Package: nodiv 1.4.1

nodiv: Compares the Distribution of Sister Clades Through a Phylogeny

An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <doi:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped.

Authors:Michael Krabbe Borregaard

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nodiv.pdf |nodiv.html✨
nodiv/json (API)

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

Peer review:

Bug tracker:https://github.com/mkborregaard/nodiv/issues

Datasets:
  • coquettes - Distribution of coquette hummingbirds in Northern South America

On CRAN:

3.45 score 2 stars 28 scripts 370 downloads 1 mentions 44 exports 15 dependencies

Last updated 2 years agofrom:a899894220. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
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R-4.5-linuxNOTENov 20 2024
R-4.4-winOKNov 20 2024
R-4.4-macOKNov 20 2024
R-4.3-winOKNov 20 2024
R-4.3-macOKNov 20 2024

Exports:add_shapeadd_sitestatadd_species_statassemblagebasal_nodecoordsDescendantsdistrib_dataGNDgridDataMostRecentAncestorNode_analysisNode_occupancyNode_sitesNode_sizeNode_speciesnodenumbersnodesNodesignodiv_dataNsitesNspeciesoccupancyoccurrencesParentphyplotplot_gridplot_nodeplot_nodes_phyloplot_pointsplot_richnessplot_sitestatplot_speciesplotSOSrichnessSistersitessitestatSOSspeciesspecies_statsubsampletwo_color_mapupdate_object

Dependencies:apeclusterdigestlatticeMASSMatrixmgcvnlmepermutepicanterasterRcppspterravegan

Readme and manuals

Help Manual

Help pageTopics
nodiv - Node-based analysis of species distributionsnodiv-package nodiv
Add a shapefile to a 'nodiv' data objectadd_shape
Identify nodes in a phylogenybasal_node Descendants MostRecentAncestor nodenumbers nodes Parent Sister
Distribution of coquette hummingbirds in Northern South Americacoquettes
Data objects for node-based analysisdistrib_data identify.distrib_data nodiv_data plot.distrib_data plot.nodiv_data print.distrib_data print.nodiv_data summary.distrib_data summary.nodiv_data
Apply a grid (2D bins) to nodiv objects of type 'points'gridData
Calculate GND and SOS scores for a phylogeny and community data setNode_analysis nodiv_result plot.nodiv_result print.nodiv_result print.summary_nodiv_result summary.nodiv_result
Attributes of individual cladesNode_occupancy Node_sites Node_size Node_species
Compare the distributions of a pair of sister cladesNodesig
Basic attributes of 'distrib_data' objectscoords Nsites Nspecies occupancy richness sites species
Access functions to the community matrix of 'distrib_data' objectsassemblage occurrences
Plot Phylogeniesphyplot
Plot a phylogeny with colored node labelsplot_nodes_phylo
Plot a variable on spatial points or a spatial grid using a color scale.plot_grid plot_points plot_species
Plot a richness map for an object of type distrib_data, nodiv_data or nodiv_resultplot_node plot_richness
Site statistics of 'nodiv' data objectsadd_sitestat plot_sitestat sitestat
Gives the SOS values for a given node.GND plotSOS SOS
Species statistics of 'nodiv' data objectsadd_species_stat species_stat
Subsampling data objects to certain species or sitessubsample subsample.distrib_data subsample.nodiv_data subsample.nodiv_result
Plot the relative amounts of two variables using a purple-green color schemetwo_color_map
Update 'distrib_data' objects to the 'nodiv' version >= 1.1 formatupdate_object