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)
#> site FRic
#> 1 s1 230967.7
# We can also compute diversity across sites
fd_fric(traits_birds, site_sp_birds)
#> site FRic
#> 1 elev_250 171543.730
#> 2 elev_500 185612.548
#> 3 elev_1000 112600.176
#> 4 elev_1500 66142.748
#> 5 elev_2000 20065.764
#> 6 elev_2500 18301.176
#> 7 elev_3000 17530.651
#> 8 elev_3500 3708.735To 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)
#> site Q
#> 1 s1 170.0519Function Summary
| Function Name | Index Name | Parallelizable[^1] | Memoizable[^2] |
|---|---|---|---|
fd_fric() | FRic | ✅ | ✅ |
fd_fric_intersect() | FRic_intersect | ✅ | ✅ |
fd_fdiv() | FDiv | ✅ | ✅ |
fd_feve() | FEve | ✅ | ❌ |
fd_fdis() | FDis | ✅ | ❌ |
fd_raoq() | Rao’s Q | ❌ | ❌ |
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)
#> site FDiv
#> 1 s1 0.7282172For more details please refer to the parallelization
vignette
or use vignette("fundiversity_1-parallel", package = "fundiversity")
within R.
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
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 | ✅ | ❌ | ❌ | |
BAT | β-diversity indices, Richness, divergence, and evenness with hypervolumes | ❌ | ❌ | ✅ | |
betapart | Functional β-diversity | ❌ | ❌ | ❌ | |
entropart | Functional Entropy | ✅ | ✅ | ✅ | |
FD | FRic, FDiv, FDis, FEve, Rao’s QE, Functional Group Richness | ❌ | ❌ | ❌ | |
hilldiv | Dendrogram-based Hill numbers for functional diversity | ❌ | ❌ | ✅ | |
hillR | Functional Diversity Hill Numbers | ❌ | ✅ | ✅ | |
hypervolume | Hypervolume measure of functional diversity (~FRic) | ✅ | ❌ | ✅ | |
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 | ✅ | ❌ | ❌ | |
vegan | Only dendrogram-based FD (treedive()) | ✅ | ✅ | ✅ |
[^1]: parallelization through the future backend please refer to the
parallelization
vignette
for details.
[^2]: memoization means that the results of the functions calls are
cached and not recomputed when recalled, to toggle it off see the
fundiversity::fd_fric() Details
section.