We begin by simulating survey data for two commensal species for the following scenario. Species 1 has a 50% probability occupancy. Species 2 benefits from the presence of species 1, so its probability of occupancy is 83% when species 1 is also present, but only 50% in the absence of species 1. One hundred sites are surveyed 10 times each. The probability of detection for both species is 0.3.

data_generator_commensal_species = function(psi, p, nSites, nReps){ # occupancy prob psi, detection prob p # true occupancy state z1 <- rbinom(nSites, 1, psi) z2 <- rbinom(nSites, 1, psi + z1/3) # sampling of true occupancy state y1 <- matrix(NA, nSites, nReps) y2 <- matrix(NA, nSites, nReps) for(i in 1:nSites) { y1[i,] <- rbinom(nReps, 1, z1[i]*p) # detection history for species 1 y2[i,] <- rbinom(nReps, 1, z2[i]*p) # "" species 2 } list(y1,y2)} y = data_generator_commensal_species(psi = .5, p = .3, nSites = 100, nReps = 10)

We specify the model structure in jags.

model { ## Priors a0 ~ dunif(-5, 5) b0 ~ dunif(-5, 5) b1 ~ dunif(-5, 5) p ~ dunif(0, 1) ## Model # State process for(i in 1:nSites) { logit(psi1[i]) <- a0 logit(psi2[i]) <- b0 + b1 * Z1[i] Z1[i] ~ dbern(psi1[i]) Z2[i] ~ dbern(psi2[i]) # Detection process for(j in 1:nOccs) { y1[i, j] ~ dbin(p, Z1[i]) y2[i, j] ~ dbin(p, Z2[i]) } } }

Then we run the model with R and jags.

library(rjags) d = list( y1 = y[[1]], y2 = y[[2]], nSites = 100, nOccs = 10) mod = jags.model("commensal_multispecies.txt", d) update(mod) post = coda.samples(mod, c("a0", "b0", "b1", "p"),1e4) summary(post) plot(post)

Here are the posterior distributions. A nice fit to the scenario for the simulated data.