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Setup Movement Processes for SPoRC

Setup_Mod_Movement.Rd

Setup Movement Processes for SPoRC

Usage

Setup_Mod_Movement(
  input_list,
  do_recruits_move = 0,
  use_fixed_movement = 0,
  Fixed_Movement = NA,
  Use_Movement_Prior = 0,
  Movement_prior = NULL,
  Movement_ageblk_spec = NULL,
  Movement_yearblk_spec = NULL,
  Movement_sexblk_spec = NULL,
  cont_vary_movement = "none",
  Movement_cont_pe_pars_spec = "none",
  ...
)

Arguments

input_list

List containing data, parameter, and map lists for the model.

do_recruits_move

Integer flag (0 or 1) indicating whether recruits move. Default is 0 (do not move).

use_fixed_movement

Integer flag (0 or 1) indicating whether to use a fixed movement matrix (1) or estimate movement parameters (0). Default is 0.

Fixed_Movement

Numeric array for fixed movement matrix dimensioned by [n_regions, n_regions, n_years, n_ages, n_sexes]. Default is an array of ones.

Use_Movement_Prior

Integer flag (0 or 1) indicating whether to use movement priors. Default is 0 (no priors).

Movement_prior

Numeric vector or array specifying prior values for movement parameters. If a vector, a constant prior is applied across all dimensions.

Movement_ageblk_spec

Either:

  • Character string "constant" for age-invariant movement, or

  • A list of numeric vectors specifying age blocks sharing parameters.

For example, list(c(1:6), c(7:10), c(11:n_ages)) defines three age blocks where:

  • ages 1 to 6 share parameters,

  • ages 7 to 10 share parameters,

  • ages 11 to n_ages share parameters.

To specify age-invariant movement, use either "constant" or list(c(1:n_ages)).

Movement_yearblk_spec

Either:

  • Character string "constant" for time-invariant movement, or

  • A list of numeric vectors specifying year blocks sharing movement parameters.

Movement_sexblk_spec

Either:

  • Character string "constant" for sex-invariant movement, or

  • A list of numeric vectors specifying sex blocks sharing movement parameters.

cont_vary_movement

Character string specifying continuous varying movement type. Available options:

  • "none"

  • "iid_y" (iid deviations by year)

  • "iid_a" (iid deviations by age)

  • "iid_y_a" (iid deviations by year and age)

  • "iid_y_s" (iid deviations by year and sex)

  • "iid_a_s" (iid deviations by age and sex)

  • "iid_y_a_s" (iid deviations by year, age, and sex)

Default is "none".

Movement_cont_pe_pars_spec

Character string specifying process error parameter sharing. Available options:

  • "est_shared_r"

  • "est_shared_a"

  • "est_shared_s"

  • "est_shared_r_a"

  • "est_shared_a_s"

  • "est_shared_r_s"

  • "est_shared_r_a_s"

  • "est_all"

  • "fix"

  • "none"

Default is "none".

...

Additional parameters such as starting values for move_pars, logit_move_devs, and move_pe_pars.