Intersection between convex hulls of pairs of sites
Source:R/fd_fric_intersect.R
fd_fric_intersect.RdCompute volume of the intersection of the convex hulls of all pairs
of sites (including self-intersection, which corresponds to their convex
hull). Note that when standardizing convex hulls of intersections,
this function uses the convex hull of all provided traits,
thus standardized volume of self-intersection hulls can be lower than one.
NB: FRic_intersect is equal to NA when there are strictly less species in
one of the sites than the number of provided traits.
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, adata.frame, or aMatrix::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, adata.frame, or aMatrix::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.
Value
a data.frame with three columns:
first_sitethe names of the first site used in the pairsp_com,second_sitethe names of the first site used in the pair,FRic_intersectthe volume of the convex hulls intersection of each pair of 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_intersect is equal to NA when there are strictly less species in
one of the sites 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.
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.
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., Grenouillet G., Brosse S. (2013), Decomposing functional \(\beta\)-diversity reveals that low functional \(\beta\)-diversity is driven by low functional turnover in European fish assemblages, Global Ecology and Biogeography, 22(6), 671–681. doi:10.1111/geb.12021 .
Zhao T., Villéger S., Cucherousset J. (2019). Accounting for intraspecific diversity when examining relationships between non-native species and functional diversity. Oecologia, 189(1), 171-183. doi:10.1007/s00442-018-4311-3 .
Examples
data(traits_birds)
fd_fric_intersect(traits_birds)
#> first_site second_site FRic_intersect
#> 1 s1 s1 230967.7