R/xu_paper_main.R

In langfob/bdpgxupaper: Package for experiments for Xu biodiversity problem generation paper

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

                        #  xu_paper_main.R

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

#  History:

#  2017 01 22 - BTL
#       Removed from old biodivprobgen project as part of splitting that
#       project into separate packages for the code specific to papers and
#       the general library of problem generator code.

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

#' Mainline for experiments and data generation for Xu bdpg paper
#'
#' This is the top level function for running experiments and generating data for
#' the problem difficulty paper that explains the Xu biodiversity problem
#' generator.
#'
#' @param parameters List of parameters controlling the current run (usually
#'   decoded from project.yaml by tzar)
#' @param emulating_tzar boolean indicating whether to run tzar_emulator; TRUE
#'   implies run emulator, FALSE implies don't run under emulator
#'
#' @return returns nothing
#'
#' @export
#'
#' @examples \dontrun{
#' xu_paper_main (parameters)
#'}

xu_paper_main = function (parameters, emulating_tzar=FALSE)
    {

#===============================================================================
#          Global variables not to be included in package.
#===============================================================================

    cat ("\n\nSTARTING xu_paper_main.R at ", date(), "\n\n")

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

        #  debugging level: 0 means don't output debugging write statements.
        #  Having this as an integer instead of binary so that I can have
        #  multiple levels of detail if I want to.
#    DEBUG_LEVEL = 0
    options (bdpg.DEBUG_LEVEL=0)
    options (bdpgxupaper.DEBUG_LEVEL=0)

        #  Turn all R warnings into errors.
#2018 06 12 temporarily turning this off to try to get something
#           working on nectar that is crashing because of a warning
#           becoming an error.  See daily log for details of the warning.
#options (warn=2)

        #  Sometimes, for debugging, bdpg needs to know if we're
        #  emulating tzar, so record the value as a global option.

    options (bdpg.emulating_tzar = emulating_tzar)

#===============================================================================
#                   Print out system environment.
#===============================================================================

    cat ("\nSystem environment variables at start of xu_paper_main():\n\n")
    sys_vars = Sys.getenv()
    print (sys_vars)
    cat ("\n\n")

#===============================================================================
#                   Initialize for use of bdpg package.
#===============================================================================

    parameters <- bdpg::init_for_bdpg (parameters)
    integerize <- bdpg::get_integerize_function (parameters$integerize_string)

#===============================================================================
#                       Do the main work.
#===============================================================================

    cat ("\n\nAt START of main work in xu_paper_main(), current dir = '",
         getwd(), "'\n\n")

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

    gen_4_basic_variants =
        bdpg::value_or_FALSE_if_null (parameters$gen_4_basic_variants)

    gen_4_simple_random_variants =
        bdpg::value_or_FALSE_if_null (parameters$gen_4_simple_random_variants)
cat ("\n>>>>> parameters$gen_4_simple_random_variants = '", parameters$gen_4_simple_random_variants, "'")
cat ("\n>>>>> gen_4_simple_random_variants = '", gen_4_simple_random_variants, "'\n")

    gen_6_basic_variants =
        bdpg::value_or_FALSE_if_null (parameters$gen_6_basic_variants)

    gen_11_variants =
        bdpg::value_or_FALSE_if_null (parameters$gen_11_variants)

    gen_20_basic_variants =
        bdpg::value_or_FALSE_if_null (parameters$gen_20_basic_variants)

    act_on_loaded_existing_tzar_run =
        bdpg::value_or_FALSE_if_null (parameters$act_on_loaded_existing_tzar_run)

    single_action_using_tzar_reps =
        bdpg::value_or_FALSE_if_null (parameters$single_action_using_tzar_reps)

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

    if (gen_20_basic_variants)
    {
    bdpg::gen_20_basic_variants_including_cost_error (parameters,
                                                      integerize)

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

    } else if (gen_4_basic_variants)
    {
    bdpg::gen_4_basic_variants (parameters, integerize)

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

    } else if (gen_4_simple_random_variants)
    {
    bdpg::gen_4_simple_random_variants_mixing_FP_FN_and_cost_error (parameters,
                                                                    integerize)

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

    } else if (gen_11_variants)
    {

    bdpg::gen_11_variants_mixing_FP_FN_and_cost_error (parameters, integerize)

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

    } else if (gen_6_basic_variants)
    {
    bdpg::gen_6_basic_variants (parameters, integerize)

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

    } else if (act_on_loaded_existing_tzar_run)
    {
    bdpg::load_existing_tzar_run_from_glass (
        parameters,
        file_of_runs_to_load = parameters$file_of_runs_to_load,
        prev_run_idx = parameters$prev_run_idx,
        tgt_filename_or_dirname_for_scp = parameters$fullOutputDir_NO_slash
        )

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

    } else if (single_action_using_tzar_reps)
    {
    bdpg::single_action_using_tzar_reps (parameters, integerize)

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

    } else
    {
    cat ("\n\n----->>>>>  In xu_paper_main.R, no matching actions found, ",
         "so, doing nothing...  <<<<<-----\n\n")
    }

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

    cat ("\n\nAt END of main work in xu_paper_main(), current dir = '", getwd(), "'\n\n")

#===============================================================================
#               Clean up tzar, console sink, etc.
#===============================================================================

    clean_up ()

    cat ("\n\n================================================================================")
    cat ("\n================================================================================\n\n")
    }

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