Summarize dataThese two functions are used to summarize up the speciestraits and assemblage data. 


Summarize Species x Traits data frame 

Summarize Assemblage x Species data frame 

Functional distances and Functional spacesThese functions compute the functional distances between species, build functional spaces (if the data gather only continuous traits or not), assess/plot the quality of functional spaces (and dendrogram if asked), plot the chosen functional space and caracterize its functional axes based on traits correlation with each functional axes. 

Compute functional distance between species 

Scale continuous traits 

Build a functional space based on continuous traits only 

Compute functional spaces and their quality 

Plot functional space quality with a chosen quality metric 

Plot species position in a functional space 

Correlation between Traits and Axes 

Compute Functional EntitiesThis function gathers species into Functional Entities (FEs) 

Compute Functional Entities composition based on a Species x Traits matrix 

Compute and Plot functional indices 

Based on FEsThese functions compute and plot functional indices based on FEs as in 

Compute the set of indices based on number of species in Functional Entities 

Illustrate Functional Diversity indices based on Functional Entities 

Based on Hill numbersThese functions compute alpha and beta indices based on Hill numbers according to the Chao et al. (2019) framework. 

Compute Functional alphaDiversity indices based on Hill Numbers 

Compute Functional betaDiversity indices based on Hill Numbers 

FUSE indexThis function computes FUSE (Functionally Unique, Specialized, and Endangered) index that combines functional uniqueness, specialisation and global endangerment to identify threatened species of particular importance for functional diversity based on 

Compute FUSE (Functionally Unique, Specialized and Endangered) 

Based on multidimensional spaceThese functions compute/plot alpha and beta indices based on a given multidimensional functional space. 

Compute a set of alpha functional indices for a set of assemblages 

Compute Functional betaDiversity indices for pairs of assemblages in a multidimensional space 

Plot functional space and chosen functional indices 

Illustrate Functional betaDiversity indices for pairs of assemblages in a multidimensional space 

Based on multidimensinal space for more complex graphsThese functions return 

Plot background of multidimensional plots 

Plot FDiv indice 

Plot FDis index 

Plot FEve index 

Plot FIde index 

Plot FNND index 

Plot FOri 

Plot FRic index 

Plot FSpe 

Plot individual plots along a pair of functional axes into a unique graph 

Plot species from the pool 

Other functionsVarious functions that can be used by the user for diverse usage 

Compute distance of a given point to its nearest neighbor in the functional space and the identity of the nearest neighbor 

Compute distances of all points to a given point in the functional space 

Merge distance object(s) into a single data frame 

Compute the Minimum Spanning Tree (MST) linking species of a given assemblage 

Retrieve information about species in a given assemblage 

Compute vertices of the Minimal Convex Hull shaping species from a single assemblage in a multidimensional functional space 

Data setsThe three data sets used for examples and tutorials in the 

Dataset: Baskets Composition in Fruits Species 

Dataset: Traits Values of Fruits Species 

Dataset: Fruits Traits Informations 