hagis

Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

https://github.com/openplantpathology/hagis

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 15 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 5 committers (20.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (17.6%) to scientific vocabulary

Keywords

pathotype-complexities plant-disease plant-pathology population-diversities

Keywords from Contributors

carpentries interpretability standardization animal hack

Last synced: 6 months ago · JSON representation

Repository

Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

Basic Info

Host: GitHub
Owner: openplantpathology
License: other
Language: R
Default Branch: main
Homepage: https://openplantpathology.github.io/hagis
Size: 19.2 MB

Statistics

Stars: 0
Watchers: 3
Forks: 1
Open Issues: 0
Releases: 2

Topics

pathotype-complexities plant-disease plant-pathology population-diversities

Created almost 2 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# {hagis}: Analysis of Plant (and Animal) Pathogen Pathotype Complexities, Distributions and Diversity
    


[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) 
[![Codecov test coverage](https://codecov.io/gh/openplantpathology/hagis/branch/main/graph/badge.svg)](https://app.codecov.io/gh/openplantpathology/hagis?branch=main)
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/hagis)](https://cran.r-project.org/package=hagis)  [![DOI](https://zenodo.org/badge/164751172.svg)](https://zenodo.org/badge/latestdoi/164751172) [![test-coverage](https://github.com/openplantpathology/hagis/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/openplantpathology/hagis/actions/workflows/test-coverage.yaml)


## Introduction

The goal of {hagis} is to provide analysis tools for plant pathogens with gene-for-gene interactions in the R programming language that the original [Habgood-Gilmour Spreadsheet, HaGiS](https://doi.org/10.1046/j.1365-3059.1999.00325.x), (Herrmann, Löwer and Schachtel) provided.

This R package has been published in *MPMI* as a resource announcement [(McCoy *et al.* 2019)](https://doi.org/10.1094/MPMI-07-19-0180-A).
You may wish to refer to that paper for further information on this package.

## Overview

{hagis} was initially created for *Phytophthora sojae* surveys by Dr. Austin McCoy and Dr. Zachary Noel at Michigan State University in the US, where the disease has been managed primarily via deployment of resistance genes (*Rps* genes, resistance to *P. sojae*) in commercial soybean cultivars and by the application of fungicide seed treatments.
However, repeated use of resistance genes can cause populations to adapt over time rendering these resistance genes ineffective.
To determine current effectiveness of resistance genes for managing *P. sojae*, state-wide surveys (in the US) are conducted to determine the pathotype (previously referred to as "race") structure within sampled population of *P. sojae*.

However, the package is not only useful for *P. sojae* work.
It was built to be useful for other plant pathogen gene-for-gene interaction systems, *e.g.*, wheat rusts, but it has been used in animal science as well, see [Cain *et al.* 2022](https://doi.org/10.1186/s13071-022-05533-y).

The goal of this package is to provide all the necessary analyses needed when conducting a pathotype surveys, including: distribution of susceptibilities (effective and non-effective resistance genes), distribution of pathotype complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes in an efficient and reproducible manner.

New users are encouraged to visit the documentation, , for detailed information on how to use {hagis} along with working examples using a built-in data set.

## Quick Start Install

### Stable Version

A CRAN version of {hagis} is available but lags behind the GitHub version.
They both will give exactly the same results.

``` r
install.packages("hagis")
```

### Development Version

A development version is available from from GitHub that may provide bug fixes or new features not yet available from CRAN.

``` r
o <- options() # store default options

options(pkg.build_vignettes = TRUE)
if (!require("pak")) {
  install.packages("pak", repos = "http://cran.rstudio.com/")
  library("pak")
}

pak("openplantpathology/hagis", build_vignettes = TRUE)
options(o) # reset options
```

## Meta

### Citation

When you use {hagis}, please cite by using:

```{r}
citation("hagis")
```

### Code of Conduct

Please note that the {hagis} project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.

## References

> Herrmann, Löwer and Schachtel. (1999), A new tool for entry and analysis of virulence data for plant pathogens. Plant Pathology, 48: 154-158. DOI: [10.1046/j.1365-3059.1999.00325.x](https://doi.org/10.1046/j.1365-3059.1999.00325.x)

> McCoy, Noel, Sparks and Chilvers. (2019). 'hagis', an R Package Resource for Pathotype Analysis of _Phytophthora sojae_ Populations Causing Stem and Root Rot of Soybean. Molecular Plant-Microbe Interactions 32.12 (Nov 2019) p. 1574-1576. DOI: [10.1094/MPMI-07-19-0180-A](https://doi.org/10.1094/MPMI-07-19-0180-A)

> Cain, Norris, Ripley, Suri, Finnerty, Gravatte, and Nielsen, 2022. The microbial community associated with _Parascaris_ spp. infecting juvenile horses. Parasites & Vectors, 15(1), pp.1-17. [10.1186/s13071-022-05533-y](https://doi.org/10.1186/s13071-022-05533-y)

Owner

Name: Open Plant Pathology
Login: openplantpathology
Kind: organization
Email: openplantpathology@gmail.com
Location: Global

Website: https://www.openplantpathology.org/
Repositories: 7
Profile: https://github.com/openplantpathology

A community that values open data and computational tools for advancing epidemiology and pathogen population biology and ecology

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GitHub Events

Total

Release event: 1
Push event: 27

Last Year

Release event: 1
Push event: 27

Committers

Last synced: about 2 years ago

All Time

Total Commits: 657
Total Committers: 5
Avg Commits per committer: 131.4
Development Distribution Score (DDS): 0.041

Past Year

Commits: 121
Committers: 2
Avg Commits per committer: 60.5
Development Distribution Score (DDS): 0.008

Top Committers

Name	Email	Commits
Adam H. Sparks	a**s@g**m	630
Austin McCoy	4****y	23
Zachary Noel	n**h@m**u	2
Zhian N. Kamvar	z**r@g**m	1
github-actions[bot]	4****]	1

Committer Domains (Top 20 + Academic)

msu.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 37
Total pull requests: 6
Average time to close issues: 11 days
Average time to close pull requests: 13 days
Total issue authors: 1
Total pull request authors: 3
Average comments per issue: 1.14
Average comments per pull request: 0.33
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

adamhsparks (37)

Pull Request Authors

adamhsparks (5)
jarioksa (2)
zkamvar (1)

Top Labels

Issue Labels

enhancement (9) bug (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 312 last-month
Total docker downloads: 21,613

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 12
Total maintainers: 1

cran.r-project.org: hagis

Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

Homepage: https://github.com/openplantpathology/hagis
Documentation: http://cran.r-project.org/web/packages/hagis/hagis.pdf
License: MIT + file LICENSE
Latest release: 4.0.0
published 7 months ago

Versions: 12
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 312 Last month
Docker Downloads: 21,613

Rankings

Forks count: 17.8%

Stargazers count: 22.5%

Average: 26.9%

Downloads: 28.8%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Maintainers (1)

adamhsparks@gmail.com

Last synced: 6 months ago

Dependencies

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DESCRIPTION cran

R >= 3.4.0 depends
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ggplot2 * imports
pander * imports
stats * imports
utils * imports
ape * suggests
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knitr * suggests
rmarkdown * suggests
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testthat * suggests
vdiffr * suggests
vegan * suggests

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