mst.computation: Compute the Minimum Spanning Tree (MST) linking species of a...

In mFD: Compute and Illustrate the Multiple Facets of Functional Diversity

Compute the Minimum Spanning Tree (MST) linking species of a given assemblage

Description

This function computes the MST linking species of a given assemblage and is used to compute FEve index.

Usage

mst.computation(sp_faxes_coord_k)

Arguments

sp_faxes_coord_k

a matrix relating species coordinates for species present in a given assemblage.

Value

A dist object summarizing the MST for all species of a given assemblage mst_asb_k.

Author(s)

Camille Magneville and Sebastien Villeger

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)
  
# 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

mFD documentation built on May 29, 2024, 7:25 a.m.