Package: bioregion 1.2.0

Maxime Lenormand

bioregion: Comparison of Bioregionalisation Methods

The main purpose of this package is to propose a transparent methodological framework to compare bioregionalisation methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).

Authors:Maxime Lenormand [aut, cre], Boris Leroy [aut], Pierre Denelle [aut]

bioregion_1.2.0.tar.gz
bioregion_1.2.0.zip(r-4.5)bioregion_1.2.0.zip(r-4.4)bioregion_1.2.0.zip(r-4.3)
bioregion_1.2.0.tgz(r-4.5-x86_64)bioregion_1.2.0.tgz(r-4.5-arm64)bioregion_1.2.0.tgz(r-4.4-x86_64)bioregion_1.2.0.tgz(r-4.4-arm64)bioregion_1.2.0.tgz(r-4.3-x86_64)bioregion_1.2.0.tgz(r-4.3-arm64)
bioregion_1.2.0.tar.gz(r-4.5-noble)bioregion_1.2.0.tar.gz(r-4.4-noble)
bioregion_1.2.0.tgz(r-4.4-emscripten)bioregion_1.2.0.tgz(r-4.3-emscripten)
bioregion.pdf |bioregion.html✨
bioregion/json (API)
NEWS

# Install 'bioregion' in R:

install.packages('bioregion', repos = c('https://biorgeo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biorgeo/bioregion/issues

Pkgdown site:https://biorgeo.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

fishdf - Spatial distribution of fish in Europe
fishmat - Spatial distribution of fish in Europe
fishsf - Spatial distribution of fish in Europe
vegedf - Spatial distribution of Mediterranean vegetation
vegemat - Spatial distribution of Mediterranean vegetation
vegesf - Spatial distribution of Mediterranean vegetation

On CRAN:

biogeography bioregion bioregionalization cpp

6.23 score 6 stars 11 scripts 741 downloads 34 exports 100 dependencies

Last updated 20 days agofrom:c58cabf179. Checks:11 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 31 2025
R-4.5-win-x86_64	OK	Jan 31 2025
R-4.5-mac-x86_64	OK	Jan 31 2025
R-4.5-mac-aarch64	OK	Jan 31 2025
R-4.5-linux-x86_64	OK	Jan 31 2025
R-4.4-win-x86_64	OK	Jan 31 2025
R-4.4-mac-x86_64	OK	Jan 31 2025
R-4.4-mac-aarch64	OK	Jan 31 2025
R-4.3-win-x86_64	OK	Jan 31 2025
R-4.3-mac-x86_64	OK	Jan 31 2025
R-4.3-mac-aarch64	OK	Jan 31 2025

Exports:betapart_to_bioregion bioregion_metrics bioregionalization_metrics compare_bioregionalizations cut_tree dissimilarity dissimilarity_to_similarity find_optimal_n hclu_diana hclu_hierarclust hclu_optics install_binaries map_bioregions mat_to_net net_to_mat netclu_beckett netclu_greedy netclu_infomap netclu_labelprop netclu_leadingeigen netclu_leiden netclu_louvain netclu_oslom netclu_walktrap nhclu_affprop nhclu_clara nhclu_clarans nhclu_dbscan nhclu_kmeans nhclu_pam similarity similarity_to_dissimilarity site_species_metrics site_species_subset

Dependencies:apcluster ape askpass base64enc bipartite bslib cachem class classInt cli cluster coda colorspace cpp11 curl data.table DBI dbscan digest dotCall64 dplyr dynamicTreeCut e1071 evaluate fansi farver fastcluster fastkmedoids fastmap fastmatch fields fontawesome fs generics ggplot2 glue gtable highr htmltools httr igraph isoband jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle magrittr maps MASS mathjaxr Matrix memoise mgcv mime munsell network nlme openssl permute phangorn pillar pkgconfig proxy purrr quadprog R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack rlang rmarkdown s2 sass scales segmented sf sna spam statnet.common stringi stringr sys tibble tidyr tidyselect tinytex units utf8 vctrs vegan viridisLite withr wk xfun yaml

Tutorial for bioregion

Maxime Lenormand, Boris Leroy and Pierre Denelle

Rendered frombioregion.Rmdusingknitr::rmarkdownon Jan 31 2025.

Last update: 2024-12-13
Started: 2023-03-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert betapart dissimilarity to bioregion dissimilarity	betapart_to_bioregion
Calculate contribution metrics for bioregions	bioregion_metrics
Calculate metrics for one or several bioregionalizations	bioregionalization_metrics
Compare cluster memberships among multiple bioregionalizations	compare_bioregionalizations
Cut a hierarchical tree	cut_tree
Compute dissimilarity metrics (beta-diversity) between sites based on species composition	dissimilarity
Convert dissimilarity metrics to similarity metrics	dissimilarity_to_similarity
Search for an optimal number of clusters in a list of bioregionalizations	find_optimal_n
Spatial distribution of fish in Europe (data.frame)	fishdf
Spatial distribution of fish in Europe (co-occurrence matrix)	fishmat
Spatial distribution of fish in Europe	fishsf
Divisive hierarchical clustering based on dissimilarity or beta-diversity	hclu_diana
Hierarchical clustering based on dissimilarity or beta-diversity	hclu_hierarclust
OPTICS hierarchical clustering algorithm	hclu_optics
Download, unzip, check permissions, and test the bioregion's binary files	install_binaries
Create a map of bioregions	map_bioregions
Create a data.frame from a contingency table	mat_to_net
Create a contingency table from a data.frame	net_to_mat
Community structure detection in weighted bipartite networks via modularity optimization	netclu_beckett
Community structure detection via greedy optimization of modularity	netclu_greedy
Infomap community finding	netclu_infomap
Finding communities based on propagating labels	netclu_labelprop
Finding communities based on the leading eigenvector of the community matrix	netclu_leadingeigen
Finding communities using the Leiden algorithm	netclu_leiden
Louvain community finding	netclu_louvain
OSLOM community finding	netclu_oslom
Community structure detection via short random walks	netclu_walktrap
Non-hierarchical clustering: Affinity Propagation	nhclu_affprop
Non-hierarchical clustering: CLARA	nhclu_clara
Non-hierarchical clustering: CLARANS	nhclu_clarans
Non-hierarchical clustering: DBSCAN	nhclu_dbscan
Non-hierarchical clustering: K-means analysis	nhclu_kmeans
Non-hierarchical clustering: Partitioning Around Medoids	nhclu_pam
Compute similarity metrics between sites based on species composition	similarity
Convert similarity metrics to dissimilarity metrics	similarity_to_dissimilarity
Calculate contribution metrics of sites and species	site_species_metrics
Extract a subset of sites or species from a 'bioregion.clusters' object	site_species_subset
Spatial distribution of Mediterranean vegetation (data.frame)	vegedf
Spatial distribution of Mediterranean vegetation (co-occurrence matrix)	vegemat
Spatial distribution of Mediterranean vegetation (spatial grid)	vegesf