inst/examples/06_cjs_robust.R

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

## CJS Robust Design example 
library(openpopscr)
RcppParallel::setThreadOptions(numThreads = 1)

# simulate data -----------------------------------------------------------

# set truth 
true_par <- list(lambda0 = 0.1, sigma = 30, phi = 0.7)

# make detectors array 
detectors <- make.grid(nx = 7, ny = 7, spacing = 20, detector = "count")

# make mesh 
mesh <- make.mask(detectors, buffer = 100, nx = 64, ny = 64, type = "trapbuffer")

# set number of total occasions to simulate
n_occasions <- 10

# set primary periods 
primary <- c(rep(1, 3), rep(2, 3), rep(3, 2), rep(4, 2))

# set number of individuals tracked
N <- 200

# simulate ScrData 
scrdat <- simulate_cjs_openscr(true_par, 
                               N, 
                               n_occasions, 
                               detectors, 
                               mesh, 
                               primary = primary, 
                               seed = 19482)

# fit model ---------------------------------------------------------------

# formulae, where phi depends on primary occasion
par <- list(lambda0 ~ 1, 
            sigma ~ 1, 
            phi ~ 1)

# get starting values 
start <- get_start_values(scrdat, model = "CjsModel")

# create model object 
oo <- CjsModel$new(par, scrdat, start)

# compute initial log-likelihood
oo$calc_llk()

# fit model
oo$fit()

# see results 
oo

oo$get_par("lambda0", k = 1, j = 1)
oo$get_par("sigma", k = 1, j = 1)
oo$get_par("phi", k = 1, m =1 )