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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
fig.path = "man/figures/",
out.width = "100%")
```
chessboard <img src="man/figures/package-sticker.png" align="right" style="float:right; height:120px;"/>
=========================================================
<!-- badges: start -->
[](https://github.com/frbcesab/chessboard/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/FRBCesab/chessboard)
[](https://github.com/frbcesab/chessboard/actions/workflows/pkgdown.yaml)
[](https://choosealicense.com/licenses/gpl-2.0/)
[](https://joss.theoj.org/papers/f709edaff050ed0cb1ffb8dd4ad2a1bb)
<!-- badges: end -->
## Table of contents
<p align="left">
• <a href="#overview">Overview</a><br>
• <a href="#features">Features</a><br>
• <a href="#installation">Installation</a><br>
• <a href="#get-started">Get started</a><br>
• <a href="#long-form-documentations">Long-form documentations</a><br>
• <a href="#citation">Citation</a><br>
• <a href="#contributing">Contributing</a><br>
• <a href="#acknowledgments">Acknowledgments</a><br>
• <a href="#references">References</a>
</p>
## Overview
The package `chessboard` provides functions to work with **directed**
(asymmetric) and **undirected** (symmetric) spatial (or non-spatial) **networks**.
It implements different methods to detect neighbors, all based on the chess game
(it goes beyond the rook and the queen) to create complex connectivity scenarios.
`chessboard` can handle spatial networks, but it does not explicitly use geographical
coordinates to find neighbors (it is not based on spatial distance).
Instead, it identifies neighbors according to **node labels**
(i.e. the node position on a two-dimension chessboard) and a specific method
(pawn, fool, rook, bishop, knight, queen, wizard, etc.).
It implements the following rules to detect neighbors and create edges:
- the **degree** of neighborhood: the number of adjacent nodes that will be used
to create direct edges.
- the **orientation** of neighborhood: can neighbors be detected horizontally,
vertically and/or diagonally?
- the **direction** of neighborhood: does the sampling has a main direction?
This can be particularly relevant for directed networks (e.g. rivers).
## Features
The main purpose of `chessboard` is to create various network objects, including:
- **node list**
- **edge list**
- **connectivity matrix**
`chessboard` also provides different plotting functions (all based on the [`ggplot2`](https://ggplot2.tidyverse.org/) package):
- [`gg_matrix()`](https://frbcesab.github.io/chessboard/reference/gg_matrix.html)
plots a (connectivity) matrix
- [`gg_chessboard()`](https://frbcesab.github.io/chessboard/reference/gg_chessboard.html)
plots the sampling as a chessboard
Read the [Visualization tools](https://frbcesab.github.io/chessboard/articles/visualization-tools.html)
vignette for further details.
Finally, the package can also produce objects that will be used later in
Moran's Eigenvector Maps
([MEM](https://search.r-project.org/CRAN/refmans/adespatial/html/mem.html),
Dray _et al._ 2006) and Asymetric Eigenvector Maps
([AEM](https://search.r-project.org/CRAN/refmans/adespatial/html/aem.html),
Blanchet _et al._ 2008), methods available in the package
[`adespatial`](https://cran.r-project.org/package=adespatial) (Dray _et al._ 2023):
- **edges weights matrix**
- **spatial weights matrix**
- **nodes by edges matrix**
- **edges weights vector**
## Installation
The package is not yet published on the CRAN but you can install the development
version from GitHub with:
```{r eval=FALSE}
# install.packages("remotes")
remotes::install_github("frbcesab/chessboard")
```
Then you can attach the package `chessboard`:
```{r eval=FALSE}
library("chessboard")
```
## Get started
For an overview of the main features of `chessboard`, please read the
[Get started](https://frbcesab.github.io/chessboard/articles/chessboard.html)
vignette.
## Long-form documentations
`chessboard` provides three vignettes to learn more about the package:
- the [Get started](https://frbcesab.github.io/chessboard/articles/chessboard.html)
vignette describes the core features of the package
- the [Chess pieces](https://frbcesab.github.io/chessboard/articles/chess-pieces.html)
vignette details the different methods implemented in `chessboard` to detect
neighbors
- the [Visualization tools](https://frbcesab.github.io/chessboard/articles/visualization-tools.html)
vignette describes the plotting functions available in `chessboard`
## Citation
A companion paper has been submitted to [Journal of Open Source Software](https://joss.theoj.org/).
In the meantime, if you want to use the package, please cite it as:
> Casajus N, Rievrs Borges E, Tabacchi E, Fried G & Mouquet N (`r format(Sys.Date(), "%Y")`) chessboard: An R
package for creating network connections based on chess moves.
R package version 0.1. URL: <https://github.com/frbcesab/chessboard>.
## Contributing
All types of contributions are encouraged and valued. For more information,
check out our [Contributor Guidelines](https://github.com/FRBCesab/chessboard/blob/main/CONTRIBUTING.md).
Please note that the `chessboard` project is released with a
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
## Acknowledgments
This package has been developed for the
[FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/)
working group
[Bridge](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/bridge/)
that aims to better understand the role of local and regional environmental
factors in shaping the taxonomic and functional diversity of plant communities
established along river corridors, roadside corridors and cultivated field
margins.
## References
Blanchet FG, Legendre P & Borcard D (2008) Modelling directional spatial processes
in ecological data. **Ecological Modelling**, 215, 325-336.
doi: [10.1016/j.ecolmodel.2008.04.001](https://doi.org/10.1016/j.ecolmodel.2008.04.001).
Csardi G & Nepusz T (2006) The igraph software package for complex network research.
**InterJournal, Complex Systems**, 1695, 1-9. <https://igraph.org/>.
Dray S, Bauman D, Blanchet G _et al._ (2023) `adespatial`: Multivariate Multiscale Spatial Analysis.
R package version 0.3-21, <https://CRAN.R-project.org/package=adespatial>.
Dray S, Legendre P & Peres-Neto PR (2006) Spatial modeling: a comprehensive
framework for principal coordinate analysis of neighbor matrices (PCNM).
**Ecological Modelling**, 196: 483–93.
doi: [10.1016/j.ecolmodel.2006.02.015](https://doi.org/10.1016/j.ecolmodel.2006.02.015).