specieschrom (version 1.0.0)

opti_eury_niche2: Optimums and amplitudes estimations along each niche dimension.

Description

Function that estimates niche optimums and amplitudes along each environmental variable and for each species.

Usage

opti_eury_niche2(sp_chr, Thres_T, z, y, k)

Value

Three matrices are returned:

amplitudes, a matrix with the degree of euryoecie (niche breadth) of each species (in column) along each environmental dimension (in line)

mean_amplitudes, a matrix with the mean degree of euryoecie of each species

optimums, a matrix with the niche optimum values of each species (in column) along each environmental dimension (in line)

Arguments

sp_chr

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

Thres_T

an integer corresponding to the min abundance threshold for niche amplitudes estimations

z

a matrix with n samples by p environmental variables (i.e. the value of each environmental variable in each sample). Same matrix as in 'chromato_env16.R'.

y

a matrix with the species abundance in the n samples

k

an integer corresponding to the percentage of samples with the highest abundance values to use to estimate the mean abundance in a given category. Should have the same value as in 'chromato_env16.R'

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)
# `opti_eury_niche2.R` can then be applied, with `Thres_T`=0 and `k`=5
opti_ampli_niche<-opti_eury_niche2(test_PS,0,environment,data_abundance[,c(3,8)],5)