Package: adiv 2.2.1

adiv: Analysis of Diversity

Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.

Authors:Sandrine Pavoine

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# Install 'adiv' in R:

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

Datasets:

RDMCCP16 - Theoretical Data Set used in Ricotta et al.
RP15EI - Theoretical Data Set used in Ricotta and Pavoine (2015) in Ecological Indicators
RP15JVS - Theoretical Data Set used in Ricotta and Pavoine (2015) in Journal of Vegetation Science
RPP16EE - Theoretical Data Set used in Ricotta et al. (2016) in Ecology and Evolution
RutorGlacier - Functional and phylogenetic composition of plant communities along a primary succession on glacial deposits.
batcomm - Bat Abundance and Phylogeny Along a Disturbance Gradient in a Neotropical Rainforest
birdData - Avian Communities along Successional Forest Gradients
rockfish - Rockfish Phylogenetic Diversity in Southern California Bight

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

105 exports 1 stars 1.16 score 101 dependencies 3 mentions 59 scripts 574 downloads

Last updated 7 months agofrom:15da21938c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 17 2024
R-4.5-win	OK	Sep 17 2024
R-4.5-linux	OK	Sep 17 2024
R-4.4-win	OK	Sep 17 2024
R-4.4-mac	OK	Sep 17 2024
R-4.3-win	OK	Sep 17 2024
R-4.3-mac	OK	Sep 17 2024

Exports:abgaptree abgdivparam abgevodivparam apd aptree barp4d betastatjac betastatsor betaTreeUniqueness betaUniqueness CFbinary CFprop crossdpcoa_maineffect crossdpcoa_version1 crossdpcoa_version2 dbMANOVAspecies dbMANOVAspecies_pairwise decdiv discomQE dislptransport dissABC dissRicotta distinctAb distinctDis distinctTopo distinctTree distinctUltra distMS divparam DJac dotp4d DP dsimcom dsimFun dsimTaxo dsimTree dspca EH EqRao EqRS EqRSintra eveparam evoCA evodiss evodiss_family evodiss_ternaryplot evodiv evodivparam evoeveparam evoNSCA evopcachord evopcahellinger evouniparam FPdivparam FunImbalance generalized_Tradidiss gridp4d Jac K Kstar Kw multiCFbinary multiCFprop optimEH orisaved PADDis pIa plot.abgdivparam plot.abgevodivparam plot.aptree plot.decdiv plot.divparam plot.dspca plot.eveparam plot.evoCA plot.evodivparam plot.evoeveparam plot.evouniparam plot.FPdivparam plot.phylo4d plot.rlqESLTP plot.rtestaptree qDT QE qHdiv randEH rare_Rao Rentropy rlqESLTP rtestaptree rtestdecdiv rtestEqRao rtestEqRS rtestEqRSintra rtestwapqe speciesdiv specieseve SQ summary.dbMANOVAspecies_pairwise summary.rlqESLTP tecAptree treeUniqueness twoHmax uniqueness wapqe

Dependencies:ade4 adegraphics ape askpass base64enc bslib cachem cli cluster clusterGeneration coda codetools combinat cpp11 crayon curl deldir DEoptim digest doParallel dplyr evaluate expm fansi fastmap fastmatch fontawesome foreach fs generics glue highr hms htmltools htmlwidgets httr igraph interp iterators jpeg jquerylib jsonlite KernSmooth knitr lattice latticeExtra lifecycle lpSolve magrittr maps MASS Matrix memoise mime mnormt nlme numDeriv openssl optimParallel phangorn phylobase phytools pillar pixmap pkgconfig plyr png prettyunits progress purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rgl rlang rmarkdown rncl RNeXML sass scatterplot3d sp stringi stringr sys tibble tidyr tidyselect tinytex utf8 uuid vctrs withr xfun XML xml2 yaml

Help page	Topics
Analysis of Diversity	adiv-package adiv
Apportionment of Parametric Indices of Diversity	abgdivparam plot.abgdivparam
Apportionment of Parametric Indices of Phylogenetic Diversity	abgevodivparam plot.abgevodivparam
Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages	abgaptree apd aptree pIa plot.aptree plot.rtestaptree rtestaptree tecAptree
Bat Abundance and Phylogeny Along a Disturbance Gradient in a Neotropical Rainforest	batcomm
Multiple-Site Dissimilarity Measure for Species Presence/Absence Data	betastatjac betastatsor
Plot-to-plot functional or phylogenetic dissimilarity and uniqueness	betaTreeUniqueness
Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity and uniqueness	betaUniqueness
Avian Communities along Successional Forest Gradients	birdData
Matrices of Intra- and Inter-Specific Similarities	CFbinary CFprop multiCFbinary multiCFprop
Crossed-DPCoA	crossdpcoa_maineffect crossdpcoa_version1 crossdpcoa_version2
Indicator species analysis in the framework of multivariate analysis of variance	dbMANOVAspecies dbMANOVAspecies_pairwise summary.dbMANOVAspecies_pairwise
Decomposition of trait-based diversity along the nodes of a phylogenetic tree	decdiv plot.decdiv rtestdecdiv
Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity	dislptransport
Phylogenetic and Functional Similarity between Communities	dissABC
Plot-to-Plot Functional or Phylogenetic Dissimilarity	dissRicotta
Abundance-based measures of species' rarity, functional or phylogenetic distinctiveness and functional or phylogenetic effective originality	distinctAb
Dissimilarity-based Species' Originality	distinctDis
Topology-based Species' Originality	distinctTopo
Tree-based Species' Originality	distinctTree
Ultrametric Tree-based Species' Originality	distinctUltra
Marczewski-Steinhaus Coefficient	distMS
Parametric Indices of Species Diversity	divparam plot.divparam
Plot-to-plot functional or phylogenetic dissimilarity	DP
Functional or Phylogenetic Similarity between Species and Communities	dsimcom dsimFun dsimTaxo dsimTree SQ
Double similarity principal component analysis	dspca plot.dspca
Faith Phylogenetic Diversity	EH
Apportionment of Diversity	EqRao EqRS EqRSintra rtestEqRao rtestEqRS rtestEqRSintra rtestwapqe wapqe
Parametric Indices of Species Evenness	eveparam plot.eveparam
Evolutionary Correspondence Analysis	evoCA plot.evoCA
Pair-wise Phylogenetic Dissimilarities between Communities	evodiss
A Family of Indices Dedicated to Pair-wise Phylogenetic Dissimilarities between Communities	evodiss_family evodiss_ternaryplot
Indices of Phylogenetic Diversity	evodiv
Parametric Indices of Phylogenetic Diversity	evodivparam plot.evodivparam
Parametric Indices of Phylogenetic evenness	evoeveparam plot.evoeveparam
Evolutionary Non-Symmetric Correspondence Analysis	evoNSCA
Evolutionary Principal Component analyses	evopcachord evopcahellinger
Parametric Indices of Phylogenetic Uniqueness	evouniparam plot.evouniparam
Parametric Indices of Functional and Phylogenetic Diversity	FPdivparam plot.FPdivparam
Indices of functional imbalance	FunImbalance
Plot-to-plot dissimilarity taking account of functional dissimilarities between species	generalized_Tradidiss
Indices K, Kstar and Kw of Phylogenetic Signal	K Kstar Kw
Nee and May's Optimizing Process	optimEH
Maximal or Minimal Amount of Originality Saved under Optimal Conditions	orisaved
Functional Dissimilarity Measures for Presence-Absence Data	DJac Jac PADDis
Plots for phylogenetic tree and data	barp4d dotp4d gridp4d plot.phylo4d
Mean Diversity along a Phylogenetic Tree	qDT
Quadratic Entropy	discomQE QE
Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components	qHdiv
Amount of Evolutionary History Preserved when Random Species are Saved	randEH
Functional Rarefaction for Species Abundance Data	rare_Rao
Theoretical Data Set used in Ricotta et al. (2016)	RDMCCP16
Pavoine et al. (2017) functional or phylogenetic entropy	Rentropy
Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space	plot.rlqESLTP rlqESLTP summary.rlqESLTP
Rockfish Phylogenetic Diversity in Southern California Bight	rockfish
Theoretical Data Set used in Ricotta and Pavoine (2015) in Ecological Indicators	RP15EI
Theoretical Data Set used in Ricotta and Pavoine (2015) in Journal of Vegetation Science	RP15JVS
Theoretical Data Set used in Ricotta et al. (2016) in Ecology and Evolution	RPP16EE
Functional and phylogenetic composition of plant communities along a primary succession on glacial deposits.	RutorGlacier
Indices of Species Diversity	speciesdiv
Indices of Species Evenvess	specieseve
Community-level phylogenetic (or functional) redundancy	treeUniqueness
Maximization of the Diversity Index TwoH	twoHmax
Functional Uniqueness and Functional Redundancy of Biological Communities	uniqueness

Package: adiv 2.2.1

adiv: Analysis of Diversity

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