djsdm: Density of a Joint Species Distribution Model

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Density of a Joint Species Distribution Model

Description

Density function for a joint species distribution model.

Usage

djsdm(x, psi, log = FALSE)

Arguments

x	Numeric vector or matrix. Binary values of species occurrence. If matrix, then a vector of probability densities is returned with an element for each record of the matrix. Matrix records represent sites, and matrix fields represent species.
psi	Numeric vector or matrix. Probabilities of site occupancy. Matrix records represent sites, and matrix fields represent species. If vector, then psi is recycled for each record of matrix x.
log	Logical scalar. If TRUE, then probabilities are given as log(density).

Details

Computes the probability density of a joint species distribution model. The probability of observing a community is calculated as the product of the probabilities of observing each species. Observations for each species are Bernoulli-distributed, and species-specific probability densities are computed with stats::dbinom.

Value

Numeric vector of probability densities.

References

Wilkinson DP, Golding N, Guillera‐Arroita G, Tingley R, and McCarthy MA. 2021. Defining and evaluating predictions of joint species distribution models. Methods in Ecology and Evolution, 12(3): 394-404. DOI: 10.1111/2041-210X.13518

See Also

stats::dbinom for density of the binomial distribution.

mlWAIC for computing widely applicable information criteria for joint species distribution models.

Examples

# Define species occurrence.
x<-c(1,0,0,1)

# Define occupancy probabilities.
psi<-c(0.886,0.391,0.139,0.991)

# Compute log probability density.
djsdm(x=x,psi=psi,log=TRUE)

LocaTT documentation built on June 14, 2026, 1:06 a.m.