SQ_optim: Main function for parameter estimation

In aafaf-arharas/SQoptimizR: A Package for Parameter Estimation for the crop model SiriusQuality

Main function for parameter estimation

Description

Main function for parameter estimation

Usage

SQ_optim(
  crit_function,
  optim_method,
  obs_daily_path,
  obs_sum_path,
  dailyVar,
  sumVar,
  obs_sim_path,
  project_path,
  output_path,
  console_path,
  param_info,
  optim_options,
  run2simulate,
  cores_nb,
  time_display,
  saves_daily_output,
  print_console
)

Arguments

crit_function	Criterium to optimise depends on the chosen method : Simplex : "crit_log_cwss", "crit_log_cwss_corr", "crit_ols" Dreamzs : "likelihood_log_ciidn" , "likelihood_log_ciidn_corr"
optim_method	Estimation method (Dreamzs, Simplex)
obs_daily_path	Path to daily observations
obs_sum_path	Path to summary observations
dailyVar	Vector of variables names to estimate (variables from daily file)
sumVar	Vector of the variables names to estimate (variables from summary file)
obs_sim_path	Path to the data frame which matches between the names of the simulated and observed variables
project_path	Path to the directory of input files
output_path	Path where to save results
console_path	Path to the console
param_info	Information on the parameters to estimate. #' Either a list containing: (named) vectors of upper and lower bounds (ub and lb) (-Inf and Inf can be used), init_values, A data.frame containing initial values to test for the parameters (optional, if not provided, or if less values than number of repetitions of the minimization are provided, the, or part of the, initial values will be randomly generated using LHS sampling within parameter bounds). or a named list containing for each parameter the list of situations per group (sit_list), the vector of upper and lower bounds (one value per group) (ub and lb) and the list of initial values per group init_values (data.frame, one column per group, optional). (see here for an example)
optim_options	List of options of the parameter estimation method, containing: path_results The path where to store the results (optional, default=getwd()) specific options depending on the method used. Click on the links to see examples with the simplex and DreamZS methods.
run2simulate	Run name to simulate
cores_nb	Number of cores to simulate on
time_display	Flag (TRUE/FALSE) for display of calculation time
saves_daily_output	Boolean to save daily output (if set to "true")
print_console	Boolean to print information on the simulation progression on the console (if set to "false")

Value

prints, graphs and a list containing the results of the parameter estimation, All results are saved in the folder optim_options$path_results.

aafaf-arharas/SQoptimizR documentation built on March 25, 2022, 12:18 a.m.