fd_fdiv {fundiversity} | R Documentation |
Compute Functional Divergence (FDiv)
Description
This function computes Functional Divergence (FDiv) following Villéger et al.
(2008). NB: when a site contains no species FDiv is equal to 0. If for a site
there are less traits than species, then FDiv is equal to NaN
.
Usage
fd_fdiv(traits, sp_com)
Arguments
traits |
Trait matrix with species as rows and traits as columns.
It has to contain exclusively numerical values. This can be
either a |
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 |
Details
By default, when loading fundiversity, the functions to
compute convex hulls are
memoised through the memoise
package if it is installed. 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.
Value
a data.frame with two columns:
-
site
the names of the sites as the row names of the inputsp_com
, -
FDiv
the values of functional divergence at each site.
NB: when a site contains no species FDiv is equal to 0. If for a site
there are less traits than species, then FDiv is equal to NaN
.
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
Villéger S., Mason N. W. H., Mouillot D. (2008), New multidimensional functional diversity indices for a multifaceted framework in functional ecology, Ecology 89(8), doi:10.1890/07-1206.1
Examples
data(traits_birds)
fd_fdiv(traits_birds)