load_data_om: Prepare the data for the operating model

In pacific-hake/pacifichakemse: Management Strategy Evaluation of Pacific Hake

Prepare the data for the operating model

Description

Prepare the data for the operating model

Usage

load_data_om(
  ss_model = NULL,
  yr_future = 0,
  n_sim_yrs = 0,
  n_season = 4,
  season_names = c("Season1", "Season2", "Season3", "Season4"),
  n_space = 2,
  space_names = c("Canada", "US"),
  n_survey = 2,
  ages = 0:20,
  age_plus_grp = 15,
  age_names = paste("age", 0:20),
  rdev_sd = 1.4,
  move_init = NULL,
  move_max_init = 0.35,
  move_fifty_init = 6,
  move_out = 0.85,
  move_south = 0.05,
  move_slope = 0.9,
  ages_no_move = 0:1,
  selectivity_change = 0,
  s_min = 1,
  s_max = 6,
  s_min_survey = 2,
  s_max_survey = 6,
  b_future = 0.5,
  sel_change_yr = 1991,
  f_space = c(0.2612, 0.7388),
  log_phi_survey = log(11.46),
  random_recruitment = TRUE,
  ...
)

Arguments

ss_model	A model input/output list representing the SS model as found in the RDS file created by create_rds_file()
yr_future	Number of years to run the OM into the future in an OM only run. If this is > 0, n_sim_yrs cannot be. This must be 0 when running from an MSE context. Use n_sim_yrs for that instead.
n_sim_yrs	Number of years to allocate OM objects for the future. If this is > 0, yr_future cannot be. All future values will be NA except for the movement matrix values.
n_season	Number of seasons
season_names	A vector of names for the seasons. Length must equal n_season
n_space	Number of spatial areas
space_names	A vector of names for the spaces. Length must equal n_space
n_survey	Survey frequency
ages	A vector of ages
age_plus_grp	Plus group for ages. Required for setup_blank_om_objects()
age_names	A vector of names for the ages. Length must equal length of ages
rdev_sd	Recruitment deviation Standard deviation
move_init	Initial distribution of fish
move_max_init	Maximum movement rate
move_fifty_init	Age at 50 percent maximum movement rate
move_out	Fraction of individuals that travel south in the last season
move_south	Fraction of individuals that move south during the year
move_slope	Slope of the movement function
ages_no_move	Ages of fish which do not move in the movement model
selectivity_change	Should selectivity change?
s_min	Minimum age in fishery selectivity
s_max	Maximum age in fishery selectivity
s_min_survey	Minimum age in survey selectivity
s_max_survey	Maximum age in survey selectivity
b_future	Bias adjustment in the future
sel_change_yr	A year in which a selectivity change took place
f_space	The proportion of TAC given to each country. First value is Canada, the second is the US
log_phi_survey	Survey phi parameter value If FALSE, they will be given random normal values based on rdev_sd
random_recruitment	Logical. If FALSE, recruitment deviations will be set to zero in the projection period. If TRUE, recruitment deviations will be set to random values in the projection period
...	Absorb arguments destined for other functions

Value

A list of Parameters, Input parameters, Survey, Catch, and others

Examples

## Not run: 
df <- load_data_om(n_season = 2, n_space = 2)

## End(Not run)

pacific-hake/pacifichakemse documentation built on June 11, 2024, 4:07 a.m.