combina_niche3 {specieschrom}

Estimate the degree of niche overlapping among species from their chromatograms.

Description

Function that returns the lowest degree of niche overlapping (index D) among all the species when 1 to p environmental variables are considered. Also return the degree of niche overlapping (index D) among each couple of species when all the environmental variables are considered simultaneously and the lowest degree of niche overlapping (index D) when each environmental variable is considered alone.

Usage

combina_niche3(sp_chr, Thres_T)

Arguments

sp_chr

a matrix with the species chromatograms (alpha categories by p-environmental variables by species). Outputs of 'chromato_env16.R'

Thres_T

an integer corresponding to the threshold of minimal abundance in a category for niche breadth estimation

Value

Return a list composed of three matrices:

combi_dim, which contains the mean degree of niche overlapping. In combi_dim, the first column displays the number of dimensions considered simultaneously and the last column displays the index D associated with the combination of dimensions. Columns between the first and the last display the combinations of dimensions considered.

sp_by_sp, a matrix with the degree of niche overlapping (index D) species by species when all the dimensions are considered.

dim_alone, a vector with the mean degree of niche overlapping (index D) when each dimension is considered alone.

D=0 when species niches are fully different and D=100 when species niches are identical; the higher the number of dimensions, the lower the value of index D.

Examples

# Load the example datasets
data("data_abundance")
data("environment")
# Characterise and display the ecological niche of 2 pseudo-species
# `alpha`=50 categories, `m`=1 sample, `k`=5 and `order_smth`=2
sp_chrom_PS3<-chromato_env16(environment,data_abundance[,3],50,1,5,2)
sp_chrom_PS8<-chromato_env16(environment,data_abundance[,8],50,1,5,2)
# Combine the species chromatograms along a third dimension with `abind`
library(abind)
test_PS<-abind::abind(sp_chrom_PS3,sp_chrom_PS8,along=3)
# Apply the function `combina_niche3.R` on the matrix `test_PS` with `Thres_T`=0
Index_D_PS<-combina_niche3(test_PS,0)