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, orA 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"
orlist(c(1:n_ages))
.- Movement_yearblk_spec
Either:
Character string
"constant"
for time-invariant movement, orA list of numeric vectors specifying year blocks sharing movement parameters.
- Movement_sexblk_spec
Either:
Character string
"constant"
for sex-invariant movement, orA 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
, andmove_pe_pars
.