fundiversity provides a lightweight package to compute common functional diversity indices. To a get a glimpse of what
fundiversity can do refer to the introductory vignette. The package is built using clear, public design principles inspired from our own experience and user feedback.
You can install the stable version from CRAN with:
Alternatively, you can install the development version with:
install.packages("fundiversity", repos = "https://bisaloo.r-universe.dev")
fundiversity lets you compute six functional diversity indices: Functional Richness with
fd_fric(), intersection with between convex hulls with
fd_fric_intersect(), Functional Divergence with
fd_fdiv(), Rao’s Quadratic Entropy with
fd_raoq(), Functional Dispersion with
fd_fdis() and Functional Evenness with
fd_feve(). You can have a brief overview of the indices in the introductory vignette.
All indices can be computed either using global trait data or at the site-level:
library(fundiversity) # Get trait data included in the package data("traits_birds") # Compute Functional Richness of all birds included fd_fric(traits_birds) #> site FRic #> 1 s1 230967.7 # Compute Functional Divergence fd_fdiv(traits_birds) #> site FDiv #> 1 s1 0.7282172 # Compute Rao's Quadratic Entropy fd_raoq(traits_birds) #> site Q #> 1 s1 170.0519 # Compute Functional Dispersion fd_fdis(traits_birds) #> site FDis #> 1 s1 146.2072 # Compute Functional Evenness fd_feve(traits_birds) #> site FEve #> 1 s1 0.3743341
To compute Rao’s Quadratic Entropy, the user can also provide a distance matrix between species directly:
|Function Name||Index Name||Parallelizable
According to Pavoine & Bonsall (2011) classification, functional diversity indices can be classified in three “domains” that assess different properties of the functional space: richness, divergence, and regularity.
fundiversity provides function to compute indices that assess this three facets at the site scale:
(= among sites)
Rao’s QE with
(= between sites)
|FRic pairwise intersection with
alternatives available in