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adiv (version 2.2)

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

475

Version

2.2

License

GPL (>= 2)

Maintainer

Sandrine Pavoine

Last Published

October 6th, 2022

Functions in adiv (2.2)

Indices of functional imbalance

Faith Phylogenetic Diversity

Matrices of Intra- and Inter-Specific Similarities

Parametric Indices of Functional and Phylogenetic Diversity

Apportionment of Diversity

Plot-to-plot functional or phylogenetic dissimilarity

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

Functional Dissimilarity Measures for Presence-Absence Data

Quadratic Entropy

Indices K, Kstar and Kw of Phylogenetic Signal

Apportionment of Parametric Indices of Diversity

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

Pavoine et al. (2017) functional or phylogenetic entropy

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

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

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

tools:::Rd_package_title("adiv")

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

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

Apportionment of Parametric Indices of Phylogenetic Diversity

Phylogenetic and Functional Similarity between Communities

betaTreeUniqueness

Plot-to-plot functional or phylogenetic dissimilarity and uniqueness

Plot-to-Plot Functional or Phylogenetic Dissimilarity

Multiple-Site Dissimilarity Measure for Species Presence/Absence Data

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

Avian Communities along Successional Forest Gradients

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

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

dbMANOVAspecies

Indicator species analysis in the framework of multivariate analysis of variance

Marczewski-Steinhaus Coefficient

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

Parametric Indices of Species Diversity

Topology-based Species' Originality

Functional or Phylogenetic Similarity between Species and Communities

Double similarity principal component analysis

Parametric Indices of Species Evenness

Dissimilarity-based Species' Originality

Ultrametric Tree-based Species' Originality

Tree-based Species' Originality

Pair-wise Phylogenetic Dissimilarities between Communities

generalized_Tradidiss

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

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

Evolutionary Non-Symmetric Correspondence Analysis

Parametric Indices of Phylogenetic Diversity

Indices of Phylogenetic Diversity

Parametric Indices of Phylogenetic Uniqueness

Parametric Indices of Phylogenetic evenness

Evolutionary Correspondence Analysis

Evolutionary Principal Component analyses

Rockfish Phylogenetic Diversity in Southern California Bight

Functional Rarefaction for Species Abundance Data

Amount of Evolutionary History Preserved when Random Species are Saved

Maximal or Minimal Amount of Originality Saved under Optimal Conditions

Nee and May's Optimizing Process

Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space

Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components

Indices of Species Diversity

Indices of Species Evenvess

Mean Diversity along a Phylogenetic Tree

Plots for phylogenetic tree and data

Community-level phylogenetic (or functional) redundancy

Maximization of the Diversity Index TwoH

Functional Uniqueness and Functional Redundancy of Biological Communities