Generate initial conditions for FLARE

Usage

generate_initial_conditions(
  states_config,
  obs_config,
  pars_config = NULL,
  obs,
  config,
  obs_non_vertical = NULL
)

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
obs_non_vertical: list; observations of variables that don't have vertical dimension. Default = NULL (non-vertical observation assimilation is not part of this build of FLAREr).

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. For new simulations (no restart file), parameters are initialized from pars_config. If config$model_settings$par_init_file is set, the per-ensemble member parameter values in that CSV (an ensemble_member column with values 1:ensemble_size plus one column per parameter named by par_names_save) overwrite the config-initialized parameters; any parameter not present as a column keeps its config-sampled value.

Author

Quinn Thomas