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<!-- 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/README-",
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# bioregion <img src="man/figures/logo.svg" align="right" alt="" width="200" />

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This **R package** gathers a comprehensive set of algorithms to perform
bioregionalisation analyses. 

Bioregionalisation methods can be based on 
hierarchical clustering algorithms, non-hierarchical clustering algorithms or 
network algorithms.

## :arrow_double_down: Installation

The package can be installed with the following command line in R session:

From the CRAN

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

or from GitHub

``` r
# install.packages("devtools")
devtools::install_github("bioRgeo/bioregion")
```

## :scroll: Vignettes

We wrote several vignettes that will help you using the **bioregion R package**.
Vignettes available are the following ones: <br>

- **[1. Installation of the executable binary files](https://bioRgeo.github.io/bioregion/articles/a1_install_binary_files.html)**  
- **[2. Matrix and network formats](https://bioRgeo.github.io/bioregion/articles/a2_matrix_and_network_formats.html)**
- **[3. Pairwise similarity/dissimilarity metrics](https://bioRgeo.github.io/bioregion/articles/a3_pairwise_metrics.html)** 
- **[4.1 Hierarchical clustering](https://bioRgeo.github.io/bioregion/articles/a4_1_hierarchical_clustering.html)** 
- **[4.2 Non-hierarchical clustering](https://bioRgeo.github.io/bioregion/articles/a4_2_non_hierarchical_clustering.html)** 
- **[4.3 Network clustering](https://bioRgeo.github.io/bioregion/articles/a4_3_network_clustering.html)** 
- **[4.4 Microbenchmark](https://bioRgeo.github.io/bioregion/articles/a4_4_microbenchmark.html)** 
- **[5.1 Visualization](https://bioRgeo.github.io/bioregion/articles/a5_1_visualization.html)** 
- **[5.2 Compare bioregionalizations](https://bioRgeo.github.io/bioregion/articles/a5_2_compare_bioregionalizations.html)** 
- **[5.3 Summary metrics](https://bioRgeo.github.io/bioregion/articles/a5_3_summary_metrics.html)** 

Alternatively, if you prefer to view the vignettes in R, you can install the
package with `build_vignettes = TRUE`. But be aware that some vignettes can be
slow to generate.

```{r, eval = FALSE}
remotes::install_github("bioRgeo/bioregion",
                        dependencies = TRUE, 
                        upgrade = "ask", 
                        build_vignettes = TRUE)

vignette("bioregion")
```

## :desktop_computer: Functions

An overview of all functions and data is given 
**[here](https://bioRgeo.github.io/bioregion/reference/index.html)**.

## :bug: Find a bug?

Thank you for finding it. Head over to the GitHub Issues tab and let us know
about it. Alternatively, you can also send us an e-mail.
We will try to get to it as soon as we can!

## References and dependencies  

`bioregion` depends on `ape`, `apcluster`, `bipartite`, `cluster`, `data.table`,
`dbscan`, `dynamicTreeCut`, `earth`, `fastcluster`, `ggplot2`, `grDevices`, 
`httr`, `igraph`, `mathjaxr`, `Matrix`, `phangorn`, `Rdpack`, `rlang`, `rmarkdown`,
`segmented`,`sf`, `stats`, `tidyr` and `utils`.