# Analysis of Diversity

## Documentation for package ‘adiv’ version 2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E 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
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 --

decdiv | Decomposition of trait-based diversity along the nodes of a phylogenetic tree
discomQE | Quadratic Entropy
dissABC | Phylogenetic and Functional Similarity between Communities
dissRicotta | Plot-to-Plot Functional or Phylogenetic Dissimilarity
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

## -- 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.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.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