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README.Rmd
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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/README-",
out.width = "100%"
)
```
# bioregion <img src="man/figures/logo.svg" align="right" alt="" width="200" />
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[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/bioregion)](https://cran.r-project.org/package=bioregion)
[![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/bioregion)](https://r-pkg.org:443/pkg/bioregion)
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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 partitions](https://bioRgeo.github.io/bioregion/articles/a5_2_compare_partitions.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`, `bipartite`, `cluster`, `data.table`, `dbscan`,
`dynamicTreeCut`, `earth`, `fastcluster`, `ggplot2`, `grDevices`, `igraph`,
`mathjaxr`, `Matrix`, `Rcpp`, `Rdpack`, `rlang`, `rmarkdown`, `segmented`,`sf`,
`stats`, `tidyr` and `utils`.