Package: bioregion 1.1.3

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_1.1.3.tar.gz
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bioregion_1.1.3.tgz(r-4.4-x86_64)bioregion_1.1.3.tgz(r-4.4-arm64)bioregion_1.1.3.tgz(r-4.3-x86_64)bioregion_1.1.3.tgz(r-4.3-arm64)
bioregion_1.1.3.tar.gz(r-4.5-noble)bioregion_1.1.3.tar.gz(r-4.4-noble)
bioregion_1.1.3.tgz(r-4.4-emscripten)bioregion_1.1.3.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'))

Peer review:

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

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:

biogeographybioregionbioregionalization

6.42 score 6 stars 10 scripts 511 downloads 33 exports 95 dependencies

Last updated 2 days agofrom:6d2d108005. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64OKNov 20 2024
R-4.5-linux-x86_64OKNov 20 2024
R-4.4-win-x86_64OKNov 20 2024
R-4.4-mac-x86_64OKNov 20 2024
R-4.4-mac-aarch64OKNov 20 2024
R-4.3-win-x86_64OKNov 20 2024
R-4.3-mac-x86_64OKNov 20 2024
R-4.3-mac-aarch64OKNov 20 2024

Exports:betapart_to_bioregioncompare_partitionscontributioncut_treedissimilaritydissimilarity_to_similarityfind_optimal_nhclu_dianahclu_hierarclusthclu_opticsinstall_binariesmap_clustersmat_to_netnet_to_matnetclu_beckettnetclu_greedynetclu_infomapnetclu_labelpropnetclu_leadingeigennetclu_leidennetclu_louvainnetclu_oslomnetclu_walktrapnhclu_affpropnhclu_claranhclu_claransnhclu_dbscannhclu_kmeansnhclu_pampartition_metricssimilaritysimilarity_to_dissimilaritysubset_node

Dependencies:apclusterapebase64encbipartitebslibcachemclassclassIntcliclustercodacolorspacecpp11data.tableDBIdbscandigestdotCall64dplyrdynamicTreeCute1071evaluatefansifarverfastclusterfastkmedoidsfastmapfastmatchfieldsfontawesomefsgenericsggplot2gluegtablehighrhtmltoolsigraphisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrmapsMASSmathjaxrMatrixmemoisemgcvmimemunsellnetworknlmepermutephangornpillarpkgconfigproxypurrrquadprogR6rappdirsrbibutilsRColorBrewerRcppRdpackrlangrmarkdowns2sassscalessegmentedsfsnaspamstatnet.commonstringistringrtibbletidyrtidyselecttinytexunitsutf8vctrsveganviridisLitewithrwkxfunyaml

5.3 Contribution

Pierre Denelle, Boris Leroy and Maxime Lenormand

Rendered froma5_3_contribution.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-11-20
Started: 2024-10-16

Tutorial for bioregion

Maxime Lenormand, Boris Leroy and Pierre Denelle

Rendered frombioregion.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-04-19
Started: 2023-03-10

Readme and manuals

Help Manual

Help pageTopics
Convert betapart Dissimilarity to bioregion Dissimilaritybetapart_to_bioregion
Compare cluster memberships among multiple partitionscompare_partitions
Calculate contribution metrics of sites and speciescontribution
Cut a hierarchical treecut_tree
Compute dissimilarity metrics (beta-diversity) between sites based on species compositiondissimilarity
Convert dissimilarity metrics to similarity metricsdissimilarity_to_similarity
Search for an optimal number of clusters in a list of partitionsfind_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 permission and test the bioregion's binary filesinstall_binaries
Create a map of bioregionsmap_clusters
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 network 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 leading eigen vector 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
dbscan clusteringnhclu_dbscan
Non hierarchical clustering: k-means analysisnhclu_kmeans
Non hierarchical clustering: partitioning around medoidsnhclu_pam
Calculate metrics for one or several partitionspartition_metrics
Compute similarity metrics between sites based on species compositionsimilarity
Convert similarity metrics to dissimilarity metricssimilarity_to_dissimilarity
Extract a subset of nodes from a bioregion.clusters objectsubset_node
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