calib_assist: Assist calibration of DYRESM-CAEDYM model.

In dycdtools: Calibration Assistant and Post-Processing Tool for Aquatic Ecosystem Model DYRESM-CAEDYM

Assist calibration of DYRESM-CAEDYM model.

Description

This function carries out simulations with a large number of possible combinations of parameter values that users regard as potentially suitable for their model calibration, and calculates the values of nominated objective functions (i.e., statistical measures of goodness of fit) for each combination. Based on the calculated objective function values, users can determine the optimal set(s) of parameter values or narrow the ranges of possible parameter values.

Usage

calib_assist(
  cal.para,
  combination = "random",
  n,
  model.var,
  phyto.group = NA,
  obs.data,
  objective.function = c("NSE", "RMSE"),
  start.date,
  end.date,
  dycd.wd,
  dycd.output,
  file.name,
  verbose = TRUE,
  parallel = FALSE,
  n.cores = NULL,
  write.out = TRUE
)

Arguments

cal.para	a data frame or a character string naming an external .csv file where below column names are mandatory: "Parameter" describing parameter names (abbreviation is allowed), "Min", "Max", and "Increment" describing the minimum and maximum parameter values and expected increment in the value range, "Input_file" and "Line_NO" listing in which configuration file at which line the parameter can be found.
combination	a vector of string character of how to pick up combinations of parameter values. "random" - the function randomly picks up a given number of combinations; "all" - the function tries all possible combinations of parameter values.
n	the number of random selections. Must be provided if combination = "random".
model.var	a vector of string character of modelled variables for calibration. the character should be from the 'var.name' column of 'data(output_name)'. Note that if model calibration needs to regard chlorophyll of multiple phytoplankton groups as a whole, model.var should use "CHLA" and individual phytoplankton group should be specified through the "phyto.group" argument. If phytoplankton groups are separately calibrated, simply list their character in this argument (model.var).
phyto.group	a vector of simulated phytoplankton groups, including CHLOR, FDIAT, NODUL, CYANO and CRYPT.
obs.data	a data frame or a character string naming a csv file of observed lake data. The observed lake data need to include below columns: 1) 'Date' in format of "%Y-%m-%d" 2) 'Depth' (integer) 3) Water quality variables (use string characters of model var as column names). see example data 'data(obs_temp)'.
objective.function	a vector of string character describing which objective function(s) to be used for calibration. Selected from the following five functions: "NSE": Nash-Sutcliffe efficiency coefficient, "RMSE": Root Mean Square Error, "MAE": Mean Absolute Error, "RAE": Relative Absolute Error, "Pearson": Pearson's r.
start.date, end.date	the beginning and end simulation dates for the intended DYRESM-CAEDYM calibration. The date format must be "%Y-%m-%d". The two dates should be consistent with model configurations.
dycd.wd	the directory where input files (including the bat file) to DYRESM-CAEDYM are stored.
dycd.output	a character string naming the output file of model simulation.
file.name	a character string naming a .csv file where the results of this function are written to. Needed if 'write.out' = TRUE.
verbose	if TRUE, model calibration information is printed.
parallel	if TRUE, the calibration process is run on multiple cores.
n.cores	When 'parallel' is TRUE, n.cores is the number of cores the calibration function will be run on. If not provided, the default value is the number of available cores on the computer -1.
write.out	if TRUE, model calibration results are saved in a file with a file name set by the "file.name" argument.

Value

a data frame of all tested values of parameters and corresponding values of the objective function(s).

Note

No executable examples are provided to illustrate the use of this function, as this function relies on the DYRESM-CAEDYM executables to work.

dycdtools documentation built on Sept. 11, 2024, 6:40 p.m.