 earlier eventsHide 4 earlier events

3.0.1
record
2019-11-18 · diff ↗
3.0.0
record
2019-08-26 · diff ↗
2.0.0
record
2019-06-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-24
Total releases: 12 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Bundled data: 2.2 KB / 2 files
Download size: 769 KB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hagis")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for hagis version 4.0.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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