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| 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 |