#### Cormack-Jolly-Seber transient example
library(openpopscr)
RcppParallel::setThreadOptions(numThreads = 1)
# simulate data -----------------------------------------------------------
# set truth
true_par <- list(lambda0 = 2, sigma = 20, phi = 0.8, sd = 10)
# 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 <- 100
# simulate ScrData
scrdat <- simulate_cjs_openscr(true_par, N, n_occasions, detectors, mesh, move = TRUE, seed = 58348)
# fit model ---------------------------------------------------------------
# formulae
par <- list(lambda0 ~ 1,
sigma ~ 1,
phi ~ 1,
sd ~ 1)
# get starting values
start <- get_start_values(scrdat, model = "CjsTransientModel")
# create model object
obj <- CjsTransientModel$new(par, scrdat, start)
# compute initial likelihood
obj$calc_llk()
# fit model
obj$fit()
# see results
obj
obj$get_par("lambda0", k = 1, j = 1)
obj$get_par("sigma", k = 1, j = 1)
obj$get_par("phi", k = 1, m = 1)
obj$get_par("sd", k = 1, m = 1)
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