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

Abbreviations used in variables and their meanings

abs - absolute app - apparent bd - biodiversity cand - candidate CF - conservation feature (usually a species) const - constant cor - correct df - data frame eg - error generator em - error model err - error gen - generator or generation mod - model par - parameter param - parameter prob - problem pg - problem generator PU - planning unit rand - random rel - relative rs - reserve selector sdm - species distribution model sel - selector or selection sol - solution unif - uniform vec - vector

Fooling around with archiving, etc.

class (archive)
    {
    is_local: "boolean"    #  is on the same disk or not
    location: "character"  #  file path if on same disk, complex locator if elsewhere [not sure how it would specify loc, maybe url?
    }

    #  Create a tiny archive for just this experiment.
    #  It may end up containing just one problem or it might end up 
    #  containing a couple of base problems and a wrapped problem and 
    #  some app problems as well as a bunch of marxan runs, etc.

create_archive <- function (archive_location, parameters)
    {
    new_archive <- blah_archive (archive_location)

    new_archive_search_set <- list (new_archive@location, unlist (parameters$archive_path_or_collection_to_search))

    return (new_archive)
    }

gen_RSprob <- function (parameters, archive_search_set)
    {
    rsprob <- blah_rsprob (parameters, archive_search_set)
    archive (rsprob, archive_search_set)
    }

gen_ILPprob <- function (parameters, archive_search_set)
    {
    ilpprob <- blah_ilpprob (parameters)

    ilpprob@UUID = getUUID()
    ilpprob@perishables <- files_etc
    ilpprob@non_perishables <- not (ilpprob@perishables)

    ilpprob@checksum <- compute_checksum (ilpprob@non_perishables)

    archive (ilpprob, archive_search_set)

    return (ilpprob)
    }

possible_duplicates <- function (object, archive_search_set)
    {
    possible_duplicate_objects <- NULL

        #  Because initial run archives are likely to be small, 
        #  you could make them just be lists or data frames and use 
        #  the dplyr kinds of functions on them...
    possible_duplicate_objects <- ldapply (archive, check (obj) { if (checksum == obj@checksum) obj })

    return (possible_duplicate_object)
    }

run_marxan <- function (rsprob, archive_search_set, parameters)
    {
    marxan_run <- blah_marxan (rsprob, parameters)
    archive (marxan_run, 
             run_archive, parameters$archive_path_or_collection_to_search)
    }

mainline <- function (parameters)
    {
    archive_search_set <- create_archive (parameters$archive_location_dir)

    rsprob <- gen_RSprob (parameters, archive_search_set)
    OR
    rsprob <- get_RSprob (parameters$marxan_rsprob_search_parameters,
                          archive_search_set)

    marxan_run <- run_marxan (rsprob, archive_search_set, parameters)
    OR
    marxan_run <- get_marxan_run (parameters$marxan_run_search_parameters,
                                  archive_search_set)
    }