Naming Convention | Regular Plots | Distribution of Trait Coverage Across Sites | Plotting the Number of Sites by Species | Plotting the Number of Species per Trait | Plotting the Number of Traits per Species | Plotting Environmental Position of Sites | Plotting Trait Coverage for All Sites | Plotting Trait Coverage per Species | Plotting Number of Species with Missing Traits | Displaying Trait Combinations | Displaying Trait Correlations | Maps | Mapping Trait Coverage of Sites | Mapping Arbitrary Site Data | Mapping Site Rasters

Wide vs. Long Format | The fb_format_*() functions | Usage | Extracting Species x Traits Data | Extracting Site x Species Data | Extracting Site x Locations Data | Extracting Species x Categories Data

Types of Data | Provided Dataset | Species x Traits | Site x Species | Site x Locations | Species x Categories | Visualizing the Data (Diagnostic plots) | Trait Completeness per Species | Number of Traits per Species | Filtering the Data | Filter trait by Species Coverage | Filter Species by Trait Coverage | Filter Sites by Trait Coverage | Computing Functional Diversity Metrics | Community-Weighted Mean (CWM) | Compute Functional Diversity Indices | Putting Variables on a Map | Mapping Diversity Indices | Mapping an Environmental Raster | Map of Average Environmental Variables in Site | Conclusion | References

Working with Categorical Traits | Considering Intraspecific Variation | Sites of Arbitrary Shapes

Preamble: Getting Site-Level Data | Aggregating Through a Square Grid | Aggregating Through Irregular Polygons | Aggregating Through a SpatRaster Grid | Specific Examples | Coarsening Site x Species Data | Obtaining Back a Site x Species data.frame | Upscaling Functional Diversity Data | Coarsen CWM of Plant Height | Coarser FRic Through fundiversity

Running code in parallel | Performance comparison

Other packages to compute FD indices | Main functions | Benchmark between packages | Functional Dispersion (FDis) | Functional Divergence (FDiv) | Functional Evenness (FEve) | Functional Richness (FRic) | Functional Richness Intersection (FRic_intersect) | Rao's Quadratic Entropy (Q) | Benchmark within fundiversity | Increasing the number of species | Functional Richness | Functional Divergence | Rao's Quadratic Entropy | Functional Evenness | Comparing between indices | Increasing the number of sites | References

Running code in parallel | Performance comparison

Other packages to compute FD indices | Main functions | Benchmark between packages | Functional Dispersion (FDis) | Functional Divergence (FDiv) | Functional Evenness (FEve) | Functional Richness (FRic) | Functional Richness Intersection (FRic_intersect) | Rao's Quadratic Entropy (Q) | Benchmark within fundiversity | Increasing the number of species | Functional Richness | Functional Divergence | Rao's Quadratic Entropy | Functional Evenness | Comparing between indices | Increasing the number of sites | References

Required data | Functional Richness (FRic) - fd_fric() | Functional volume intersect (FRic_intersect) - fd_fric_intersect() | Functional Divergence (FDiv) - fd_fdiv() | Functional Evenness (FEve) - fd_feve() | Functional Dispersion (FDis) - fd_fdis() | Rao's Quadratic Entropy (Q) - fd_raoq() | Large site-species data / sparse matrices | Standardizing trait data | Non-continuous traits? | Missing values in traits? | Functions summary table | References

Required data | Functional Richness (FRic) - fd_fric() | Functional volume intersect (FRic_intersect) - fd_fric_intersect() | Functional Divergence (FDiv) - fd_fdiv() | Functional Evenness (FEve) - fd_feve() | Functional Dispersion (FDis) - fd_fdis() | Rao's Quadratic Entropy (Q) - fd_raoq() | Large site-species data / sparse matrices | Standardizing trait data | Non-continuous traits? | Missing values in traits? | Functions summary table | References

Changes of abundance | Changes of coordinates (= traits)

Changes of abundance | Changes of coordinates (= traits)

Scope | Dependencies | Functions | Each index should be computed in its own separate function | Input data should not be transformed without any explicit action from the user | Inputs | Outputs | Functions should output data.frames | The outputs of functions should be similar in structure

Scope | Dependencies | Functions | Each index should be computed in its own separate function | Input data should not be transformed without any explicit action from the user | Inputs | Outputs | Functions should output data.frames | The outputs of functions should be similar in structure

General Population Growth Equation | Limiting similarity ($\delta_{ij}$ & $\sigma_{ij}$) | Basic Limiting Similarity | Variable contribution of traits to limiting similarity | Considering non-linear of traits on limiting similarity | Adding intra-specific competition | Variable contribution of traits to environmental filtering | Adding Hierarchical Competition | Basic Hierarchical Competition | Variable contribution of traits to hierarchical competition | Considering non-linear effect of hierarchical competiton | Updated final equation | Considering Species Dispersal Across Patches | Final equation | Single trait contributing to everything | Multiple traits co-contributing to some processes

Compute Distinctiveness from Global Pool - distinctiveness_global() | Compute functional rarity indices across combinations of traits | Compare Distinctiveness computed on all traits and each trait - distinctiveness_dimensions() | Compare Uniqueness computed on all traits and each trait - uniqueness_dimensions() | Compute Relative Abundances - make_relative()

Introduction | Framework | Dataset example | Functional rarity indices | Inputs of functions | Indices | Distance matrix computation | Functional Distinctiveness computation | Formula | Computation with site-species matrix | Computation with stacked data.frame | Scarcity | Computation | Uniqueness | Geographical Restrictedness | funrar | Plots | References

Sparse Matrices Usefulness | Benchmark | Systematic benchmark

Presence-Absence | Theoretical definition | Implementation | Using real data | Considering Abundance | Definitive formula | Reconciling with presence-absence definition

Searching for a taxon name | Retrieving the status of species | Additional info | Getting interaction data | Linking this information to other databases

Get Image(s) - bi_image() | Single Image | Image Crop | Image size | Rotation | Color | Format | Saving the image | Multiple Images | Get Image(s) Metadata - bi_metadata() | Get Both Images and Metadata - bi_all_data() | Rate Limitation

Neutral dynamics in species pool and communities | User-defined species pool | Trait distribution in communities | Environmental filtering | Filtering of multiple traits | Investigating phylogenetic structure in communities | Forward-in-time simulation | References

What is an API key? | Why use one? | Registering for an API key for SHERPA/RoMEO | How to set up your API key in rromeo | Using Sys.setenv() during an interactive session | Using the dedicated function rr_auth() | Setting up your API key in an .Rprofile file | Setting up your API key in an .Renviron file | Using the key function argument (NOT RECOMMENDED)

Query Journal Data | Query using ISSN | Query by Journal Title | Query Publisher Data | Query by Publisher's Name | Query by RoMEO's ID | Query by Country or Region | Query by RoMEO colour | Setting up an API key | Visualization Example

Appendix 3: ABC estimation of neutral parameters in Barro Colorado Island rainforest, using coalescent-based simulation