How I change a function not to need an input

There is a function does need an input as selected genomic site across genomic regions. But my genomic region bed file already is a subset of interesting site (like promoters). I want this function to work not complaining about genomic site
However when I leave genomic site says

> prepare_elements_regions_tf <- prepare_elements("regions.bed",
+                                                 window_size = 50000)
Successfully read elements
 Error in utils::read.delim(sites_file, stringsAsFactors = FALSE, header = FALSE) : 
  argument "sites_file" is missing, with no default 

The whole function is here

https://github.com/wenmm/ActiveDriverWGS/blob/master/R/ActiveDriverWGS.R

But part of function that nags is this

prepare_elements = function(elements_file, sites_file, window_size = 50000, mc.cores = 1, recovery_dir = NA) {

    try_error = "try-error"



    element_coords_filename = paste0(recovery_dir, "/ADWGS_elements_coords_recovery_file.rsav")

    element_coords_1 = NULL

    load_result = suppressWarnings(try(load(element_coords_filename), silent = TRUE))

    if (class(load_result) == try_error) {

        element_coords_1 = prepare_element_coords_from_BED(elements_file)

        if (!is.na(recovery_dir)) {

            save(element_coords_1, file = element_coords_filename)

        }

        cat("Successfully read elementsn")

    } else {

        cat("Recovered elementsn")

    }



    element_coords = coords_sanity(element_coords_1)



    element_3n_filename = paste0(recovery_dir, "/ADWGS_element_3n_recovery_file.rsav")

    element_3n = NULL

    load_result = suppressWarnings(try(load(element_3n_filename), silent = TRUE))

    if (class(load_result) == try_error) {

        element_3n = add_trinucs_by_elements(get_3n(element_coords))

        if (!is.na(recovery_dir)) {

            save(element_3n, file = element_3n_filename)

        }

    }



    window_coords_filename = paste0(recovery_dir, "/ADWGS_window_coords_recovery_file.rsav")

    window_coords = NULL

    load_result = suppressWarnings(try(load(window_coords_filename), silent = TRUE))

    if (class(load_result) == try_error) {

        window_coords = coords_sanity(get_window_coords(element_coords, window_size))

        if (!is.na(recovery_dir)) {

            save(window_coords, file = window_coords_filename)

        }

    }



    window_3n_filename = paste0(recovery_dir, "/ADWGS_window_3n_recovery_file.rsav")

    window_3n = NULL

    load_result = suppressWarnings(try(load(window_3n_filename), silent = TRUE))

    if (class(load_result) == try_error) {

        window_3n = add_trinucs_by_elements(get_3n(window_coords))

        if (!is.na(recovery_dir)) {

            save(window_3n, file = window_3n_filename)

        }

    }



    raw_site_coords_filename = paste0(recovery_dir, "/ADWGS_raw_site_coords_recovery_file.rsav")

    site_coords_filename = paste0(recovery_dir, "/ADWGS_site_coords_recovery_file.rsav")

    raw_site_coords = NULL

    site_coords = NULL

    sites_load_result = suppressWarnings(try(load(site_coords_filename), silent = TRUE))

    if (class(sites_load_result) == try_error) {

        load_result = suppressWarnings(try(load(raw_site_coords_filename), silent = TRUE))

        if (class(load_result) == try_error) {

            raw_site_coords = utils::read.delim(sites_file, stringsAsFactors = FALSE, header = FALSE)

            colnames(raw_site_coords) = c("chr", "starts", "ends", "site_info")

            raw_site_coords$chr = gsub("chr", "", raw_site_coords$chr, ignore.case = TRUE)

            raw_site_coords$chr = paste0("chr", raw_site_coords$chr)

            if (!is.na(recovery_dir)) {

                save(raw_site_coords, file = raw_site_coords_filename)

            }

            cat("Successfully read active sitesn")

        } else {

            cat("Recovered active sitesn")

        }



        if (!is.null(raw_site_coords[[1]])) {

            # first only keep sites that overlap with element coordinates

            site_gr = GenomicRanges::GRanges(raw_site_coords$chr,

                IRanges::IRanges(start=raw_site_coords$starts, end=raw_site_coords$ends))

            element_gr = GenomicRanges::GRanges(element_coords$chr, 

                IRanges::IRanges(start=element_coords$starts, end=element_coords$ends))



            rm(raw_site_coords)



            overlaps_found = GenomicRanges::findOverlaps(element_gr, site_gr)

            site_here_gr = site_gr[S4Vectors::subjectHits(overlaps_found)]



            rm(site_gr, element_gr, overlaps_found)



            site_coords = do.call(rbind, parallel::mclapply(1:nrow(element_coords), 

                get_sites_per_element, element_coords, site_here_gr, mc.cores=mc.cores))

            rm(site_here_gr)

            site_coords = coords_sanity(site_coords)

        }

        if (!is.na(recovery_dir)) {

            save(site_coords, file = site_coords_filename)

        }

    } else {

        cat("Recovered active sitesn")

    }

    rm(sites_load_result, element_coords)



    site_3n_filename = paste0(recovery_dir, "/ADWGS_site_3n_recovery_file.rsav")

    site_3n = NULL

    load_result = suppressWarnings(try(load(site_3n_filename), silent = TRUE))

    if (class(load_result) == try_error) {

        site_3n = get_3n(site_coords)

        if (!is.na(recovery_dir)) {

            save(site_3n, file = site_3n_filename)

        }

    }



    list(element_coords=element_coords_1, element_3n=element_3n, window_coords=window_coords, window_3n=window_3n, site_coords=site_coords, site_3n=site_3n)



}

How I get rid of nagging part?