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shar

shar: An R package to analyze species-habitat associations using point pattern analysis - Published in JOSS (2021)

https://github.com/r-spatialecology/shar

Science Score: 93.0%

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 8 DOI reference(s) in README and JOSS metadata
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

habitat-association landscape-ecology point-pattern-analysis spatial-analysis
Last synced: 4 months ago · JSON representation

Repository

:package: Analyse species-habitat associations in R

Basic Info
Statistics
  • Stars: 21
  • Watchers: 2
  • Forks: 10
  • Open Issues: 0
  • Releases: 25
Topics
habitat-association landscape-ecology point-pattern-analysis spatial-analysis
Created almost 8 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Codemeta

README.Rmd 

---
output: 
    github_document:
      html_preview: false
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE, 
  fig.path = "man/figures/README-"
)
```

# **shar** | **S**pecies **h**abitat **a**ssociations in **R** 

README Last updated: `r Sys.Date()`



| CI | Development | CRAN | License |
|----|-------------|------|---------|
| [![R-CMD](https://github.com/r-spatialecology/shar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatialecology/shar/actions/workflows/R-CMD-check.yaml) | [![Project-status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![CRAN-status](https://www.r-pkg.org/badges/version/shar)](https://cran.r-project.org/package=shar) | [![DOI](https://img.shields.io/badge/JOSS-10.21105/joss.03811-yellow.svg)](https://doi.org/10.21105/joss.03811) | 
[![Codecov](https://codecov.io/gh/r-spatialecology/shar/graph/badge.svg)](https://app.codecov.io/gh/r-spatialecology/shar) | [![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN-logs](https://cranlogs.r-pkg.org/badges/grand-total/shar)](http://cran.rstudio.com/web/packages/shar/index.html) | [![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) |



**S**pecies-**h**abitat **a**ssociations in **R** provides a toolset of functions in the `R` programming language to analyze species-habitat associations. Therefore, information about the location of the species (as a point pattern) and the environmental conditions (as a raster) is needed. In order to analyse the data for significant habitat associations either the location data or the environmental data is randomized *n*-times. Then, counts within the habitats are compared between the observed and the randomized data. Positive or negative associations are present if the observed counts are higher or lower than the randomized counts (using quantile thresholds). Methods are described in Plotkin et al. (2000), Harms et al. (2001) and Wiegand & Moloney (2014). **shar** is mainly based on the [`spatstat`](http://spatstat.org) (Baddeley et al. 2015) and [`terra`](https://rspatial.org/terra/) (Hijmans 2022) package.

You can find more information and help using the corresponding [homepage](https://r-spatialecology.github.io/shar/).

## Installation

You can install the released version of **shar** from [CRAN](https://cran.r-project.org/web/packages/shar/index.html) with:

```{r install-CRAN, eval = FALSE}
install.packages("shar")
```

And the development version from [GitHub](https://github.com/r-spatialecology/shar) with:

```{r install-github, eval = FALSE}
# install.packages("remotes")
remotes::install_github("r-spatialecology/shar")
```

This also automatically installs all non-base `R` package dependencies, namely: `classInt`, `spatstat.explore`, `spatstat.geom`, `spatstat.model`, `spatstat.random`, and `terra`.

## How to use **shar**

Please refer to `vignette("Get started")` and the [homepage](https://r-spatialecology.github.io/shar/) to get an introduction to **shar**.

### Citation

The **shar** package is part of our academic work. To cite the package or acknowledge its use in publications, please cite the following paper.

> Hesselbarth, M.H.K., (2021). shar: A R package to analyze species-habitat associations using point pattern analysis. Journal of Open Source Software, 6(67), 3811. .

If you use the `reconstruct_pattern_multi()` function, please also cite.

> Wudel C., Schlicht R., Berger U. (2023). Multi-trait point pattern reconstruction of plant ecosystems. Methods in Ecology and Evolution, 14, 2668–2679. .

The get a BibTex entry, please use `citation("shar")`.

## Contributing and Code of Conduct

Contributions to **shar** are highly welcomed and appreciated. This includes any form of feedback, bug reports, feature requests/suggestions, or general questions about the usage.

Please note that the **shar** package is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

To contribute to this project, please see the [Contributing guidelines](CONTRIBUTING.md).

Owner

  • Name: r-spatialecology
  • Login: r-spatialecology
  • Kind: organization

JOSS Publication

shar: An R package to analyze species-habitat associations using point pattern analysis
Published
December 06, 2021
DOI
Volume 6, Issue 68, Page 3811
Authors
Maximilian H. k. Hesselbarth ORCID
Department of Ecosystem Modelling, University of Goettingen, Buesgenweg 4, 37077, Goettingen, Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, Michigan 48109, USA
Editor
Hugo Gruson ORCID
Tags
open source software spatial point pattern analysis gamma-test pattern reconstruction torus-translation test randomized-habitats procedure;
View PDF Review Thread Software Archive

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GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Push event: 30
  • Pull request event: 3
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 1
  • Push event: 30
  • Pull request event: 3
  • Create event: 1

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 625
  • Total Committers: 9
  • Avg Commits per committer: 69.444
  • Development Distribution Score (DDS): 0.082
Past Year
  • Commits: 22
  • Committers: 1
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
mhesselbarth m****h@g****m 574
GitHub Actions a****s@g****m 31
marcosci s****o@g****m 6
ZekeMarshall m****e@o****m 6
ChrisWudel c****l@w****e 3
rubak r****k@m****k 2
tretherington t****n 1
Hugo Gruson B****o 1
Darío Hereñú m****a@g****m 1
Committer Domains (Top 20 + Academic)
math.aau.dk: 1 github.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 50
  • Total pull requests: 71
  • Average time to close issues: 2 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 5
  • Total pull request authors: 7
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.21
  • Merged pull requests: 67
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mhesselbarth (36)
  • tretherington (8)
  • lionel68 (4)
  • Bisaloo (1)
  • kiranaw (1)
Pull Request Authors
  • mhesselbarth (63)
  • ZekeMarshall (5)
  • rubak (2)
  • tretherington (1)
  • kant (1)
  • ChrisWudel (1)
  • Bisaloo (1)
Top Labels
Issue Labels
enhancement (8) question (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 602 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 25
  • Total maintainers: 1
cran.r-project.org: shar

Species-Habitat Associations

  • Versions: 25
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 602 Last month
Rankings
Forks count: 7.7%
Stargazers count: 13.3%
Average: 22.1%
Downloads: 24.2%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
mhk.hesselbarth@gmail.com
Last synced: 4 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.0 depends
  • classInt * imports
  • grDevices * imports
  • graphics * imports
  • methods * imports
  • spatstat.core * imports
  • spatstat.geom * imports
  • spatstat.random * imports
  • stats * imports
  • terra * imports
  • utils * imports
  • covr * suggests
  • dplyr * suggests
  • future * suggests
  • future.apply * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • spatstat >= 2.0.0 suggests
  • testthat >= 2.1.0 suggests
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