Compute the Minimum Spanning Tree (MST) linking species of a given assemblage
Source:R/fcts_used_for_ind_comp.R
mst.computation.RdThis function computes the MST linking species of a given assemblage and is used to compute FEve index.
Examples
# 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):
mst_fruits <- mst.computation(sp_faxes_coord_fruits)
mst_fruits
#> apple apricot banana currant blackberry blueberry cherry grape
#> apricot 0
#> banana 0 0
#> currant 0 0 0
#> blackberry 0 0 0 1
#> blueberry 0 0 0 0 0
#> cherry 0 0 0 0 0 0
#> grape 0 0 0 0 0 0 0
#> grapefruit 0 0 1 0 0 0 0 0
#> kiwifruit 0 0 0 0 0 0 0 1
#> lemon 0 0 0 0 0 0 0 0
#> lime 0 0 0 0 0 0 0 0
#> litchi 0 0 0 0 0 0 0 0
#> mango 0 0 1 0 0 0 0 0
#> melon 0 0 0 0 0 0 0 0
#> orange 0 0 0 0 0 0 0 0
#> passion_fruit 0 0 0 0 0 0 0 0
#> peach 1 0 0 0 0 0 0 0
#> pear 1 0 0 0 0 0 0 0
#> pineapple 0 0 1 0 0 0 0 0
#> plum 0 1 0 0 0 0 1 0
#> raspberry 0 0 0 0 1 0 0 0
#> strawberry 0 0 0 0 0 1 0 0
#> tangerine 0 0 0 0 0 0 0 0
#> water_melon 0 0 0 0 0 0 0 0
#> grapefruit kiwifruit lemon lime litchi mango melon orange
#> apricot
#> banana
#> currant
#> blackberry
#> blueberry
#> cherry
#> grape
#> grapefruit
#> kiwifruit 0
#> lemon 1 0
#> lime 0 0 1
#> litchi 0 0 0 0
#> mango 0 0 0 0 1
#> melon 0 0 0 0 0 0
#> orange 1 0 0 0 0 0 0
#> passion_fruit 0 0 0 0 0 0 0 0
#> peach 0 0 0 0 0 0 0 0
#> pear 0 1 0 0 0 0 1 1
#> pineapple 0 0 0 0 0 0 0 0
#> plum 0 0 0 0 0 0 0 0
#> raspberry 0 0 0 0 0 0 0 0
#> strawberry 0 0 0 0 0 0 0 0
#> tangerine 0 0 0 0 0 0 0 1
#> water_melon 0 0 0 0 0 0 1 0
#> passion_fruit peach pear pineapple plum raspberry strawberry
#> apricot
#> banana
#> currant
#> blackberry
#> blueberry
#> cherry
#> grape
#> grapefruit
#> kiwifruit
#> lemon
#> lime
#> litchi
#> mango
#> melon
#> orange
#> passion_fruit
#> peach 0
#> pear 0 0
#> pineapple 0 0 0
#> plum 0 1 0 0
#> raspberry 0 0 1 0 0
#> strawberry 0 0 0 0 0 1
#> tangerine 1 0 0 0 0 0 0
#> water_melon 0 0 0 0 0 0 0
#> tangerine
#> apricot
#> banana
#> currant
#> blackberry
#> blueberry
#> cherry
#> grape
#> grapefruit
#> kiwifruit
#> lemon
#> lime
#> litchi
#> mango
#> melon
#> orange
#> passion_fruit
#> peach
#> pear
#> pineapple
#> plum
#> raspberry
#> strawberry
#> tangerine
#> water_melon 0