In Bisaloo/fundiversity: Easy Computation of Functional Diversity Indices

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

temp_dir = tempdir(check = TRUE)

pkg_has_vignettes_and_test = function(pkg_name, pkg_dir = temp_dir) {
  pkg_archive = download.packages(pkg_name, destdir = pkg_dir,
                                  repos = "https://cran.r-project.org")

  files_list = untar(pkg_archive[1, 2], list = TRUE)

  has_vignette = paste0(pkg_archive[1, 1], "/vignettes/") %in% files_list

  has_tests = paste0(pkg_archive[1, 1], "/tests/") %in% files_list

  c(ifelse(has_vignette, "✅", "❌"), ifelse(has_tests, "✅", "❌"))
}

fundiversity

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.

Installation

You can install the stable version from CRAN with:

install.packages("fundiversity")

Alternatively, you can install the development version with:

install.packages("fundiversity", repos = "https://bisaloo.r-universe.dev")

Examples

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")

# If only the trait dataset is specified, considers all species together
# by default
fd_fric(traits_birds)

# We can also compute diversity across sites
fd_fric(traits_birds, site_sp_birds)

To compute Rao's Quadratic Entropy, the user can also provide a distance matrix between species directly:

dist_traits_birds = as.matrix(dist(traits_birds))

fd_raoq(traits = NULL, dist_matrix = dist_traits_birds)

Function Summary

Parallelization

Thanks to the future.apply package, all functions (except fd_raoq()) within fundiversity support parallelization through the future backend. To toggle parallelization follow the future syntax:

future::plan(future::multisession)
fd_fdiv(traits_birds)

For more details please refer to the parallelization vignette or use vignette("fundiversity_1-parallel", package = "fundiversity") within R. Note: parallelization and memoization are mutually exclusive, when doing computation in parallel, fundiversity falls back on unmemoised versions of function.

Available functional diversity indices

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. We made sure that the computations in the package are correct in our correctness vignette. fundiversity provides function to compute indices that assess this three facets at the site scale:

| Scale | Richness | Divergence | Evenness | |------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------| | α-diversity
(= among sites) | FRic with fd_fric() | FDiv with fd_fdiv()
Rao's QE with fd_raoq()
FDis with fd_fdis() | FEve with fd_feve() | | β-diversity
(= between sites) | FRic pairwise intersection with fd_fric_intersect()
alternatives available in betapart | available in entropart, betapart or hillR | available in BAT |

Related Packages

adiv        = pkg_has_vignettes_and_test("adiv")
bat         = pkg_has_vignettes_and_test("BAT")
betapart    = pkg_has_vignettes_and_test("betapart")
entropart   = pkg_has_vignettes_and_test("entropart")
fd          = pkg_has_vignettes_and_test("FD")
hilldiv     = pkg_has_vignettes_and_test("hilldiv")
hillr       = pkg_has_vignettes_and_test("hillR")
hypervolume = pkg_has_vignettes_and_test("hypervolume")
tpd         = pkg_has_vignettes_and_test("TPD")
vegan       = pkg_has_vignettes_and_test("vegan")

Several other packages exist that compute functional diversity indices. We did a performance comparison between related packages. We here mention some of them (but do not mention the numerous wrappers around these packages):

| Package Name | Indices included | Has vignettes | Has tests | On GitHub | On CRAN (last updated) | |-------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------|--------------------|--------------------|-----------|-----------------------------------------------------------| | adiv | Functional Entropy, Functional Redundancy |r adiv[[1]] |r adiv[[2]] | ❌ | | | BAT | β-diversity indices, Richness, divergence, and evenness with hypervolumes |r bat[[1]] |r bat[[2]] | ✅ | |
| betapart | Functional β-diversity |r betapart[[1]] |r betapart[[2]] | ❌ | | | entropart| Functional Entropy |r entropart[[1]] |r entropart[[2]] | ✅ | |
| FD | FRic, FDiv, FDis, FEve, Rao's QE, Functional Group Richness |r fd[[1]] |r fd[[2]] | ❌ | | | hilldiv | Dendrogram-based Hill numbers for functional diversity |r hilldiv[[1]] |r hilldiv[[2]] | ✅ | | | hillR | Functional Diversity Hill Numbers |r hillr[[1]] |r hillr[[2]] | ✅ | |
| hypervolume | Hypervolume measure of functional diversity (~FRic) |r hypervolume[[1]]|r hypervolume[[2]]| ✅ | | | mFD | Functional α- and β-diversity indices, including FRic, FDiv, FDis, FEve, FIde, FMPD, FNND, FOri, FSpe, Hill Numbers | ✅ | ❌ | ✅ | | | TPD | FRic, FDiv, FEve but for probability distributions |r tpd[[1]] |r tpd[[2]] | ❌ | | | vegan | Only dendrogram-based FD (treedive()) |r vegan[[1]] |r vegan[[2]] | ✅ | |