This function computes names of species present in an given assemblage,
their coordinates in the functional space and their weights. It is used in
the alpha_FD_multidim function to filter species and compute each
functional indices for each community.
sp.filter(asb_nm, sp_faxes_coord, asb_sp_w)a string object referring to the name of a given community.
a matrix of species coordinates in a chosen functional
space. Species coordinates have been retrieved thanks to
tr.cont.fspace or quality.fspaces.
a matrix linking weight of species (columns) and a set of assemblages (rows).
A vector containing names of species present in a given assemblage
sp_name_asb_k, a matrix containing coordinates of species present
in a given assemblage sp_faxes_coord_k, a matrix containing weight
of species present in a given assemblage asb_sp_w_k, a matrix
containing relative weight of species present in a given assemblage
asb_sp_relatw_k.
# 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
# Filter species of basket_1 assemblage:
sp.filter(asb_nm = "basket_1",
sp_faxes_coord = sp_faxes_coord_fruits,
asb_sp_w = baskets_fruits_weights)
#> $`species names`
#> [1] "apple" "banana" "cherry" "lemon"
#> [5] "melon" "passion_fruit" "pear" "strawberry"
#>
#> $`species coordinates`
#> PC1 PC2 PC3 PC4 PC5
#> apple 0.0265193144 0.01305413 -0.043717435 -0.02121146 -0.14821854
#> banana -0.3346937349 0.09137141 -0.070877547 0.06988872 -0.05000085
#> cherry 0.1532479527 -0.25099690 -0.135570593 0.05621669 0.02650788
#> lemon -0.1116123197 0.05271882 0.138487467 -0.10319375 0.02307706
#> melon 0.0475710274 0.22821444 -0.009073564 -0.13015462 0.03728241
#> passion_fruit -0.1743734750 -0.09195180 0.051587716 0.22053201 -0.14745293
#> pear -0.0008010876 0.01968943 -0.013204612 -0.07056511 -0.07014583
#> strawberry 0.2743910893 0.09325097 0.046622086 0.09331814 0.04954010
#> PC6 PC7 PC8 PC9 PC10
#> apple 0.040965006 0.039965979 -0.02257727 -0.012017348 -0.010675722
#> banana 0.020752971 -0.041476147 -0.08303923 0.042337245 0.015830902
#> cherry -0.020780891 0.004803343 -0.04262059 0.030307476 -0.022668724
#> lemon 0.101128620 0.044498483 -0.03408272 -0.023135838 -0.021535320
#> melon -0.136045993 0.036709357 0.01345963 -0.022081148 0.005067072
#> passion_fruit 0.066901090 -0.006120818 0.06645768 0.020143504 -0.008008755
#> pear -0.004973365 0.023163490 -0.05589114 -0.008962102 0.038038792
#> strawberry 0.001191018 0.094872368 0.01891473 0.012390681 -0.018860955
#>
#> $`species weight`
#> apple banana cherry lemon melon passion_fruit pear strawberry
#> basket_1 400 100 150 200 200 100 600 250
#>
#> $`species relative weight`
#> apple banana cherry lemon melon passion_fruit pear strawberry
#> basket_1 0.2 0.05 0.075 0.1 0.1 0.05 0.3 0.125
#>