Analysis of Diversity


[Up] [Top]

Documentation for package ‘adiv’ version 1.1

Help Pages

adiv-package Analysis of Diversity
abgaptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
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
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
birdData Avian Communities along Successional Forest Gradients
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
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
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
EH Faith Phylogenetic Diversity
EqRao Apportionment of Diversity
EqRS Apportionment of Diversity
EqRSintra Apportionment of Diversity
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
evoNSCA Evolutionary Non-Symmetric Correspondence Analysis
evopcachord Evolutionary Principal Component analyses
evopcahellinger Evolutionary Principal Component analyses
Jac Functional Dissimilarity Measures for Presence-Absence Data
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
multiCFbinary Matrices of Intra- and Inter-Specific Similarities
multiCFprop Matrices of Intra- and Inter-Specific Similarities
optimEH Nee and May's Optimizing Process
orisaved Maximal or Minimal Amount of Originality Saved under Optimal Conditions
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.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.divparam Parametric Indices of Species Diversity
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
QE Quadratic Entropy
qHdiv Biodiversity Measure that Includes Consistent Interspecific and Intraspecific Components
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)
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
rtestEqRao Apportionment of Diversity
rtestEqRS Apportionment of Diversity
rtestEqRSintra Apportionment of Diversity
rtestwapqe Apportionment of Diversity
SQ Functional or Phylogenetic Similarity between Species and Communities
summary.rlqESLTP Linking Patterns in Phylogeny, Traits, Abiotic Variables and Space
tecAptree Hierarchical Partitioning of Evolutionary and Ecological Patterns in the Organization of Phylogenetically-Structured Species Assemblages
twoHmax Maximization of the Diversity Index TwoH
uniqueness Functional Uniqueness and Functional Redundancy of Biological Communities
wapqe Apportionment of Diversity