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adiv (version 2.2.1)

Analysis of Diversity

Description

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.

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Version

Install

install.packages('adiv')

Monthly Downloads

441

Version

2.2.1

License

GPL (>= 2)

Maintainer

Sandrine Pavoine

Last Published

February 19th, 2024

Functions in adiv (2.2.1)

Matrices of Intra- and Inter-Specific Similarities

Plot-to-plot functional or phylogenetic dissimilarity

Indices of functional imbalance

Faith Phylogenetic Diversity

Indices K, Kstar and Kw of Phylogenetic Signal

Functional Dissimilarity Measures for Presence-Absence Data

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

Apportionment of Diversity

Quadratic Entropy

Parametric Indices of Functional and Phylogenetic Diversity

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

tools:::Rd_package_title("adiv")

Pavoine et al. (2017) functional or phylogenetic entropy

Apportionment of Parametric Indices of Diversity

Apportionment of Parametric Indices of Phylogenetic Diversity

Functional and phylogenetic composition of plant communities along a primary succession on glacial deposits.

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

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

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

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

betaTreeUniqueness

Plot-to-plot functional or phylogenetic dissimilarity and uniqueness

Phylogenetic and Functional Similarity between Communities

Plot-to-Plot Functional or Phylogenetic Dissimilarity

Multiple-Site Dissimilarity Measure for Species Presence/Absence Data

Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity and uniqueness

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

Avian Communities along Successional Forest Gradients

dbMANOVAspecies

Indicator species analysis in the framework of multivariate analysis of variance

Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity

Parametric Indices of Species Diversity

Marczewski-Steinhaus Coefficient

Abundance-based measures of species' rarity, functional or phylogenetic distinctiveness and functional or phylogenetic effective originality

Topology-based Species' Originality

Double similarity principal component analysis

Functional or Phylogenetic Similarity between Species and Communities

Dissimilarity-based Species' Originality

Parametric Indices of Species Evenness

Pair-wise Phylogenetic Dissimilarities between Communities

Evolutionary Correspondence Analysis

Indices of Phylogenetic Diversity

Tree-based Species' Originality

Evolutionary Non-Symmetric Correspondence Analysis

Parametric Indices of Phylogenetic Uniqueness

Nee and May's Optimizing Process

generalized_Tradidiss

Plot-to-plot dissimilarity taking account of functional dissimilarities between species

Parametric Indices of Phylogenetic Diversity

Maximal or Minimal Amount of Originality Saved under Optimal Conditions

Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components

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

Amount of Evolutionary History Preserved when Random Species are Saved

Ultrametric Tree-based Species' Originality

Functional Rarefaction for Species Abundance Data

Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space

Rockfish Phylogenetic Diversity in Southern California Bight

Parametric Indices of Phylogenetic evenness

Indices of Species Diversity

Mean Diversity along a Phylogenetic Tree

Maximization of the Diversity Index TwoH

Plots for phylogenetic tree and data

Indices of Species Evenvess

Evolutionary Principal Component analyses

Functional Uniqueness and Functional Redundancy of Biological Communities

Community-level phylogenetic (or functional) redundancy