Run a model and calculate model fit.

Usage

run_and_fit(
  aeme,
  param,
  model,
  vars_sim,
  path,
  model_controls = NULL,
  FUN_list = NULL,
  weights,
  na_value = 999,
  var_indices = NULL,
  return_indices = FALSE,
  include_wlev = FALSE,
  return_df = FALSE,
  method = "calib",
  sa_ctrl = NULL,
  fit = TRUE,
  timeout = Inf
)

Arguments

aeme: aeme; object.
param: dataframe; of parameters read in from a csv file. Requires the columns c("model", "file", "name", "value", "min", "max", "log")
model: string; for which model. Options are c("dy_cd", "glm_aed" and "gotm_wet")
vars_sim: vector; of variables names to be used in the calculation of model fit. Currently only supports using one variable.
path: filepath; where input files are located relative to `config`.
model_controls: dataframe; of configuration loaded from "model_controls.csv".
FUN_list: function; of the form function(O, P) which will be used in to calculate model fit. If NULL, uses mean absolute error (MAE).
weights: vector; of weights to be used in the calculation of model fit.
na_value: numeric; value to be returned if model fails to run.
var_indices: list; generated from running run_and_fit() with return indices = TRUE on the first simulation.
return_indices: boolean; return the indices (depths, time and dates) of each variable. Used when running calibration and the time period does not change between simulations.
include_wlev: boolean; include water level in the calculation of model fit.
return_df: boolean; return dataframe of modelled and observed.
method: string; of the method of the model run. Options are c("sa", "calib").
sa_ctrl: list; of control parameters for the sensitivity analysis. Only required if method = "sa".
fit: boolean; fit model or not. If FALSE, only return netCDF file connection.
timeout: numeric; time in seconds to run each simulation. Default is Inf.

Value

A single value of model fit, calculated by FUN_list.