indicspecies
Studying the statistical relationship between species and groups of sites
Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 8 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Last synced: 11 months ago
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Repository
Studying the statistical relationship between species and groups of sites
Basic Info
- Host: GitHub
- Owner: emf-creaf
- Language: R
- Default Branch: main
- Homepage: https://emf-creaf.github.io/indicspecies/
- Size: 10.8 MB
Statistics
- Stars: 11
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 1
Created about 7 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
Changelog
README.Rmd
---
output: github_document
---
```{r setup, echo = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.path = "README-")
```
# Relationship between species and groups of sites 
[](https://cran.r-project.org/package=indicspecies)
[](https://cran.rstudio.com/web/packages/indicspecies/index.html)
[](https://github.com/emf-creaf/indicspecies/actions/workflows/R-CMD-check.yaml)
## Introduction
Package `indicspecies` provides functions to conduct:
* **Indicator species analysis**: Assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites (De Cáceres & Legendre 2009; De Cáceres et al. 2010; De Cáceres et al. 2012).
* **Species niche analysis**: Measure species niche metrics using resource categories (De Cáceres et al. 2011).
## Package installation
Package`indicspecies` can be found at [CRAN](https://cran.r-project.org/) package repository. In addition, the latest stable `indicspecies` R package can be installed from GitHub as follows:
```{r installation, eval = FALSE}
remotes::install_github("emf-creaf/indicspecies")
```
Additionally, users can have help to run package functions directly as package vignettes, by forcing their inclusion in installation:
```{r installation vignettes, eval = FALSE}
remotes::install_github("emf-creaf/indicspecies",
build_opts = c("--no-resave-data", "--no-manual"),
build_vignettes = TRUE)
```
## Usage
Use `strassoc()` for assessing strength of associations and `signassoc()` to assess the statistical significance of the associations (De Cáceres & Legendre 2009). Much more complete functions are `multipatt()` (De Cáceres et al. 2010) and `indicators()` (De Cáceres et al. 2012).
## Maintenance
Although not in active development, the R package is maintained by the [*Ecosystem Modelling Facility*](https://emf.creaf.cat) unit at CREAF (in Spain).
## References
+ De Cáceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566–3574 (https://doi.org/10.1890/08-1823.1).
+ De Cáceres, M., Legendre, P., & Moretti, M. (2010). Improving indicator species analysis by combining groups of sites. Oikos, 119(10), 1674–1684 (https://doi.org/10.1111/j.1600-0706.2010.18334.x).
+ De Cáceres, M., Legendre, P., Wiser, S. K., & Brotons, L. (2012). Using species combinations in indicator value analyses. Methods in Ecology and Evolution, 3, 973–982 (https://doi.org/10.1111/j.2041-210X.2012.00246.x).
+ De Cáceres, M., Sol, D., Lapiedra, O., & Legendre, P. (2011). A framework for estimating niche metrics using the resemblance between qualitative resources. Oikos, 120(February), 1341–1350 (https://doi.org/10.1111/J.1600-0706.2011.19679.x).
Owner
- Name: Ecosystem Modelling Facility (CREAF)
- Login: emf-creaf
- Kind: organization
- Email: ecosystemmodellingfacility@creaf.uab.cat
- Website: https://emf.creaf.cat/
- Repositories: 10
- Profile: https://github.com/emf-creaf
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 2
- Issue comment event: 4
- Push event: 5
- Pull request event: 2
Last Year
- Create event: 1
- Release event: 1
- Issues event: 3
- Watch event: 2
- Issue comment event: 4
- Push event: 5
- Pull request event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Miquel De Cáceres | m****s@g****m | 50 |
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 3
- Total pull requests: 2
- Average time to close issues: 7 months
- Average time to close pull requests: 3 months
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 1.67
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 2
- Average time to close issues: 3 months
- Average time to close pull requests: 3 months
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rsbivand (1)
- see24 (1)
- MalditoBarbudo (1)
Pull Request Authors
- see24 (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 2,258 last-month
- Total dependent packages: 3
- Total dependent repositories: 2
- Total versions: 23
- Total maintainers: 1
cran.r-project.org: indicspecies
Relationship Between Species and Groups of Sites
- Homepage: https://emf-creaf.github.io/indicspecies/
- Documentation: http://cran.r-project.org/web/packages/indicspecies/indicspecies.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
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Latest release: 1.8.0
published over 1 year ago
Rankings
Downloads: 9.8%
Dependent packages count: 13.7%
Average: 18.5%
Dependent repos count: 19.2%
Stargazers count: 21.9%
Forks count: 27.8%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- permute * depends
- knitr * suggests
- rgeos * suggests
- rmarkdown * suggests
- sp * suggests