point transect distance sampling in Nimble (half-normal with 2 detection function covariates)

dhnpt.R

  # need to define half-normal point transect detection function pdf
  dhnpt <<- nimbleFunction(
      run = function(x = double(0), b0 = double(0), b1 = double(0),
                     covar = double(0), width = double(0),
                     log = integer(0, default = 0)) {
          returnType(double(0))

        # calculate scale parameter
        sigma <- exp(b0 + b1*covar)

        # analytic expression for integral of 2*r*g(r)/width^2 when
        #  g(r) is half-normal (Intro distance book eqn 3.45)
        nu <- sigma^2 * (1 - exp(-(width^2)/(2*sigma^2)))

        # evaluate the detection function at distance/chaparral combination
        g <- exp(-(x^2)/(2*sigma^2))

        # pdf
        L <- (x * g)/nu

        if(log) return(log(L))
        else return(L)
      }
  )
  rhnpt <<- nimbleFunction(
      run = function(n = integer(0), b0 = double(0), b1 = double(0),
                     covar = double(0), width = double(0),
                     log = integer(0, default = 0)) {
          returnType(double())
          return(0)
      }
  )
  nimble::registerDistributions(list(
    dhnpt = list(BUGSdist="dhnpt(b0, b1, covar, width)",
                 pqAvail = FALSE,
                 range = c(0, 1000))))