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adiv (version 1.2)

Analysis of Diversity

Description

Includes 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. It 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.

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Version

Install

install.packages('adiv')

Monthly Downloads

441

Version

1.2

License

GPL (>= 2)

Maintainer

Sandrine Pavoine

Last Published

August 24th, 2018

Functions in adiv (1.2)

rlqESLTP

Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space
K

Indices K, Kstar and Kw of Phylogenetic Signal
EqRao

Apportionment of Diversity
RDMCCP16

Theoretical Data Set used in Ricotta et al. (2016)
RP15JVS

Theoretical Data Set used in Ricotta and Pavoine (2015) in Journal of Vegetation Science
eveparam

Parametric Indices of Species Evenness
RP15EI

Theoretical Data Set used in Ricotta and Pavoine (2015) in Ecological Indicators
evopca

Evolutionary Principal Component analyses
CF

Matrices of Intra- and Inter-Specific Similarities
dsimcom

Functional or Phylogenetic Similarity between Species and Communities
optimEH

Nee and May's Optimizing Process
aptree

Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
decdiv

Decomposition of trait-based diversity along the nodes of a phylogenetic tree
divparam

Parametric Indices of Species Diversity
twoHmax

Maximization of the Diversity Index TwoH
EH

Faith Phylogenetic Diversity
rockfish

Rockfish Phylogenetic Diversity in Southern California Bight
RPP16EE

Theoretical Data Set used in Ricotta et al. (2016) in Ecology and Evolution
rare_Rao

Functional Rarefaction for Species Abundance Data
betastat

Multiple-Site Dissimilarity Measure for Species Presence/Absence Data
batcomm

Bat Abundance and Phylogeny Along a Disturbance Gradient in a Neotropical Rainforest
distinctTree

Tree-based Species' Originality
distMS

Marczewski-Steinhaus Coefficient
dissABC

Phylogenetic and Functional Similarity between Communities
randEH

Amount of Evolutionary History Preserved when Random Species are Saved
abgevodivparam

Apportionment of Parametric Indices of Phylogenetic Diversity
birdData

Avian Communities along Successional Forest Gradients
crossdpcoa

Crossed-DPCoA
uniqueness

Functional Uniqueness and Functional Redundancy of Biological Communities
distinctUltra

Ultrametric Tree-based Species' Originality
dissRicotta

Plot-to-Plot Functional or Phylogenetic Dissimilarity
qHdiv

Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components
evoCA

Evolutionary Correspondence Analysis
speciesdiv

Indices of Species Diversity
distinctDis

Dissimilarity-based Species' Originality
orisaved

Maximal or Minimal Amount of Originality Saved under Optimal Conditions
evodiss

Pair-wise Phylogenetic Dissimilarities between Communities
distinctTopo

Topology-based Species' Originality
specieseve

Indices of Species Evenvess
evoNSCA

Evolutionary Non-Symmetric Correspondence Analysis
QE

Quadratic Entropy
PADDis

Functional Dissimilarity Measures for Presence-Absence Data
Rentropy

Pavoine et al. (2017) functional or phylogenetic entropy
adiv-package

adiv
evodiss_family

A Family of Indices Dedicated to Pair-wise Phylogenetic Dissimilarities between Communities
evodivparam

Parametric Indices of Phylogenetic Diversity