R/gen_4_basic_variants.R

In langfob/bdpg: Package For Building and Testing Biodiversity Problem Generators

#===============================================================================

                        #  gen_4_basic_variants.R

#===============================================================================

#' Create 1 of each of the 4 types of problems and run reserve selector on each
#'
#' This is what used to be the mainline for bdpgxupaper.  It creates a correct
#' biodiversity problem, then from that correct, it creates a wrapped problem.
#' It also creates an apparent problem for the original correct problem
#' and another for the wrapped problem.  It also runs marxan on each of these
#' four problems.
#'
#-------------------------------------------------------------------------------

#' @inheritParams std_param_defns
#'
#' @return Returns nothing.
#' @export

#-------------------------------------------------------------------------------

gen_4_basic_variants <- function (parameters, starting_dir, integerize)
    {
                    cat ("\n\nAT START OF gen_4_basic_variants().\n\n")

    #===============================================================================
    #       Generate a base problem, i.e, create the Xu graph nodes and edge_list.
    #===============================================================================

    base_COR_bd_prob = gen_single_bdprob_COR (parameters,
                                              starting_dir,
                                              integerize,
                                              base_prob_name_stem = "base_prob",
                                              cor_dir_name_stem = "cor"
                                              )

                    cat ("\n\n-----  base_COR_bd_prob@UUID = '", base_COR_bd_prob@UUID,
                         "', checksum = '", base_COR_bd_prob@checksum, "'  -----\n\n")

    do_rs_analysis_and_output (base_COR_bd_prob,
                                   base_COR_bd_prob,
                                   parameters,
                               starting_dir)

                    cat("\n\njust after do_rs_analysis_and_output() for Base COR problem")
                    cat ("\n\n================================================================================")
                    cat ("\n================================================================================\n\n")

    #===============================================================================
    #  Generate an APPARENT problem from the base problem, i.e., apply errors.
    #===============================================================================

    # base_APP_bd_prob = gen_single_bdprob_APP (base_COR_bd_prob,
    #                                           parameters)
#    base_APP_bd_prob =
                       gen_1_app_variant (base_COR_bd_prob,
                                          parameters,
                                          starting_dir,
                                          gen_cost_errors        = FALSE,
                                          cost_error_frac_bound  = 0,
                                          gen_FP_FN_errors       = TRUE,
                                          spp_occ_FP_const_rate  = parameters$spp_occ_FP_const_rate,
                                          spp_occ_FN_const_rate  = parameters$spp_occ_FN_const_rate,
                                          match_error_counts     = parameters$match_error_counts
                                          )

    # do_rs_analysis_and_output (base_APP_bd_prob,
    #                                base_COR_bd_prob,
    #                                parameters,
    #                            starting_dir)

                    cat("\n\njust after gen_1_app_variant() for Base APP problem")
                    cat ("\n\n================================================================================")
                    cat ("\n================================================================================\n\n")

    #===============================================================================
    #       Generate a wrapped problem around the base problem.
    #===============================================================================

    if (value_or_FALSE_if_null (parameters$wrap_lognormal_dist_around_Xu) &
        ! value_or_FALSE_if_null (parameters$read_Xu_problem_from_Xu_bench_file))
        {
        wrapped_COR_bd_prob =
#            gen_bdprob (parameters,
            gen_multi_bdprob (parameters,
                              starting_dir,
                              integerize,
                              base_COR_bd_prob)

        do_rs_analysis_and_output (wrapped_COR_bd_prob,
                                       wrapped_COR_bd_prob,
                                       parameters,
                                   starting_dir)

                        cat("\n\njust after do_rs_analysis_and_output() for Wrapped COR problem")
                        cat ("\n\n================================================================================")
                        cat ("\n================================================================================\n\n")

    #===============================================================================
    #  Generate an APPARENT problem from the wrapped problem, i.e., apply errors.
    #===============================================================================

        # wrapped_APP_bd_prob = gen_single_bdprob_APP (wrapped_COR_bd_prob,
        #                                              parameters)
#        wrapped_APP_bd_prob =
                              gen_1_app_variant (wrapped_COR_bd_prob,
                                                 parameters,
                                                 starting_dir,
                                                 gen_cost_errors        = FALSE,
                                                 cost_error_frac_bound  = 0,
                                                 gen_FP_FN_errors       = TRUE,
                                                 spp_occ_FP_const_rate  = parameters$spp_occ_FP_const_rate,
                                                 spp_occ_FN_const_rate  = parameters$spp_occ_FN_const_rate,
                                                 match_error_counts     = parameters$match_error_counts
                                                 )

        # do_rs_analysis_and_output (wrapped_APP_bd_prob,
        #                                wrapped_COR_bd_prob,
        #                                parameters,
        #                            starting_dir)

                        cat("\n\njust after gen_1_app_variant() for Wrapped APP problem")
                        cat ("\n\n================================================================================")
                        cat ("\n================================================================================\n\n")
        }  #  end if - wrap_lognormal_dist_around_Xu

    }  #  end function - gen_4_basic_variants()

#===============================================================================