mFD (version 1.0.7)

sp.filter: Retrieve information about species in a given assemblage

Description

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.

Usage

sp.filter(asb_nm, sp_faxes_coord, asb_sp_w)

Value

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.

Arguments

asb_nm

a string object referring to the name of a given community.

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.

asb_sp_w

a matrix linking weight of species (columns) and a set of assemblages (rows).

Author

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

# 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)