from.spfe.to.feasb: Build the assemblage-FEs dataframe from the...

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

Build the assemblage-FEs dataframe from the assemblages-species one

Description

This function computes an occurrence data frame with assemblages in rows and Functional Entities (FEs) in columns, from the dataframe of assemblage-species and the output of the mFD::sp.to.fe() function.

Usage

from.spfe.to.feasb(sp_fe, asb_sp_w)

Arguments

sp_fe	list gathering to which FE belongs eac species. It is the output of the mFD::sp.to.fe() function - $sp_fe.
asb_sp_w	the assemblage * species data frame with assemblages being rows and species being columns

Value

an occurrence dataframe with studied FEs in columns and assemblages in rows. Be careful: It's an occurrence data frame, not an abundance one

Author(s)

Camille Magneville

Examples

# Load species traits data:
 data("fruits_traits", package = "mFD")

# Transform species traits data:
# Only keep the first 4 traits to illustrate FEs:
 fruits_traits <- fruits_traits[ , c(1:4)]   

# Load trait types data:
 data("fruits_traits_cat", package = "mFD")

# Transform the trait types data to only keep traits 1 - 4:
 fruits_traits_cat <- fruits_traits_cat[c(1:4), ]
 
 # Load Assemblages*Species matrix:
data('baskets_fruits_weights', package = 'mFD')

# Gather species into FEs:
## gathering species into FEs (FEs named according to the decreasing...
## ...  number of species they gather):
 sp_FEs_fruits <- mFD::sp.to.fe(
      sp_tr      = fruits_traits, 
      tr_cat     = fruits_traits_cat, 
      fe_nm_type = "fe_rank")
      
# Get the list which gather to which FE belongs each species:
sp_fes_list <- sp_FEs_fruits$sp_fe
      
# Build the Assemblages*FEs data frame:
asb_fes <- mFD::from.spfe.to.feasb(sp_fe = sp_fes_list,
                                   asb_sp_w = baskets_fruits_weights)
asb_fes

CmlMagneville/mFD documentation built on Dec. 21, 2024, 7:36 p.m.