inst/devel/simulateSCR_noneuc.R

In r-glennie/openpopscr: Open Population Spatial Capture-Recapture

#### Simple script to simulate SCR data with pairwise non-euclidean distances 

## Set parameters 
D <- 1000
lambda0 <- 0.5
sigma <-  30
noneuc <- 1.5

## Survey setup 
# number of occasions
K <- 5
# make detectors array 
detectors <- make.grid(nx = 7, ny = 7, spacing = 20, detector = "count")
rownames(detectors) <- 1:nrow(detectors)
# make mesh 
mesh <- make.mask(detectors, buffer = 100, nx = 64, ny = 64, type = "trapbuffer")

# set non-euclidean pairwise distance effect
euc <- matrix(0, nrow = nrow(detectors), nc = nrow(mesh))
euc[1:10, 1:1500] <- 1 
sigma_mesh <- exp(log(sigma) + noneuc * euc)

## Simulate activity centres
A <- nrow(mesh) * attr(mesh, "area") / 100
N <- rpois(1, D*A)
pt <- sample(1:nrow(mesh), size = N, replace = TRUE)
x <- mesh[pt, 1]
y <- mesh[pt, 2]

## Simulate survey 
cap <- data.frame(session = numeric(), 
                  ID = numeric(), 
                  occasion = numeric(), 
                  trap = numeric())

seen <- rep(FALSE, N)
id <- rep(0, N)
for (k in 1:K) {
  for (i in 1:N) {
    d2 <- (x[i] - detectors[,1])^2 + (y[i] - detectors[,2])^2
    er <- lambda0 * exp(-d2 / (2 * sigma_mesh[,pt[i]]^2))
    c <- rpois(length(er), er)
    if (any(c > 0)) {
      if (!seen[i]) {
        id[i] <- max(id) + 1
        seen[i] <- TRUE
      } 
      dets <- which(c > 0)
      for (r in 1:length(dets)) {
        nc <- c[dets[r]]
        rec <- data.frame(session = rep(1, nc), 
                          ID = rep(id[i], nc), 
                          occasion = rep(k, nc), 
                          trap = rep(dets[r], nc))
        cap <- rbind(cap, rec)
      }
    }
  }
}
if (max(cap$occasion) != K) cap <- rbind(cap, data.frame(session = 1, ID = "NONE", occasion = K, trap = 1))
ch <- make.capthist(cap, detectors)

scrdat <- ScrData$new(ch, mesh = mesh)