Package: phyloregion 1.0.9

Barnabas H. Daru

phyloregion: Biogeographic Regionalization and Macroecology

Computational infrastructure for biogeography, community ecology, and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>. It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>. The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013> on patterns and processes of biogeographical regionalization. Additionally, the package contains fast and efficient functions to compute more standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment, as well as compositional turnover (e.g., beta diversity).

Authors:Barnabas H. Daru [aut, cre, cph], Piyal Karunarathne [aut], Klaus Schliep [aut], Xiaobei Zhao [ctb], Albin Sandelin [ctb], Luciano Pataro [ctb]

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phyloregion.pdf |phyloregion.html
phyloregion/json (API)
NEWS

# Install 'phyloregion' in R:
install.packages('phyloregion', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/darunabas/phyloregion/issues

Datasets:
  • africa - Plants of southern Africa

On CRAN:

software

7.51 score 18 stars 1 packages 50 scripts 424 downloads 1 mentions 61 exports 68 dependencies

Last updated 30 days agofrom:99bf571ed3. Checks:OK: 5 NOTE: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winNOTENov 21 2024
R-4.5-linuxNOTENov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:arc_labelsbackgbeta_corebeta_disschoroplethcoldspotscollapse_rangecountsdense2longdense2sparsedirpathEDGEevol_distinctfishnetfitgomfunctional_betaget_cladeshexcolshotspotsindicatorsinfomaplong2denselong2sparsemap_traitmatch_phylo_commMatrixmean_distnodepieoptimal_phyloregionPDPD_sesphylo_endemismphylobetaphylobeta_corephylobeta_sesphylobuilderphyloregionplot_NMDSplot_pieplot.phyloregionplot.sparsepoints2commpolys2commrandom_speciesrandpointsrast_hotspotrast_quantilerast2commread.communityRPDsdmselect_linkageselectbylocationsparse2densesparse2longsparseMatrixtext_NMDStimeslicetree_samplerunifracweighted_endemism

Dependencies:abindapebetapartclassclassIntcliclusterclustMixTypecodetoolscolorspacecombinatcpp11DBIdigestdoSNOWdplyre1071fansifastmatchforeachgenericsgeometryglueigraphiteratorsitertoolsKernSmoothlatticelifecyclelinproglpSolvemagicmagrittrmaptpxMASSMatrixmgcvminpack.lmnlmepermutephangornpicantepillarpkgconfigpredictsproxyquadprogR6rcddRColorBrewerRcppRcppArmadilloRcppProgressrlangs2sfslamsmoothrsnowterratibbletidyselectunitsutf8vctrsveganwithrwk

An introduction to the phyloregion package

Rendered fromphyloregion-intro.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2022-11-16
Started: 2020-01-14

Benchmarking phyloregion

Rendered fromBenchmark.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2022-11-16
Started: 2020-01-14

Fast Evolutionary Distinctiveness

Rendered fromed.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2022-11-16
Started: 2020-12-14

Readme and manuals

Help Manual

Help pageTopics
Biogeographic regionalization and macroecologyphyloregion-package
Plants of southern Africaafrica
Add arc labels to plotted phylogenyarc_labels arc_labels.default
Sample background pointsbackg randpoints
Taxonomic (non-phylogenetic) beta diversitybeta_core beta_diss
Bin valueschoropleth
Computes biodiversity coldspots and hotspotscoldspots hotspots rast_hotspot
Collapse nodes and ranges based on divergence timescollapse_range
Phyloregions for functional traits and phylogenycounts
Get current directorydirpath
Evolutionary Distinctiveness and Global EndangermentEDGE
Species' evolutionary distinctivenessevol_distinct
Create fishnet of regular gridsfishnet
Fits Grade of membership models for biogeographic regionalizationfitgom
Functional beta diversity for mixed-type functional traitsfunctional_beta
Get descendant nodes of phylogeny at a given time depthget_clades
Generate diverging colors in HCL colour space.hexcols
Top driving species in phyloregionsindicators
Conversion of community datadense2long dense2sparse long2dense long2sparse sparse2dense sparse2long
Map species' trait values in geographic spacemap_trait
Match taxa and in phylogeny and community matrixmatch_phylo_comm
Mean distance matrix from a set of distance matricesmean_dist
Label phylogenetic nodes using pienodepie
Determine optimal number of clustersoptimal_phyloregion
Phylogenetic diversityPD RPD
Phylogenetic diversity standardized for species richnessPD_ses
Phylogenetic Endemismphylo_endemism
Phylogenetic beta diversityphylobeta phylobeta_core
Phylogenetic beta diversity standardized for species beta diversityphylobeta_ses
Create a subtree with largest overlap from a species list.phylobuilder
Compute phylogenetic regionalization and evolutionary distinctiveness of phyloregionsinfomap phyloregion
Visualize biogeographic patterns using pie chartsplot_pie
Visualize biogeographic patternsplot.phyloregion plot_NMDS text_NMDS
Create illustrative sparse matrixplot.sparse
Generate random species distributions in spacerandom_species
Standardizes raster values for mappingrast_quantile
Convert raw input distribution data to communitypoints2comm polys2comm rast2comm
Read in sparse community matricesread.community
Fast species distribution modelsdm
Cluster algorithm selection and validationselect_linkage
Select polygon features from another layer and adds polygon attributes to layerselectbylocation
Slice phylogenetic tree at various time depthstimeslice
Subset trees from posterior distribution of trees.tree_sampler
UniFrac distanceunifrac
Measure the distribution of narrow-ranged or endemic species.weighted_endemism