#### Jolly-Seber example
library(openpopscr)
RcppParallel::setThreadOptions(numThreads = 1)
# simulate data -----------------------------------------------------------
# set truth
true_par <- list(D = 1000, lambda0 = 1.0, sigma = 30, phi = 0.8, beta = 0.5)
# make detectors array
detectors <- make.grid(nx = 7, ny = 7, spacing = 20, detector = "proximity")
# make mesh
mesh <- make.mask(detectors, buffer = 100, nx = 64, ny = 64, type = "trapbuffer")
# set number of occasions to simulate
n_occasions <- 5
# simulate ScrData
scrdat <- simulate_js_openscr(true_par, n_occasions, detectors, mesh, seed = 19592)
# fit model ---------------------------------------------------------------
# create formulae
par <- list(lambda0 ~ 1,
sigma ~ 1,
beta ~ 1,
phi ~ 1,
D ~ 1)
# get start values
start <- get_start_values(scrdat, model = "JsModel")
# create model object
oo <- JsModel$new(par, scrdat, start)
# compute initial likelihood
oo$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)
oo$get_par("beta", k = 1, m = 1)
oo$get_par("D")
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