`R/fcts_used_for_ind_comp.R`

`dist.nearneighb.Rd`

This function is used in functional indices computation.

`dist.nearneighb(sp_faxes_coord, ref_sp)`

- sp_faxes_coord
a matrix of species coordinates in a chosen functional space. Species coordinates have been retrieved thanks to

`tr.cont.fspace`

or`quality.fspaces`

.- ref_sp
a character string referring to the name of the reference species.

A list containing the nearest neighbor identity `nn_id`

and a
list of the distance of the reference point to its nearest neighbor
`nn_ref_sp_dist`

.

```
# Load Species*Traits dataframe:
data("fruits_traits", package = "mFD")
# Load Assemblages*Species dataframe:
data("baskets_fruits_weights", package = "mFD")
# Load Traits categories dataframe:
data("fruits_traits_cat", package = "mFD")
# Compute functional distance
sp_dist_fruits <- mFD::funct.dist(sp_tr = fruits_traits,
tr_cat = fruits_traits_cat,
metric = "gower",
scale_euclid = "scale_center",
ordinal_var = "classic",
weight_type = "equal",
stop_if_NA = TRUE)
#> [1] "Running w.type=equal on groups=c(Size)"
#> [1] "Running w.type=equal on groups=c(Plant)"
#> [1] "Running w.type=equal on groups=c(Climate)"
#> [1] "Running w.type=equal on groups=c(Seed)"
#> [1] "Running w.type=equal on groups=c(Sugar)"
#> [1] "Running w.type=equal on groups=c(Use,Use,Use)"
# Compute functional spaces quality to retrieve species coordinates matrix:
fspaces_quality_fruits <- mFD::quality.fspaces(
sp_dist = sp_dist_fruits,
maxdim_pcoa = 10,
deviation_weighting = "absolute",
fdist_scaling = FALSE,
fdendro = "average")
# Retrieve species coordinates matrix:
sp_faxes_coord_fruits <- fspaces_quality_fruits$details_fspaces$sp_pc_coord
# Compute the distance of "pear" to its nearest neighbor(s):
dist_nn_pear <- dist.nearneighb(sp_faxes_coord_fruits, ref_sp = "pear")
dist_nn_pear
#> $`nearest neighbour identity`
#> [1] "apple"
#>
#> $`distance of the reference species to its nearest neighbour`
#> [1] 0.1270335
#>
```