Analysis of Diversity

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Documentation for package ‘adiv’ version 2.2.1

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A B C D E F G J K M O P Q R S T U W

adiv-package Analysis of Diversity

-- A --

abgaptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
abgdivparam Apportionment of Parametric Indices of Diversity
abgevodivparam Apportionment of Parametric Indices of Phylogenetic Diversity
adiv Analysis of Diversity
apd Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
aptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages

-- B --

barp4d Plots for phylogenetic tree and data
batcomm Bat Abundance and Phylogeny Along a Disturbance Gradient in a Neotropical Rainforest
betastatjac Multiple-Site Dissimilarity Measure for Species Presence/Absence Data
betastatsor Multiple-Site Dissimilarity Measure for Species Presence/Absence Data
betaTreeUniqueness Plot-to-plot functional or phylogenetic dissimilarity and uniqueness
betaUniqueness Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity and uniqueness
birdData Avian Communities along Successional Forest Gradients

-- C --

CFbinary Matrices of Intra- and Inter-Specific Similarities
CFprop Matrices of Intra- and Inter-Specific Similarities
crossdpcoa_maineffect Crossed-DPCoA
crossdpcoa_version1 Crossed-DPCoA
crossdpcoa_version2 Crossed-DPCoA

-- D --

dbMANOVAspecies Indicator species analysis in the framework of multivariate analysis of variance
dbMANOVAspecies_pairwise Indicator species analysis in the framework of multivariate analysis of variance
decdiv Decomposition of trait-based diversity along the nodes of a phylogenetic tree
discomQE Quadratic Entropy
dislptransport Algorithmic index of plot-to-plot functional (or phylogenetic) dissimilarity
dissABC Phylogenetic and Functional Similarity between Communities
dissRicotta Plot-to-Plot Functional or Phylogenetic Dissimilarity
distinctAb Abundance-based measures of species' rarity, functional or phylogenetic distinctiveness and functional or phylogenetic effective originality
distinctDis Dissimilarity-based Species' Originality
distinctTopo Topology-based Species' Originality
distinctTree Tree-based Species' Originality
distinctUltra Ultrametric Tree-based Species' Originality
distMS Marczewski-Steinhaus Coefficient
divparam Parametric Indices of Species Diversity
DJac Functional Dissimilarity Measures for Presence-Absence Data
dotp4d Plots for phylogenetic tree and data
DP Plot-to-plot functional or phylogenetic dissimilarity
dsimcom Functional or Phylogenetic Similarity between Species and Communities
dsimFun Functional or Phylogenetic Similarity between Species and Communities
dsimTaxo Functional or Phylogenetic Similarity between Species and Communities
dsimTree Functional or Phylogenetic Similarity between Species and Communities
dspca Double similarity principal component analysis

-- E --

EH Faith Phylogenetic Diversity
EqRao Apportionment of Diversity
EqRS Apportionment of Diversity
EqRSintra Apportionment of Diversity
eveparam Parametric Indices of Species Evenness
evoCA Evolutionary Correspondence Analysis
evodiss Pair-wise Phylogenetic Dissimilarities between Communities
evodiss_family A Family of Indices Dedicated to Pair-wise Phylogenetic Dissimilarities between Communities
evodiss_ternaryplot A Family of Indices Dedicated to Pair-wise Phylogenetic Dissimilarities between Communities
evodiv Indices of Phylogenetic Diversity
evodivparam Parametric Indices of Phylogenetic Diversity
evoeveparam Parametric Indices of Phylogenetic evenness
evoNSCA Evolutionary Non-Symmetric Correspondence Analysis
evopcachord Evolutionary Principal Component analyses
evopcahellinger Evolutionary Principal Component analyses
evouniparam Parametric Indices of Phylogenetic Uniqueness

-- F --

FPdivparam Parametric Indices of Functional and Phylogenetic Diversity
FunImbalance Indices of functional imbalance

-- G --

generalized_Tradidiss Plot-to-plot dissimilarity taking account of functional dissimilarities between species
gridp4d Plots for phylogenetic tree and data

-- J --

Jac Functional Dissimilarity Measures for Presence-Absence Data

-- K --

K Indices K, Kstar and Kw of Phylogenetic Signal
Kstar Indices K, Kstar and Kw of Phylogenetic Signal
Kw Indices K, Kstar and Kw of Phylogenetic Signal

-- M --

multiCFbinary Matrices of Intra- and Inter-Specific Similarities
multiCFprop Matrices of Intra- and Inter-Specific Similarities

-- O --

optimEH Nee and May's Optimizing Process
orisaved Maximal or Minimal Amount of Originality Saved under Optimal Conditions

-- P --

PADDis Functional Dissimilarity Measures for Presence-Absence Data
pIa Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
plot.abgdivparam Apportionment of Parametric Indices of Diversity
plot.abgevodivparam Apportionment of Parametric Indices of Phylogenetic Diversity
plot.aptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
plot.decdiv Decomposition of trait-based diversity along the nodes of a phylogenetic tree
plot.divparam Parametric Indices of Species Diversity
plot.dspca Double similarity principal component analysis
plot.eveparam Parametric Indices of Species Evenness
plot.evoCA Evolutionary Correspondence Analysis
plot.evodivparam Parametric Indices of Phylogenetic Diversity
plot.evoeveparam Parametric Indices of Phylogenetic evenness
plot.evouniparam Parametric Indices of Phylogenetic Uniqueness
plot.FPdivparam Parametric Indices of Functional and Phylogenetic Diversity
plot.phylo4d Plots for phylogenetic tree and data
plot.rlqESLTP Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space
plot.rtestaptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages

-- Q --

qDT Mean Diversity along a Phylogenetic Tree
QE Quadratic Entropy
qHdiv Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components

-- R --

randEH Amount of Evolutionary History Preserved when Random Species are Saved
rare_Rao Functional Rarefaction for Species Abundance Data
RDMCCP16 Theoretical Data Set used in Ricotta et al. (2016)
Rentropy Pavoine et al. (2017) functional or phylogenetic entropy
rlqESLTP Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space
rockfish Rockfish Phylogenetic Diversity in Southern California Bight
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
rtestaptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
rtestdecdiv Decomposition of trait-based diversity along the nodes of a phylogenetic tree
rtestEqRao Apportionment of Diversity
rtestEqRS Apportionment of Diversity
rtestEqRSintra Apportionment of Diversity
rtestwapqe Apportionment of Diversity
RutorGlacier Functional and phylogenetic composition of plant communities along a primary succession on glacial deposits.

-- S --

speciesdiv Indices of Species Diversity
specieseve Indices of Species Evenvess
SQ Functional or Phylogenetic Similarity between Species and Communities
summary.dbMANOVAspecies_pairwise Indicator species analysis in the framework of multivariate analysis of variance
summary.rlqESLTP Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space

-- T --

tecAptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
treeUniqueness Community-level phylogenetic (or functional) redundancy
twoHmax Maximization of the Diversity Index TwoH

-- U --

uniqueness Functional Uniqueness and Functional Redundancy of Biological Communities

-- W --

wapqe Apportionment of Diversity