Generate initial conditions for FLARE

Usage

generate_initial_conditions(
  states_config,
  obs_config,
  pars_config = NULL,
  obs,
  config,
  historical_met_error = FALSE
)

Arguments

states_config: list; list of state configurations
obs_config: list; list of observation configurations
pars_config: list; list of parameter configurations (Default = NULL)
obs: array; array of the observations. Required dimensions are [nobs, time, depth]
config: list; list of configurations
historical_met_error: boolean; producted by generate_glm_met_files()
restart_file: string; netcdf file with full path from FLARE output that is used as initial conditions

Value

list; list contains the initial conditions objects required by run_da_forecast()

Details

Function to generate initial conditions from either default values in the states_config, observations (if available), or a previous run using the output as a restart file.

Author

Quinn Thomas

Examples

if (FALSE) {
  init <- generate_initial_conditions(states_config, obs_config,
    pars_config, obs, config, restart_file = config$run_config$restart_file,
    historical_met_error = met_out$historical_met_error)
  }