fd_fric: Compute Functional Richness (FRic)

In Bisaloo/fundiversity: Easy Computation of Functional Diversity Indices

Compute Functional Richness (FRic)

Description

Functional Richness is computed as the volume of the convex hull from all included traits following Villéger et al. (2008). NB: FRic is equal to NA when there are strictly less species in a site than the number of provided traits.

Usage

fd_fric(traits, sp_com, stand = FALSE)

Arguments

traits	Trait matrix with species as rows and traits as columns. It has to contain exclusively numerical values. This can be either a matrix, a data.frame, or a Matrix::Matrix() object.
sp_com	Site-species matrix with sites as rows and species as columns if not provided, the function considers all species with equal abundance in a single site. This can be either a matrix, a data.frame, or a Matrix::Matrix() object.
stand	a boolean indicating whether to standardize FRic values over the observed maximum over all species (default: FALSE). This scales FRic between 0 and 1. NB: The maximum FRic values only considers species that are present in both site-species and trait matrices. If you want to consider species that are absent in the site-species matrix, add corresponding columns of 0s.

Details

By default, when loading fundiversity, the functions to compute convex hulls are memoised through the memoise package if it is installed (their results are cached to avoid recomputing the same functional volume twice). To deactivate this behavior you can set the option fundiversity.memoise to FALSE by running the following line: options(fundiversity.memoise = FALSE). If you use it interactively it will only affect your current session. Add it to your script(s) or .Rprofile file to avoid toggling it each time. By changing the option, the behavior will automatically change the next time you run the function. Note: memoisation is only available when the memoise package has been installed and without parallelization, otherwise fundiversity will use unmemoised versions of the functions. In other words, memoization and parallelization are mutually exclusive.

Value

a data.frame with two columns:

• site the names of the sites as the row names of the input sp_com,

• FRic the values of functional richness at each site.

If the sp_com argument is not provided or if sp_com doesn't have rownames, arbitrary rownames s1, s2, s3, etc. will be used.

NB: FRic is equal to NA when there are strictly less species in a site than the number of provided traits. Note that only species with strictly different trait combinations are considered unique, species that share the exact same trait values across all traits are considered as one species.

Parallelization

The computation of this function can be parallelized thanks to future::plan(). To get more information on how to parallelize your computation please refer to the parallelization vignette with: vignette("fundiversity_1-parallel", package = "fundiversity").

References

Cornwell W. K., Schwilk D. W., Ackerly D. D. (2006), A trait-based test for habitat filtering; convex hull volume, Ecology 84(6), \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1890/0012-9658(2006)87[1465:ATTFHF]2.0.CO;2")}

Examples

data(traits_birds)
fd_fric(traits_birds)

Bisaloo/fundiversity documentation built on April 4, 2024, 12:24 a.m.