Run ensemble data assimilation and/or produce forecasts

Usage

run_da_forecast(
  states_init,
  pars_init = NULL,
  aux_states_init,
  obs,
  obs_sd,
  model_sd,
  working_directory,
  met_file_names,
  inflow_file_names = NULL,
  outflow_file_names = NULL,
  config,
  pars_config = NULL,
  states_config,
  obs_config,
  management = NULL,
  da_method = "enkf",
  par_fit_method = "inflate",
  debug = FALSE,
  log_wq = FALSE,
  obs_secchi = NULL,
  obs_depth = NULL
)

Arguments

states_init: array of the initial states. Required dimensions are [states, depths, ensemble]
pars_init: array of the initial states. Required dimensions are [pars, depths, ensemble]. (Default = NULL)
aux_states_init: list of initial conditions for auxillary states. These are states in the GLM that are require for restarting the model but are not included in data assimilation. These are states that are not associated with a value in model_sd.
obs: array; array of the observations. Required dimensions are [nobs, time, depth]
obs_sd: vector; vector of standard deviation for observation
model_sd: vector vector of standard deviations describing the model error for each state
working_directory: string; full path to directory where model executes
met_file_names: vector; vector of full path meteorology file names
inflow_file_names: vector or matrix;; vector of inflow file names
outflow_file_names: vector or matrix; vector of outflow file names
config: list; list of configurations
pars_config: list; list of parameter configurations (Default = NULL)
states_config: list; list of state configurations
obs_config: list; list of observation configurations
management: list; list of management inputs and configuration (Default = NULL)
da_method: string; data assimilation method (enkf or pf; Default = enkf)
par_fit_method: string; method for adding noise to parameters during calibration
debug: boolean; add extra diagnostics for debugging (Default = FALSE)

Value

a list is passed to write_forecast_netcdf() to write the netcdf output and create_flare_eml() to generate the EML metadata

Details

Uses the ensemble data assimilation to predict water quality for a lake or reservoir. The function requires the initial conditions (states_init) for each state and ensemble member using an array with the following dimension order: states, depth, ensembles member. If you are fitting parameters, it also requires initial conditions for each parameter and ensemble member using an array (par_init) with the following dimension order: parameters, ensemble member. The arrays for states_init and pars_init can be created using the generate_initial_conditions() function, if starting from initial conditions in the states_config data frame or from observations in first time column of the obs array.

Examples

if (FALSE) {
da_forecast_output <- FLAREr::run_da_forecast(states_init = init$states,
    pars_init = init$pars, aux_states_init = init$aux_states_init,
    obs = obs, obs_sd = obs_config$obs_sd, model_sd = model_sd,
    working_directory = config$file_path$execute_directory,
    met_file_names = met_file_names, inflow_file_names = inflow_file_names,
    outflow_file_names = outflow_file_names, config = config,
    pars_config = pars_config, states_config = states_config,
    obs_config = obs_config)
}