Package: rdiversity 2.2.0

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) <arxiv:1404.6520v3>.

Authors:Sonia Mitchell [aut], Richard Reeve [cre, aut, ths], Tom White [ctb], Daniel Dörrhöfer [ctb], Aaron Rudkin [ctb]

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rdiversity.pdf |rdiversity.html✨
rdiversity/json (API)
NEWS

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

Peer review:

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

On CRAN:

biodiversitydiversity-measurementpartitioning-diversity

38 exports 7 stars 2.11 score 12 dependencies 1 dependents 3 mentions 65 scripts 257 downloads

Last updated 2 years agofrom:77e4212827. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winOKSep 13 2024
R-4.5-linuxOKSep 13 2024
R-4.4-winOKSep 13 2024
R-4.4-macOKSep 13 2024
R-4.3-winOKSep 13 2024
R-4.3-macOKSep 13 2024

Exports:as.binarychainsawdist2simdistancegen2distinddivmeta_gammametacommunitymetadivnorm_alphanorm_betanorm_meta_alphanorm_meta_betanorm_meta_rhonorm_rhonorm_sub_alphanorm_sub_betanorm_sub_rhophy_abundancephy_structphy2branchphy2distpower_meanraw_alpharaw_betaraw_gammaraw_meta_alpharaw_meta_betaraw_meta_rhoraw_rhoraw_sub_alpharaw_sub_betaraw_sub_rhorepartitionsimilaritysub_gammasubdivtax2dist

Dependencies:cligluelifecyclemagrittrplyrRcppreshape2rlangstringdiststringistringrvctrs

rdiversity examples

Sonia Mitchell

Rendered fromexamples.Rmdusingknitr::knitron Sep 13 2024.

Last update: 2020-12-21
Started: 2020-12-21

Readme and manuals

Help Manual

Help pageTopics
rdiversity: diversity measurement in Rrdiversity-package rdiversity
as binary digit.as.binary
Binary Addition (+)binAdd
Binary digit.binary
Binary sequencebinSeq
A simple helper function to return the size of one bytebyte
Minimum number of "byte" needed to hold n "bit"bytesNeeded
Function to cut the phylogeny to a specified depth from the tip with the greatest distance from the root.chainsaw
Distance to similaritydist2sim
Generate distance objectdistance distance,matrix,character-method distance,matrix,missing-method
distance-classdistance-class show,distance-method
Fill up to bit (000..)fillUpToBit
Fill up to Byte (00000000..)fillUpToByte
Genetic distance matrixgen2dist
Calculate individual-level diversityinddiv inddiv,metacommunity-method inddiv,powermean-method inddiv,relativeentropy-method
is Binary Vectoris.binary
loadAttributesloadAttributes
Metacommunity gamma diversitymeta_gamma
Metacommunitymetacommunity 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-classmetacommunity-class show,metacommunity-method
Metacommunity-level diversitymetadiv metadiv,metacommunity-method metadiv,powermean-method metadiv,relativeentropy-method
Binary Negation (!)negate
Normalised alpha (low level diversity component)norm_alpha
Normalised beta (low level diversity component)norm_beta
Normalised metacommunity alpha diversitynorm_meta_alpha
Normalised metacommunity beta diversitynorm_meta_beta
Normalised metacommunity rho diversitynorm_meta_rho
Normalised rho (low level diversity component)norm_rho
Normalised subcommunity alpha diversitynorm_sub_alpha
Normalised subcommunity beta diversitynorm_sub_beta
Normalised subcommunity rho diversitynorm_sub_rho
Group Generic OpsOps.binary
Relative abundance of historical speciesphy_abundance
Calculate phylogenetic structure matrixphy_struct
Phylogenetic similarityphy2branch
Phylogenetic pairwise tip distance matrixphy2dist
Power mean of vector elementspower_mean
powermean-classpowermean-class
Print method for binary number.print.binary
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 diversityraw_meta_alpha
Raw metacommunity beta diversityraw_meta_beta
Raw metacommunity rho diversityraw_meta_rho
Raw rho (low level diversity component)raw_rho
Raw subcommunity alpha diversityraw_sub_alpha
Raw subcommunity beta diversityraw_sub_beta
Raw subcommunity rho diversityraw_sub_rho
relativeentropy-classrelativeentropy-class
Repartition metacommunityrepartition
saveAttributessaveAttributes
Generate similarity objectsimilarity similarity,matrix,character-method similarity,matrix,missing-method
similarity-classshow,similarity-method similarity-class
Subcommunity gamma diversitysub_gamma
Calculate subcommunity-level diversitysubdiv subdiv,metacommunity-method subdiv,powermean-method subdiv,relativeentropy-method
Summary method for binary number.summary.binary
Switch Endianess.switchEndianess
Generate taxonomic distance matrixtax2dist