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

Source: R/fit_cjs.R
fit_s4t_cjs_ml.Rd

Fits the time- and age-specific space-for-time mark-recapture model using maximum likelihood.

Usage

fit_s4t_cjs_ml(
  p_formula,
  theta_formula,
  ageclass_formula,
  groups = NULL,
  s4t_ch,
  ndeps = 0.001,
  lmm = 5,
  maxit = 500,
  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. Default is no groups (groups = NULL).

s4t_ch

a s4t_ch object

ndeps

a numeric value passed to optim. See optim documentation.

lmm

an integer value passed to optim. See optim documentation.

maxit

an integer value passed to optim. See optim documentation.

fixed_age

a logical value that determines whether the age-class model will be run as a separate model (TRUE) or whether it is estimated along with the mark-recapture model (FALSE).

Value

a s4t_cjs_ml object.

Details

Additional details...

Examples

if (FALSE) { # \dontrun{
sim.dat <- sim_simple_s4t_ch(N = 2000)
m1 <- fit_s4t_cjs_ml(p_formula = ~ t,
                     theta_formula = ~ a1 * a2 * s * j,
                     ageclass_formula = ~ FL,
                     fixed_age = TRUE,
                     s4t_ch = sim.dat$s4t_ch)
} # }