inst/examples/05_cjs_basic.R

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

#### Cormack-Jolly-Seber example 
library(openpopscr)
RcppParallel::setThreadOptions(numThreads = 1)

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

# set truth 
true_par <- list(lambda0 = 0.2, 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 occasions to simulate
n_occasions <- 5

# set number of individuals tracked
N <- 250

# simulate ScrData 
scrdat <- simulate_cjs_openscr(true_par, N, n_occasions, detectors, mesh, seed = 19295)

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

# set formulae
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 likelihood at starting values 
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)