Fit space-for-time mark-recapture model in Bayesian framework

Fits the time- and age-specific space-for-time mark-recapture model in a Bayesian framework using Stan.

Usage

fit_s4t_cjs_rstan(
  p_formula,
  theta_formula,
  ageclass_formula,
  groups = NULL,
  s4t_ch,
  chains = 3,
  warmup = 500,
  iter = 1000,
  fixed_age = FALSE,
  ...
)

Arguments

p_formula: a formula for detection probabilities using default indices (a1, a2, s, t, j, k, r, and g) or covariates.
theta_formula: a formula for transition probabilities using default indices (a1, a2, s, t, j, k, r, and g) or covariates.
ageclass_formula: a formula for the effect structure of the age-class sub-model.
groups: a character vector containing the names of the covariates that comprise the groups.
s4t_ch: a s4t_ch object
chains: an integer of the number of chains to run.
warmup: an integer of the number of warmup iterations.
iter: an integer of the number of total (warmup + actual) iterations.
fixed_age: a logical object that determines whether the ageclass model will be run as a separate model (TRUE) or whether it is estimated along with the CJS model (FALSE).
...: further arguents to pass to rstan::sampling

Value

a s4t_cjs_rstan object.

Examples

if (FALSE) { # \dontrun{
sim.dat <- sim_simple_s4t_ch(N = 2000)
m1 <- fit_s4t_cjs_rstan(p_formula = ~ t,
                        theta_formula = ~ a1 * a2 * s * j,
                        ageclass_formula = ageclass ~ FL,
                        fixed_age = TRUE,
                        s4t_ch = sim.dat$s4t_ch)
} # }