Package: rdiversity 2.3.0

Richard Reeve

rdiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

Provides a framework for the measurement and partitioning of the (similarity-sensitive) biodiversity of a metacommunity and its constituent subcommunities. Richard Reeve, et al. (2016) <doi:10.48550/arXiv.1404.6520>.

Authors:Sonia Mitchell [aut], Richard Reeve [cre, aut, ths], Tom White [ctb]

rdiversity_2.3.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rdiversity/json (API)

# Install 'rdiversity' in R:

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

Bug tracker:https://github.com/boydorr/rdiversity/issues

On CRAN:

biodiversity diversity-measurement partitioning-diversity

6.64 score 10 stars 72 scripts 298 downloads 3 mentions 37 exports 1 dependencies

Last updated from:fae9cf877e. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	126
source / vignettes	OK	189
linux-release-x86_64	OK	134
macos-release-arm64	OK	80
macos-oldrel-arm64	OK	107
windows-devel	OK	74
windows-release	OK	76
windows-oldrel	OK	92
wasm-release	OK	131

Exports:chainsaw dist2sim distance gen2dist inddiv meta_gamma metacommunity metadiv norm_alpha norm_beta norm_meta_alpha norm_meta_beta norm_meta_rho norm_rho norm_sub_alpha norm_sub_beta norm_sub_rho phy_abundance phy_struct phy2branch phy2dist power_mean raw_alpha raw_beta raw_gamma raw_meta_alpha raw_meta_beta raw_meta_rho raw_rho raw_sub_alpha raw_sub_beta raw_sub_rho repartition similarity sub_gamma subdiv tax2dist

Dependencies:stringdist

rdiversity examples

Rendered fromexamples.Rmdusingknitr::knitr

Last update: 2026-07-15
Started: 2020-12-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
rdiversity: diversity measurement in R	rdiversity-package rdiversity
Function to cut the phylogeny to a specified depth from the tip with the greatest distance from the root.	chainsaw
Distance to similarity	dist2sim
Generate distance object	distance distance,matrix,character-method distance,matrix,missing-method
distance-class	distance-class show,distance-method
Genetic distance matrix	gen2dist
Calculate individual-level diversity	inddiv inddiv,metacommunity-method inddiv,powermean-method inddiv,relativeentropy-method
Metacommunity gamma diversity	meta_gamma
Metacommunity	metacommunity metacommunity,data.frame,missing-method metacommunity,data.frame,similarity-method metacommunity,data.frame-method metacommunity,matrix,missing-method metacommunity,matrix,similarity-method metacommunity,matrix-method metacommunity,missing,similarity-method metacommunity,numeric,missing-method metacommunity,numeric,similarity-method metacommunity,numeric-method metacommunity,similarity-method
metacommunity-class	metacommunity-class show,metacommunity-method
Metacommunity-level diversity	metadiv metadiv,metacommunity-method metadiv,powermean-method metadiv,relativeentropy-method
Normalised alpha (low level diversity component)	norm_alpha
Normalised beta (low level diversity component)	norm_beta
Normalised metacommunity alpha diversity	norm_meta_alpha
Normalised metacommunity beta diversity	norm_meta_beta
Normalised metacommunity rho diversity	norm_meta_rho
Normalised rho (low level diversity component)	norm_rho
Normalised subcommunity alpha diversity	norm_sub_alpha
Normalised subcommunity beta diversity	norm_sub_beta
Normalised subcommunity rho diversity	norm_sub_rho
Relative abundance of historical species	phy_abundance
Calculate phylogenetic structure matrix	phy_struct
Phylogenetic similarity	phy2branch
Phylogenetic pairwise tip distance matrix	phy2dist
Power mean of vector elements	power_mean
powermean-class	powermean-class
Raw alpha (low level diversity component)	raw_alpha
Raw beta (low level diversity component)	raw_beta
Gamma (low level diversity component)	raw_gamma
Raw metacommunity alpha diversity	raw_meta_alpha
Raw metacommunity beta diversity	raw_meta_beta
Raw metacommunity rho diversity	raw_meta_rho
Raw rho (low level diversity component)	raw_rho
Raw subcommunity alpha diversity	raw_sub_alpha
Raw subcommunity beta diversity	raw_sub_beta
Raw subcommunity rho diversity	raw_sub_rho
relativeentropy-class	relativeentropy-class
Repartition metacommunity	repartition
Generate similarity object	similarity similarity,matrix,character-method similarity,matrix,missing-method
similarity-class	show,similarity-method similarity-class
Subcommunity gamma diversity	sub_gamma
Calculate subcommunity-level diversity	subdiv subdiv,metacommunity-method subdiv,powermean-method subdiv,relativeentropy-method
Generate taxonomic distance matrix	tax2dist