Package: bioregion 1.4.0.9000

Maxime Lenormand

bioregion: Comparison of Bioregionalization Methods

The main purpose of this package is to propose a transparent methodological framework to compare bioregionalization 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_1.4.0.9000.tar.gz
bioregion_1.4.0.9000.zip(r-4.7)bioregion_1.4.0.9000.zip(r-4.6)bioregion_1.4.0.9000.zip(r-4.5)
bioregion_1.4.0.9000.tgz(r-4.6-x86_64)bioregion_1.4.0.9000.tgz(r-4.6-arm64)bioregion_1.4.0.9000.tgz(r-4.5-x86_64)bioregion_1.4.0.9000.tgz(r-4.5-arm64)
bioregion_1.4.0.9000.tar.gz(r-4.7-arm64)bioregion_1.4.0.9000.tar.gz(r-4.7-x86_64)bioregion_1.4.0.9000.tar.gz(r-4.6-arm64)bioregion_1.4.0.9000.tar.gz(r-4.6-x86_64)
bioregion_1.4.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs 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:

Conda:

biogeographybioregionbioregionalizationcpp

5.27 score 11 stars 12 scripts 710 downloads 38 exports 100 dependencies

Last updated from:a9f10b539e. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK221
linux-devel-x86_64OK236
source / vignettesOK269
linux-release-arm64OK213
linux-release-x86_64OK251
macos-release-arm64OK233
macos-release-x86_64OK580
macos-oldrel-arm64OK225
macos-oldrel-x86_64OK334
windows-develOK187
windows-releaseOK192
windows-oldrelOK176
wasm-releaseOK156

Exports:as_bioregion_pairwisebetapart_to_bioregionbind_pairwisebioregion_colorsbioregion_metricsbioregionalization_metricscompare_bioregionalizationscut_treedissimilaritydissimilarity_to_similarityexportGDFfind_optimal_nhclu_dianahclu_hierarclusthclu_opticsinstall_binariesmap_bioregionsmat_to_netnet_to_matnetclu_beckettnetclu_greedynetclu_infomapnetclu_labelpropnetclu_leadingeigennetclu_leidennetclu_louvainnetclu_oslomnetclu_walktrapnhclu_affpropnhclu_claranhclu_claransnhclu_dbscannhclu_kmeansnhclu_pamsimilaritysimilarity_to_dissimilaritysite_species_metricssite_species_subset

Dependencies:apclusterapeaskpassbase64encbipartitebslibcachemclassclassIntcliclustercodacorpcorcpp11curldata.tableDBIdbscandigestdotCall64dplyrdynamicTreeCute1071evaluatefarverfastclusterfastkmedoidsfastmapfastmatchfieldsfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshttrigraphisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrmapsMASSmathjaxrMatrixmemoisemgcvmimenetworknlmeopensslpermutephangornpillarpkgconfigproxypurrrquadprogR6rappdirsrbibutilsrcartocolorRColorBrewerRcppRdpackrlangrmarkdowns2S7sassscalessegmentedsfsnaspamstatnet.commonstringistringrsystibbletidyrtidyselecttinytexunitsutf8vctrsveganviridisLitewithrwkxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Convert a matrix or list of matrices to a bioregion (dis)similarity objectas_bioregion_pairwise
Convert betapart dissimilarity to bioregion dissimilarity (DEPRECATED)betapart_to_bioregion
Combine and enrich bioregion (dis)similarity object(s)bind_pairwise
Add color palettes to bioregion cluster objectsbioregion_colors
Calculate metrics for bioregionsbioregion_metrics
Calculate metrics for one or several bioregionalizationsbioregionalization_metrics
Compare cluster memberships among multiple bioregionalizationscompare_bioregionalizations
Cut a hierarchical treecut_tree
Compute dissimilarity metrics (beta-diversity) between sites based on species compositiondissimilarity
Convert dissimilarity metrics to similarity metricsdissimilarity_to_similarity
Export a network to GDF format for Gephi visualizationexportGDF
Search for an optimal number of clusters in a list of bioregionalizationsfind_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 Europefishsf
Divisive hierarchical clustering based on dissimilarity or beta-diversityhclu_diana
Hierarchical clustering based on dissimilarity or beta-diversityhclu_hierarclust
OPTICS hierarchical clustering algorithmhclu_optics
Download, unzip, check permissions, and test the bioregion's binary filesinstall_binaries
Create a map of bioregionsmap_bioregions
Create a data.frame from a contingency tablemat_to_net
Create a contingency table from a data.framenet_to_mat
Community structure detection in weighted bipartite networks via modularity optimizationnetclu_beckett
Community structure detection via greedy optimization of modularitynetclu_greedy
Infomap community findingnetclu_infomap
Finding communities based on propagating labelsnetclu_labelprop
Finding communities based on the leading eigenvector of the community matrixnetclu_leadingeigen
Finding communities using the Leiden algorithmnetclu_leiden
Louvain community findingnetclu_louvain
OSLOM community findingnetclu_oslom
Community structure detection via short random walksnetclu_walktrap
Non-hierarchical clustering: Affinity Propagationnhclu_affprop
Non-hierarchical clustering: CLARAnhclu_clara
Non-hierarchical clustering: CLARANSnhclu_clarans
Non-hierarchical clustering: DBSCANnhclu_dbscan
Non-hierarchical clustering: K-means analysisnhclu_kmeans
Non-hierarchical clustering: Partitioning Around Medoidsnhclu_pam
Compute similarity metrics between sites based on species compositionsimilarity
Convert similarity metrics to dissimilarity metricssimilarity_to_dissimilarity
Calculate metrics for sites and species relative to bioregions and chorotypessite_species_metrics
Extract a subset of sites or species from a 'bioregion.clusters' objectsite_species_subset
Spatial distribution of Mediterranean vegetation (data.frame)vegedf
Spatial distribution of Mediterranean vegetation (co-occurrence matrix)vegemat
Spatial distribution of Mediterranean vegetation (sf data.frame)vegesf