R/fn_write.R

In ready4-dev/ready4show: Author Health Economic Analysis Programs and Reporting Templates

#' Write all output directories
#' @description write_all_outp_dirs() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write all output directories. The function returns Paths (a list).
#' @param paths_ls Paths (a list)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @return Paths (a list)
#' @rdname write_all_outp_dirs
#' @export 
#' @importFrom here here
#' @importFrom ready4 write_new_dirs
#' @keywords internal
write_all_outp_dirs <- function (paths_ls, consent_1L_chr = "", consent_indcs_int = 1L, 
    options_chr = c("Y", "N")) 
{
    output_data_dir_1L_chr <- paste0(here::here(paths_ls$path_from_top_level_1L_chr), 
        "/", paths_ls$write_to_dir_nm_1L_chr, "/Output")
    reports_dir_1L_chr <- paste0(here::here(paths_ls$path_from_top_level_1L_chr), 
        "/", paths_ls$write_to_dir_nm_1L_chr, "/Reports")
    mkdn_data_dir_1L_chr <- paste0(here::here(paths_ls$path_from_top_level_1L_chr), 
        "/", paths_ls$write_to_dir_nm_1L_chr, "/Markdown")
    descv_outp_dir_1L_chr <- paste0(output_data_dir_1L_chr, "/_Descriptives")
    dv_dir_1L_chr <- paste0(output_data_dir_1L_chr, "/H_Dataverse")
    c(paste0(here::here(paths_ls$path_from_top_level_1L_chr), 
        "/", paths_ls$write_to_dir_nm_1L_chr), mkdn_data_dir_1L_chr, 
        output_data_dir_1L_chr, reports_dir_1L_chr, descv_outp_dir_1L_chr, 
        dv_dir_1L_chr) %>% ready4::write_new_dirs(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    paths_ls <- append(paths_ls, list(output_data_dir_1L_chr = output_data_dir_1L_chr, 
        mkdn_data_dir_1L_chr = mkdn_data_dir_1L_chr, reports_dir_1L_chr = reports_dir_1L_chr, 
        descv_outp_dir_1L_chr = descv_outp_dir_1L_chr, dv_dir_1L_chr = dv_dir_1L_chr))
    return(paths_ls)
}
#' Write complete study program output
#' @description write_csp_output() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write complete study program output. The function is called for its side effects and does not return a value.
#' @param path_to_csp_1L_chr Path to complete study program (a character vector of length one)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param description_1L_chr Description (a character vector of length one), Default: 'Methods Report 1: Complete Study Program'
#' @param dv_ds_doi_1L_chr Dataverse dataset digital object identifier (a character vector of length one), Default: NULL
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param execute_1L_lgl Execute (a logical vector of length one), Default: T
#' @return No return value, called for side effects.
#' @rdname write_csp_output
#' @export 
#' @importFrom purrr map_chr
#' @importFrom ready4 write_with_consent
#' @importFrom stringr str_sub
#' @importFrom knitr purl
#' @importFrom DescTools SplitPath
#' @seealso [rmarkdown::render()]
#' @importFrom dataverse add_dataset_file
#' @keywords internal
write_csp_output <- function (path_to_csp_1L_chr, consent_1L_chr = "", consent_indcs_int = 1L, 
    description_1L_chr = "Methods Report 1: Complete Study Program", 
    dv_ds_doi_1L_chr = NULL, options_chr = c("Y", "N"), execute_1L_lgl = T) 
{
    file_chr <- readLines(path_to_csp_1L_chr) %>% purrr::map_chr(~ifelse(.x == 
        "knitr::opts_chunk$set(eval = F)", "knitr::opts_chunk$set(eval = T)", 
        .x))
    ready4::write_with_consent(consented_fn = writeLines, prompt_1L_chr = paste0("Do you confirm that you want to edit the file ", 
        path_to_csp_1L_chr, " to reset the default chunk evaluation setting to 'TRUE'?"), 
        consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
        consented_args_ls = list(text = file_chr, con = path_to_csp_1L_chr), 
        consented_msg_1L_chr = paste0("File ", path_to_csp_1L_chr, 
            " has been edited (overwritten)."), declined_msg_1L_chr = "Edit request cancelled - no files have been modified.", 
        options_chr = options_chr)
    path_to_r_script_1L_chr <- stringr::str_sub(path_to_csp_1L_chr, 
        end = -3)
    ready4::write_with_consent(consented_fn = knitr::purl, prompt_1L_chr = paste0("Do you confirm that you want to write the file ", 
        path_to_r_script_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(input = path_to_csp_1L_chr, 
            output = path_to_r_script_1L_chr), consented_msg_1L_chr = paste0("File ", 
            path_to_r_script_1L_chr, " has been written."), declined_msg_1L_chr = "Write request cancelled - no new file has been written.", 
        options_chr = options_chr)
    file_chr <- readLines(path_to_csp_1L_chr) %>% purrr::map_chr(~ifelse(.x == 
        "knitr::opts_chunk$set(eval = T)", "knitr::opts_chunk$set(eval = F)", 
        .x))
    ready4::write_with_consent(consented_fn = writeLines, prompt_1L_chr = paste0("Do you confirm that you want to edit the file ", 
        path_to_csp_1L_chr, " to reset the default chunk evaluation setting to 'FALSE'?"), 
        consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
        consented_args_ls = list(text = file_chr, con = path_to_csp_1L_chr), 
        consented_msg_1L_chr = paste0("File ", path_to_csp_1L_chr, 
            " has been edited (overwritten)."), declined_msg_1L_chr = "Edit request cancelled - no files have been modified.", 
        options_chr = options_chr)
    if (execute_1L_lgl) {
        old_wd_1L_chr <- getwd()
        path_info_ls <- DescTools::SplitPath(path_to_r_script_1L_chr)
        setwd(path_info_ls$dirname)
        source(path_info_ls$fullfilename)
        setwd(old_wd_1L_chr)
    }
    ready4::write_with_consent(consented_fn = rmarkdown::render, 
        prompt_1L_chr = paste0("Do you confirm that you want to render the file ", 
            path_to_csp_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(input = path_to_csp_1L_chr), 
        consented_msg_1L_chr = paste0("File ", path_to_csp_1L_chr, 
            " has been rendered."), declined_msg_1L_chr = "Render request cancelled.", 
        options_chr = options_chr)
    if (!is.null(dv_ds_doi_1L_chr)) {
        ready4::write_with_consent(consented_fn = dataverse::add_dataset_file, 
            prompt_1L_chr = paste0("Do you confirm that you want to upload the file ", 
                paste0(stringr::str_sub(path_to_csp_1L_chr, end = -4), 
                  "pdf"), " to dataverse dataset ", dv_ds_doi_1L_chr, 
                "?"), consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
            consented_args_ls = list(file = paste0(stringr::str_sub(path_to_csp_1L_chr, 
                end = -4), "pdf"), dataset = dv_ds_doi_1L_chr, 
                description = description_1L_chr), consented_msg_1L_chr = character(0), 
            declined_msg_1L_chr = "Upload request cancelled.", 
            options_chr = options_chr)
    }
}
#' Write custom authors
#' @description write_custom_authors() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write custom authors. The function is called for its side effects and does not return a value.
#' @param paths_ls Paths (a list)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param rmd_fl_nms_ls R Markdown file names (a list), Default: make_rmd_fl_nms_ls()
#' @return No return value, called for side effects.
#' @rdname write_custom_authors
#' @export 
#' @importFrom stringr str_remove_all str_sub str_replace
#' @importFrom purrr map flatten flatten_chr map_chr map_int reduce
#' @importFrom stringi stri_replace_last_regex
#' @importFrom ready4 write_with_consent
#' @keywords internal
write_custom_authors <- function (paths_ls, consent_1L_chr = "", consent_indcs_int = 1L, 
    options_chr = c("Y", "N"), rmd_fl_nms_ls = make_rmd_fl_nms_ls()) 
{
    original_chr <- readLines(paste0(paths_ls$path_to_ms_mkdn_dir_1L_chr, 
        "/Parent_PDF/", rmd_fl_nms_ls$PDF, ".Rmd"))
    placeholder_idx_1L_int <- which(original_chr == "## CUSTOM_AUTHORS_PLACEHOLDER ##")
    if (!identical(placeholder_idx_1L_int, integer(0))) {
        header_chr <- readLines(paste0(paths_ls$path_to_ms_mkdn_dir_1L_chr, 
            "/Header/header_common.yaml"))
        names_indcs_int <- c(which(header_chr == "author:") + 
            1, (1:length(header_chr))[header_chr %>% startsWith("  - name: ")])
        affiliations_indcs_int <- c(1:length(header_chr))[header_chr %>% 
            startsWith("    institute: ") | header_chr %>% startsWith("      institute: ")]
        affiliations_ls <- header_chr[affiliations_indcs_int] %>% 
            stringr::str_remove_all("      institute: ") %>% 
            stringr::str_remove_all("    institute: ") %>% purrr::map(~stringr::str_sub(.x, 
            start = 2, end = -2) %>% strsplit(", "))
        affiliations_chr <- affiliations_ls %>% purrr::flatten() %>% 
            purrr::flatten_chr() %>% unique()
        affiliations_chr <- affiliations_ls %>% purrr::map_chr(~paste0("    affiliation: ", 
            .x[[1]] %>% purrr::map_int(~which(affiliations_chr == 
                .x)) %>% paste0(collapse = ",")))
        replacement_chr <- purrr::reduce(1:length(names_indcs_int), 
            .init = c("authors:"), ~{
                if (.y == 1) {
                  c(.x, header_chr[names_indcs_int[.y]] %>% stringr::str_replace("  - ", 
                    "  - name: ") %>% stringi::stri_replace_last_regex(":", 
                    ""), affiliations_chr[.y])
                }
                else {
                  c(.x, header_chr[names_indcs_int[.y]] %>% stringr::str_replace("  - name: ", 
                    "  - name: "), affiliations_chr[.y])
                }
            })
        file_chr <- c(original_chr[1:(placeholder_idx_1L_int - 
            1)], replacement_chr, original_chr[(placeholder_idx_1L_int + 
            1):length(original_chr)])
        file_path_1L_chr <- paste0(paths_ls$path_to_ms_mkdn_dir_1L_chr, 
            "/Parent_PDF/", rmd_fl_nms_ls$PDF, ".Rmd")
        ready4::write_with_consent(consented_fn = writeLines, 
            prompt_1L_chr = paste0("Do you confirm that you want to write the file ", 
                file_path_1L_chr, " to ", dir_path_1L_chr, "?"), 
            consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
            consented_args_ls = list(text = file_chr, con = file_path_1L_chr), 
            consented_msg_1L_chr = paste0("File ", paste0(rmd_fl_nms_ls$PDF, 
                ".Rmd"), " has been written to ", paste0(paths_ls$path_to_ms_mkdn_dir_1L_chr, 
                "/Parent_PDF"), "."), declined_msg_1L_chr = "Write request cancelled - no new files have been written.", 
            options_chr = options_chr)
    }
}
#' Write header files
#' @description write_header_fls() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write header files. The function is called for its side effects and does not return a value.
#' @param path_to_header_dir_1L_chr Path to header directory (a character vector of length one)
#' @param header_yaml_args_ls Header yaml arguments (a list)
#' @param abstract_args_ls Abstract arguments (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @return No return value, called for side effects.
#' @rdname write_header_fls
#' @export 
#' @importFrom ready4 write_new_dirs write_with_consent
#' @importFrom rlang exec
#' @keywords internal
write_header_fls <- function (path_to_header_dir_1L_chr, header_yaml_args_ls, abstract_args_ls = NULL, 
    consent_1L_chr = "", consent_indcs_int = 1L, options_chr = c("Y", 
        "N")) 
{
    ready4::write_new_dirs(path_to_header_dir_1L_chr, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    header_yaml_args_ls <- validate_args_inc_consent(header_yaml_args_ls, 
        consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
        options_chr = options_chr)
    rlang::exec(write_header_yaml, path_to_header_dir_1L_chr, 
        !!!header_yaml_args_ls)
    if (!is.null(abstract_args_ls)) {
        file_chr <- abstract_args_ls$abstract_ls %>% make_abstract_lines()
        file_path_1L_chr <- paste0(path_to_header_dir_1L_chr, 
            "/", abstract_args_ls$fl_nm_1L_chr)
        ready4::write_with_consent(consented_fn = writeLines, 
            prompt_1L_chr = paste0("Do you confirm that you want to write the file ", 
                file_path_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
            consent_indcs_int = consent_indcs_int, consented_args_ls = list(text = file_chr, 
                con = file_path_1L_chr), consented_msg_1L_chr = paste0("File ", 
                file_path_1L_chr, " has been written."), declined_msg_1L_chr = "Write request cancelled - no new files have been written.", 
            options_chr = options_chr)
    }
}
#' Write header yaml
#' @description write_header_yaml() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write header yaml. The function is called for its side effects and does not return a value.
#' @param path_to_header_dir_1L_chr Path to header directory (a character vector of length one)
#' @param authors_tb Authors (a tibble)
#' @param institutes_tb Institutes (a tibble)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param fl_nm_1L_chr File name (a character vector of length one), Default: 'header.yaml'
#' @param inc_quals_1L_lgl Include qualifications (a logical vector of length one), Default: F
#' @param keywords_chr Keywords (a character vector), Default: c("Example keyword one", "Example keyword two")
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param path_to_tmpl_header_1L_chr Path to template header (a character vector of length one), Default: NULL
#' @param title_1L_chr Title (a character vector of length one), Default: 'Example title'
#' @return No return value, called for side effects.
#' @rdname write_header_yaml
#' @export 
#' @importFrom dplyr arrange
#' @importFrom purrr map flatten_chr discard
#' @importFrom stringr str_detect str_replace str_replace_all
#' @importFrom ready4 write_with_consent
#' @keywords internal
write_header_yaml <- function (path_to_header_dir_1L_chr, authors_tb, institutes_tb, 
    consent_1L_chr = "", consent_indcs_int = 1L, fl_nm_1L_chr = "header.yaml", 
    inc_quals_1L_lgl = F, keywords_chr = c("Example keyword one", 
        "Example keyword two"), options_chr = c("Y", "N"), path_to_tmpl_header_1L_chr = NULL, 
    title_1L_chr = "Example title") 
{
    if (is.null(path_to_tmpl_header_1L_chr)) {
        tmpl_header_chr <- c("title: TITLE_PLACEHOLDER", "author:", 
            "AUTHOR_PLACEHOLDER", "institute:", "INSTITUTE_PLACEHOLDER", 
            "keywords:  KEYWORDS_PLACEHOLDER")
    }
    else {
        tmpl_header_chr <- readLines(path_to_tmpl_header_1L_chr)
    }
    authors_tb <- authors_tb %>% dplyr::arrange(sequence_int)
    file_chr <- tmpl_header_chr %>% purrr::map(~{
        if (.x == "AUTHOR_PLACEHOLDER") {
            make_authorship_lines(authors_tb, inc_quals_1L_lgl = inc_quals_1L_lgl)
        }
        else {
            if (.x == "INSTITUTE_PLACEHOLDER") {
                make_institutes_lines(authors_tb, institutes_tb = institutes_tb)
            }
            else {
                if (stringr::str_detect(.x, "KEYWORDS_PLACEHOLDER")) {
                  if (is.na(keywords_chr[1])) {
                    NA_character_
                  }
                  else {
                    stringr::str_replace(.x, "KEYWORDS_PLACEHOLDER", 
                      paste0(keywords_chr, collapse = ", "))
                  }
                }
                else {
                  .x %>% stringr::str_replace_all("TITLE_PLACEHOLDER", 
                    title_1L_chr)
                }
            }
        }
    }) %>% purrr::flatten_chr() %>% purrr::discard(is.na)
    file_path_1L_chr <- paste0(path_to_header_dir_1L_chr, "/", 
        fl_nm_1L_chr)
    ready4::write_with_consent(consented_fn = writeLines, prompt_1L_chr = paste0("Do you confirm that you want to write the file ", 
        file_path_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(text = file_chr, 
            con = file_path_1L_chr), consented_msg_1L_chr = paste0("File ", 
            file_path_1L_chr, " has been written."), declined_msg_1L_chr = "Write request cancelled - no new files have been written.", 
        options_chr = options_chr)
}
#' Write main output directory
#' @description write_main_outp_dir() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write main output directory. The function returns Paths (a list).
#' @param params_ls Parameters (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param R_fl_nm_1L_chr R file name (a character vector of length one), Default: 'aaaaaaaaaa.txt'
#' @param use_fake_data_1L_lgl Use fake data (a logical vector of length one), Default: F
#' @return Paths (a list)
#' @rdname write_main_outp_dir
#' @export 
#' @importFrom ready4 write_new_files write_new_dirs
#' @importFrom purrr pluck
#' @importFrom here i_am here
#' @keywords internal
write_main_outp_dir <- function (params_ls = NULL, consent_1L_chr = "", consent_indcs_int = 1L, 
    options_chr = c("Y", "N"), R_fl_nm_1L_chr = "aaaaaaaaaa.txt", 
    use_fake_data_1L_lgl = F) 
{
    ready4::write_new_files(R_fl_nm_1L_chr, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    R_fl_nm_1L_chr <- list.files() %>% purrr::pluck(1)
    paths_ls <- make_paths_ls(append(params_ls, list(use_fake_data_1L_lgl = use_fake_data_1L_lgl)), 
        depth_1L_int = 0)
    paths_ls$path_to_current_1L_chr <- ifelse(!is.null(paths_ls$path_to_current_1L_chr), 
        paths_ls$path_to_current_1L_chr, params_ls$path_to_current_1L_chr)
    here::i_am(paste0(paths_ls$path_from_top_level_1L_chr, "/", 
        paths_ls$path_to_current_1L_chr, "/", R_fl_nm_1L_chr))
    ready4::write_new_dirs(paste0(here::here(paths_ls$path_from_top_level_1L_chr), 
        "/", paths_ls$write_to_dir_nm_1L_chr), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    paths_ls$R_fl_nm_1L_chr <- R_fl_nm_1L_chr
    paths_ls <- write_all_outp_dirs(paths_ls, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    return(paths_ls)
}
#' Write manuscript
#' @description write_manuscript() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write manuscript. The function returns Results (a list).
#' @param abstract_args_ls Abstract arguments (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param input_params_ls Input parameters (a list), Default: NULL
#' @param figures_in_body_lgl Figures in body (a logical vector), Default: NULL
#' @param ms_mkdn_fl_nm_1L_chr Manuscript markdown file name (a character vector of length one), Default: 'TTU_Study_Manuscript'
#' @param ms_mkdn_parent_1L_chr Manuscript markdown parent (a character vector of length one), Default: 'ready4-dev'
#' @param ms_mkdn_repo_1L_chr Manuscript markdown repository (a character vector of length one), Default: 'ttu_lng_ss'
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param output_type_1L_chr Output type (a character vector of length one), Default: NULL
#' @param results_ls Results (a list), Default: NULL
#' @param tables_in_body_lgl Tables in body (a logical vector), Default: NULL
#' @param title_1L_chr Title (a character vector of length one), Default: 'Scientific manuscript'
#' @param version_1L_chr Version (a character vector of length one), Default: '0.5'
#' @param write_to_dv_1L_lgl Write to dataverse (a logical vector of length one), Default: F
#' @return Results (a list)
#' @rdname write_manuscript
#' @export 
#' @importFrom ready4 write_with_consent write_to_dv_with_wait
#' @seealso [rmarkdown::render()]
#' @importFrom tibble tibble
#' @keywords internal
write_manuscript <- function (abstract_args_ls = NULL, consent_1L_chr = "", consent_indcs_int = 1L, 
    input_params_ls = NULL, figures_in_body_lgl = NULL, ms_mkdn_fl_nm_1L_chr = "TTU_Study_Manuscript", 
    ms_mkdn_parent_1L_chr = "ready4-dev", ms_mkdn_repo_1L_chr = "ttu_lng_ss", 
    options_chr = c("Y", "N"), output_type_1L_chr = NULL, results_ls = NULL, 
    tables_in_body_lgl = NULL, title_1L_chr = "Scientific manuscript", 
    version_1L_chr = "0.5", write_to_dv_1L_lgl = F) 
{
    mkdn_data_dir_1L_chr <- ifelse(!is.null(input_params_ls), 
        input_params_ls$path_params_ls$paths_ls$mkdn_data_dir_1L_chr, 
        results_ls$path_params_ls$paths_ls$mkdn_data_dir_1L_chr)
    outp_dir_1L_chr <- ifelse(!is.null(input_params_ls), input_params_ls$path_params_ls$paths_ls$output_data_dir_1L_chr, 
        results_ls$path_params_ls$paths_ls$output_data_dir_1L_chr)
    output_type_1L_chr <- ifelse(!is.null(output_type_1L_chr), 
        output_type_1L_chr, ifelse(!is.null(input_params_ls), 
            input_params_ls$output_format_ls$manuscript_outp_1L_chr, 
            results_ls$output_format_ls$manuscript_outp_1L_chr))
    path_to_ms_mkdn_1L_dir <- paste0(mkdn_data_dir_1L_chr, "/", 
        ms_mkdn_repo_1L_chr, "-", version_1L_chr)
    path_to_results_dir_1L_chr <- ifelse(!is.null(input_params_ls), 
        input_params_ls$path_params_ls$paths_ls$reports_dir_1L_chr, 
        results_ls$path_params_ls$paths_ls$reports_dir_1L_chr)
    if (!dir.exists(path_to_ms_mkdn_1L_dir)) {
        write_mkdn_from_repo(consent_1L_chr = consent_1L_chr, 
            consent_indcs_int = consent_indcs_int, mkdn_data_dir_1L_chr = mkdn_data_dir_1L_chr, 
            ms_mkdn_parent_1L_chr = ms_mkdn_parent_1L_chr, ms_mkdn_repo_1L_chr = ms_mkdn_repo_1L_chr, 
            options_chr = options_chr, version_1L_chr = version_1L_chr)
    }
    if (!is.null(input_params_ls)) {
        header_yaml_args_ls <- input_params_ls$header_yaml_args_ls
    }
    else {
        header_yaml_args_ls <- results_ls$header_yaml_args_ls
    }
    if (is.null(abstract_args_ls)) {
        abstract_args_ls <- make_abstract_args_ls(results_ls)
    }
    write_header_fls(path_to_header_dir_1L_chr = paste0(path_to_ms_mkdn_1L_dir, 
        "/Header"), header_yaml_args_ls = header_yaml_args_ls, 
        abstract_args_ls = abstract_args_ls, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    params_ls <- list(output_type_1L_chr = output_type_1L_chr, 
        results_ls = results_ls)
    if (!is.null(figures_in_body_lgl)) 
        params_ls$figures_in_body_lgl <- figures_in_body_lgl
    if (!is.null(tables_in_body_lgl)) 
        params_ls$tables_in_body_lgl <- tables_in_body_lgl
    file_to_render_1L_chr <- paste0(path_to_ms_mkdn_1L_dir, "/", 
        output_type_1L_chr, "/", output_type_1L_chr, ".Rmd")
    ready4::write_with_consent(consented_fn = rmarkdown::render, 
        prompt_1L_chr = paste0("Do you confirm that you want to render the file ", 
            file_to_render_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(input = file_to_render_1L_chr, 
            output_format = NULL, params = params_ls, output_file = paste0(ms_mkdn_fl_nm_1L_chr, 
                ifelse(output_type_1L_chr == "Word", ".docx", 
                  ".pdf")), output_dir = path_to_results_dir_1L_chr), 
        consented_msg_1L_chr = paste0("File ", file_to_render_1L_chr, 
            " has been rendered."), declined_msg_1L_chr = "Render request cancelled.", 
        options_chr = options_chr)
    if (write_to_dv_1L_lgl) {
        if (!is.null(input_params_ls)) {
            paths_ls <- input_params_ls$path_params_ls$paths_ls
        }
        else {
            paths_ls <- results_ls$path_params_ls$paths_ls
        }
        ready4::write_to_dv_with_wait(consent_1L_chr = consent_1L_chr, 
            consent_indcs_int = consent_indcs_int, dss_tb = tibble::tibble(ds_obj_nm_chr = ms_mkdn_fl_nm_1L_chr, 
                title_chr = title_1L_chr), dv_nm_1L_chr = ifelse(!is.null(input_params_ls), 
                input_params_ls$path_params_ls$dv_ds_nm_and_url_chr[1], 
                results_ls$path_params_ls$dv_ds_nm_and_url_chr[1]), 
            ds_url_1L_chr = ifelse(!is.null(input_params_ls), 
                input_params_ls$path_params_ls$dv_ds_nm_and_url_chr[2], 
                results_ls$path_params_ls$dv_ds_nm_and_url_chr[2]), 
            inc_fl_types_chr = ifelse(output_type_1L_chr == "Word", 
                ".docx", ".pdf"), options_chr = options_chr, 
            parent_dv_dir_1L_chr = paths_ls$dv_dir_1L_chr, paths_to_dirs_chr = paths_ls$reports_dir_1L_chr, 
            paths_are_rltv_1L_lgl = F)
    }
    results_ls$path_params_ls$paths_ls$path_to_ms_mkdn_1L_dir <- path_to_ms_mkdn_1L_dir
    file_to_write_1L_chr <- paste0(outp_dir_1L_chr, "/results_ls.RDS")
    ready4::write_with_consent(consented_fn = saveRDS, prompt_1L_chr = paste0("Do you confirm that you want to write the file ", 
        file_to_write_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(object = results_ls, 
            file = file_to_write_1L_chr), consented_msg_1L_chr = paste0("File ", 
            file_to_write_1L_chr, " has been written."), declined_msg_1L_chr = "Write request cancelled - no files have been written.", 
        options_chr = options_chr)
    return(results_ls)
}
#' Write model plot file
#' @description write_mdl_plt_fl() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write model plot file. The function returns Path to plot (a character vector of length one).
#' @param plt_fn Plot (a function), Default: NULL
#' @param path_to_write_to_1L_chr Path to write to (a character vector of length one)
#' @param plt_nm_1L_chr Plot name (a character vector of length one)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param fn_args_ls Function arguments (a list), Default: NULL
#' @param grpx_fn Graphics (a function), Default: grDevices::png
#' @param height_1L_dbl Height (a double vector of length one), Default: 6
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param rsl_1L_dbl Resolution (a double vector of length one), Default: 300
#' @param units_1L_chr Units (a character vector of length one), Default: 'in'
#' @param width_1L_dbl Width (a double vector of length one), Default: 6
#' @return Path to plot (a character vector of length one)
#' @rdname write_mdl_plt_fl
#' @export 
#' @importFrom grDevices png dev.off
#' @importFrom rlang exec
#' @importFrom ready4 write_with_consent
write_mdl_plt_fl <- function (plt_fn = NULL, path_to_write_to_1L_chr, plt_nm_1L_chr, 
    consent_1L_chr = "", consent_indcs_int = 1L, fn_args_ls = NULL, 
    grpx_fn = grDevices::png, height_1L_dbl = 6, options_chr = c("Y", 
        "N"), rsl_1L_dbl = 300, units_1L_chr = "in", width_1L_dbl = 6) 
{
    if (!is.null(plt_fn)) {
        path_to_plot_1L_chr <- paste0(path_to_write_to_1L_chr, 
            "/", plt_nm_1L_chr, ifelse(identical(grpx_fn, grDevices::png), 
                ".png", ".tiff"))
        consented_fn <- function(path_to_plot_1L_chr, fn_args_ls, 
            grpx_fn, height_1L_dbl, plt_fn, rsl_1L_dbl, units_1L_chr, 
            width_1L_dbl) {
            rlang::exec(grpx_fn, !!!list(path_to_plot_1L_chr, 
                units = units_1L_chr, width = width_1L_dbl, height = height_1L_dbl, 
                res = rsl_1L_dbl))
            plt <- rlang::exec(plt_fn, !!!fn_args_ls)
            print(plt)
            grDevices::dev.off()
        }
        ready4::write_with_consent(consented_fn = consented_fn, 
            prompt_1L_chr = paste0("Do you confirm that you want to write the file ", 
                path_to_plot_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
            consent_indcs_int = consent_indcs_int, consented_args_ls = list(path_to_plot_1L_chr = path_to_plot_1L_chr, 
                fn_args_ls = fn_args_ls, grpx_fn = grpx_fn, height_1L_dbl = height_1L_dbl, 
                plt_fn = plt_fn, rsl_1L_dbl = rsl_1L_dbl, units_1L_chr = units_1L_chr, 
                width_1L_dbl = width_1L_dbl), consented_msg_1L_chr = paste0("File ", 
                path_to_plot_1L_chr, " has been written."), declined_msg_1L_chr = "Write request cancelled - no files have been written.", 
            options_chr = options_chr)
    }
    else {
        path_to_plot_1L_chr <- NA_character_
    }
    return(path_to_plot_1L_chr)
}
#' Write markdown from package
#' @description write_mkdn_from_pkg() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write markdown from package. The function is called for its side effects and does not return a value.
#' @param pkg_nm_1L_chr Package name (a character vector of length one)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param dest_dir_1L_chr Destination directory (a character vector of length one), Default: 'Markdown'
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param overwrite_1L_lgl Overwrite (a logical vector of length one), Default: F
#' @return No return value, called for side effects.
#' @rdname write_mkdn_from_pkg
#' @export 
#' @importFrom purrr map_lgl map_chr discard
#' @importFrom ready4 write_new_dirs write_new_files
write_mkdn_from_pkg <- function (pkg_nm_1L_chr, consent_1L_chr = "", consent_indcs_int = 1L, 
    dest_dir_1L_chr = "Markdown", options_chr = c("Y", "N"), 
    overwrite_1L_lgl = F) 
{
    all_mkdn_chr <- system.file("Markdown", package = pkg_nm_1L_chr) %>% 
        list.files()
    is_dir_lgl <- all_mkdn_chr %>% purrr::map_lgl(~system.file(paste0("Markdown/", 
        .x), package = pkg_nm_1L_chr) %>% dir.exists())
    all_mkdn_chr[is_dir_lgl] %>% ready4::write_new_dirs(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    all_mkdn_files_chr <- system.file("Markdown", package = pkg_nm_1L_chr) %>% 
        list.files(recursive = T)
    all_mkdn_files_chr %>% purrr::map_chr(~{
        if (!file.exists(paste0(dest_dir_1L_chr, "/", .x)) | 
            (file.exists(paste0(dest_dir_1L_chr, "/", .x)) & 
                overwrite_1L_lgl)) {
            paste0(dest_dir_1L_chr, "/", .x)
        }
        else {
            NA_character_
        }
    }) %>% purrr::discard(is.na) %>% ready4::write_new_files(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
}
#' Write markdown from repository
#' @description write_mkdn_from_repo() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write markdown from repository. The function is called for its side effects and does not return a value.
#' @param mkdn_data_dir_1L_chr Markdown data directory (a character vector of length one)
#' @param ms_mkdn_parent_1L_chr Manuscript markdown parent (a character vector of length one)
#' @param ms_mkdn_repo_1L_chr Manuscript markdown repository (a character vector of length one)
#' @param version_1L_chr Version (a character vector of length one)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @return No return value, called for side effects.
#' @rdname write_mkdn_from_repo
#' @export 
#' @importFrom utils unzip
#' @importFrom ready4 write_with_consent
#' @keywords internal
write_mkdn_from_repo <- function (mkdn_data_dir_1L_chr, ms_mkdn_parent_1L_chr, ms_mkdn_repo_1L_chr, 
    version_1L_chr, consent_1L_chr = "", consent_indcs_int = 1L, 
    options_chr = c("Y", "N")) 
{
    consented_fn <- function(mkdn_data_dir_1L_chr, ms_mkdn_parent_1L_chr, 
        ms_mkdn_repo_1L_chr, version_1L_chr) {
        tmp_fl <- tempfile()
        download.file(paste0("https://github.com/", ms_mkdn_parent_1L_chr, 
            "/", ms_mkdn_repo_1L_chr, "/archive/refs/tags/v", 
            version_1L_chr, ".zip"), tmp_fl)
        utils::unzip(tmp_fl, exdir = mkdn_data_dir_1L_chr)
        unlink(tmp_fl)
    }
    ready4::write_with_consent(consented_fn = consented_fn, prompt_1L_chr = paste0("Do you confirm that you want to write a local copy of version ", 
        version_1L_chr, " of RMarkdown program ", paste0("https://github.com/", 
            ms_mkdn_parent_1L_chr, "/", ms_mkdn_repo_1L_chr), 
        " to ", mkdn_data_dir_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(mkdn_data_dir_1L_chr = mkdn_data_dir_1L_chr, 
            ms_mkdn_parent_1L_chr = ms_mkdn_parent_1L_chr, ms_mkdn_repo_1L_chr = ms_mkdn_repo_1L_chr, 
            version_1L_chr = version_1L_chr), consented_msg_1L_chr = paste0("RMarkdown program files written to ", 
            mkdn_data_dir_1L_chr, "."), declined_msg_1L_chr = "Write request cancelled - no new local copy of the RMarkdown program has been written.", 
        options_chr = options_chr)
}
#' Write report
#' @description write_report() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write report. The function is called for its side effects and does not return a value.
#' @param params_ls Parameters (a list)
#' @param paths_ls Paths (a list)
#' @param rprt_lup Report (a lookup table)
#' @param rprt_nm_1L_chr Report name (a character vector of length one)
#' @param abstract_args_ls Abstract arguments (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param header_yaml_args_ls Header yaml arguments (a list), Default: NULL
#' @param nm_of_mkdn_dir_1L_chr Name of markdown directory (a character vector of length one), Default: 'Markdown'
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param reports_dir_1L_chr Reports directory (a character vector of length one), Default: 'Reports'
#' @param rltv_path_to_data_dir_1L_chr Relative path to data directory (a character vector of length one), Default: '../Output'
#' @return No return value, called for side effects.
#' @rdname write_report
#' @export 
#' @importFrom here i_am here
#' @importFrom rlang exec
#' @keywords internal
write_report <- function (params_ls, paths_ls, rprt_lup, rprt_nm_1L_chr, abstract_args_ls = NULL, 
    consent_1L_chr = "", consent_indcs_int = 1L, header_yaml_args_ls = NULL, 
    nm_of_mkdn_dir_1L_chr = "Markdown", options_chr = c("Y", 
        "N"), reports_dir_1L_chr = "Reports", rltv_path_to_data_dir_1L_chr = "../Output") 
{
    rprt_type_ls <- rprt_lup %>% make_rprt_type_ls(rprt_nm_1L_chr = rprt_nm_1L_chr)
    here::i_am(paste0(paths_ls$path_from_top_level_1L_chr, "/", 
        paths_ls$path_to_current_1L_chr, "/", paths_ls$R_fl_nm_1L_chr))
    args_ls <- list(rprt_type_ls = rprt_type_ls, params_ls = params_ls, 
        output_type_1L_chr = params_ls$output_type_1L_chr, path_to_prjs_dir_1L_chr = here::here(paths_ls$path_from_top_level_1L_chr), 
        prj_dir_1L_chr = paths_ls$write_to_dir_nm_1L_chr, header_yaml_args_ls = header_yaml_args_ls, 
        abstract_args_ls = abstract_args_ls, reports_dir_1L_chr = reports_dir_1L_chr, 
        rltv_path_to_data_dir_1L_chr = rltv_path_to_data_dir_1L_chr, 
        nm_of_mkdn_dir_1L_chr = nm_of_mkdn_dir_1L_chr, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    rlang::exec(write_rprt_from_tmpl, !!!args_ls)
}
#' Write reporting directory
#' @description write_reporting_dir() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write reporting directory. The function returns Path to program (a character vector of length one).
#' @param path_to_write_to_1L_chr Path to write to (a character vector of length one), Default: getwd()
#' @param path_to_rmd_dir_1L_chr Path to Markdown directory (a character vector of length one)
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param path_to_main_rmd_fl_1L_chr Path to main Markdown file (a character vector of length one), Default: '/CSP/CSP.Rmd'
#' @param new_dir_nm_1L_chr New directory name (a character vector of length one), Default: 'TTU_Project'
#' @param overwrite_1L_lgl Overwrite (a logical vector of length one), Default: FALSE
#' @return Path to program (a character vector of length one)
#' @rdname write_reporting_dir
#' @export 
#' @importFrom ready4 write_new_dirs write_with_consent
#' @keywords internal
write_reporting_dir <- function (path_to_write_to_1L_chr = getwd(), path_to_rmd_dir_1L_chr, 
    consent_1L_chr = "", consent_indcs_int = 1L, options_chr = c("Y", 
        "N"), path_to_main_rmd_fl_1L_chr = "/CSP/CSP.Rmd", new_dir_nm_1L_chr = "TTU_Project", 
    overwrite_1L_lgl = FALSE) 
{
    path_to_prjt_dir_1L_chr <- paste0(path_to_write_to_1L_chr, 
        "/", new_dir_nm_1L_chr)
    path_to_prjt_dir_1L_chr %>% ready4::write_new_dirs(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    ready4::write_with_consent(consented_fn = file.copy, prompt_1L_chr = paste0("Do you confirm that you want to copy the directory ", 
        path_to_rmd_dir_1L_chr, " along with its contents to ", 
        path_to_prjt_dir_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(from = path_to_rmd_dir_1L_chr, 
            to = path_to_prjt_dir_1L_chr, recursive = T, overwrite = overwrite_1L_lgl), 
        consented_msg_1L_chr = paste0("The directory ", path_to_rmd_dir_1L_chr, 
            " along with its contents has been copied to ", path_to_prjt_dir_1L_chr, 
            "."), declined_msg_1L_chr = "Copy request cancelled - no files or directories have been written.", 
        options_chr = options_chr)
    path_to_program_1L_chr <- paste0(path_to_prjt_dir_1L_chr, 
        path_to_main_rmd_fl_1L_chr)
    return(path_to_program_1L_chr)
}
#' Write rendered report
#' @description write_rndrd_rprt() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write rendered report. The function is called for its side effects and does not return a value.
#' @param rprt_type_ls Report type (a list)
#' @param abstract_args_ls Abstract arguments (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param header_yaml_args_ls Header yaml arguments (a list), Default: NULL
#' @param nm_of_mkdn_dir_1L_chr Name of markdown directory (a character vector of length one), Default: 'Markdown'
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param overwrite_1L_lgl Overwrite (a logical vector of length one), Default: T
#' @param params_ls Parameters (a list), Default: list(output_type_1L_chr = "HTML")
#' @param path_to_rprt_dir_1L_chr Path to report directory (a character vector of length one), Default: './'
#' @param path_to_write_dirs_to_1L_chr Path to write directories to (a character vector of length one), Default: 'NA'
#' @return No return value, called for side effects.
#' @rdname write_rndrd_rprt
#' @export 
#' @importFrom ready4 write_with_consent write_new_dirs
#' @importFrom purrr pluck
#' @seealso [rmarkdown::render()]
#' @keywords internal
write_rndrd_rprt <- function (rprt_type_ls, abstract_args_ls = NULL, consent_1L_chr = "", 
    consent_indcs_int = 1L, header_yaml_args_ls = NULL, nm_of_mkdn_dir_1L_chr = "Markdown", 
    options_chr = c("Y", "N"), overwrite_1L_lgl = T, params_ls = list(output_type_1L_chr = "HTML"), 
    path_to_rprt_dir_1L_chr = "./", path_to_write_dirs_to_1L_chr = NA_character_) 
{
    if (!is.na(path_to_write_dirs_to_1L_chr)) {
        ready4::write_with_consent(consented_fn = file.copy, 
            prompt_1L_chr = paste0("Do you confirm that you want to copy the directory ", 
                rprt_type_ls$path_to_RMD_dir_1L_chr, " along with its contents to ", 
                path_to_write_dirs_to_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
            consent_indcs_int = consent_indcs_int, consented_args_ls = list(from = rprt_type_ls$path_to_RMD_dir_1L_chr, 
                to = path_to_write_dirs_to_1L_chr, recursive = T, 
                overwrite = overwrite_1L_lgl), consented_msg_1L_chr = paste0("The directory ", 
                rprt_type_ls$path_to_RMD_dir_1L_chr, " along with its contents has been copied to ", 
                path_to_write_dirs_to_1L_chr, "."), declined_msg_1L_chr = "Copy request cancelled - no files or directories have been written.", 
            options_chr = options_chr)
        dir_nm_1L_chr <- rprt_type_ls$path_to_RMD_dir_1L_chr %>% 
            normalizePath() %>% strsplit("\\\\") %>% purrr::pluck(1) %>% 
            tail(1)
        path_to_mkdn_dir_1L_chr <- paste0(path_to_write_dirs_to_1L_chr, 
            "/", nm_of_mkdn_dir_1L_chr)
        if (dir_nm_1L_chr != nm_of_mkdn_dir_1L_chr) 
            ready4::write_with_consent(consented_fn = file.copy, 
                prompt_1L_chr = paste0("Do you confirm that you want to rename the file ", 
                  paste0(path_to_write_dirs_to_1L_chr, "/", dir_nm_1L_chr), 
                  " to ", path_to_mkdn_dir_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
                consent_indcs_int = consent_indcs_int, consented_args_ls = list(from = paste0(path_to_write_dirs_to_1L_chr, 
                  "/", dir_nm_1L_chr), to = path_to_mkdn_dir_1L_chr), 
                consented_msg_1L_chr = paste0("The file ", paste0(path_to_write_dirs_to_1L_chr, 
                  "/", dir_nm_1L_chr), " has been renamed ", 
                  path_to_mkdn_dir_1L_chr, "."), declined_msg_1L_chr = "Rename request cancelled - no file have been renamed.", 
                options_chr = options_chr)
        path_to_wd_1L_chr <- path_to_mkdn_dir_1L_chr
    }
    else {
        path_to_wd_1L_chr <- rprt_type_ls$path_to_RMD_dir_1L_chr
    }
    path_to_rprt_dir_1L_chr %>% ready4::write_new_dirs(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    if (!is.null(header_yaml_args_ls)) {
        write_header_fls(path_to_header_dir_1L_chr = paste0(path_to_mkdn_dir_1L_chr, 
            "/Header"), header_yaml_args_ls, abstract_args_ls = abstract_args_ls, 
            consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
            options_chr = options_chr)
    }
    path_to_RMD_1L_chr <- paste0(path_to_wd_1L_chr, "/", rprt_type_ls$nm_of_RMD_1L_chr)
    ready4::write_with_consent(consented_fn = rmarkdown::render, 
        prompt_1L_chr = paste0("Do you confirm that you want to render the file ", 
            path_to_RMD_1L_chr, "?"), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, consented_args_ls = list(input = path_to_RMD_1L_chr, 
            output_format = switch(params_ls$output_type_1L_chr, 
                PDF = "bookdown::pdf_book", HTML = "bookdown::html_document2", 
                Word = "officedown::rdocx_document"), output_yaml = paste0(path_to_wd_1L_chr, 
                "/", rprt_type_ls$rltv_path_to_outp_yaml_1L_chr), 
            params = params_ls, envir = new.env(), output_file = paste0(rprt_type_ls$file_nm_1L_chr, 
                ".", ifelse(params_ls$output_type_1L_chr == "Word", 
                  "docx", tolower(params_ls$output_type_1L_chr))), 
            output_dir = path_to_rprt_dir_1L_chr), consented_msg_1L_chr = paste0("File ", 
            path_to_RMD_1L_chr, " has been rendered."), declined_msg_1L_chr = "Render request cancelled.", 
        options_chr = options_chr)
}
#' Write report
#' @description write_rprt() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write report. The function returns Output summary (a list).
#' @param rprt_type_ls Report type (a list)
#' @param outp_smry_ls Output summary (a list)
#' @param append_params_ls Append parameters (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param output_type_1L_chr Output type (a character vector of length one), Default: 'PDF'
#' @param nm_of_mkdn_dir_1L_chr Name of markdown directory (a character vector of length one), Default: 'Markdown'
#' @param path_to_prjs_dir_1L_chr Path to projects directory (a character vector of length one), Default: '../../../../Data/Project'
#' @param prj_dir_dir_1L_chr Project directory directory (a character vector of length one), Default: 'My_Project'
#' @param push_copy_to_dv_1L_lgl Push copy to dataverse (a logical vector of length one), Default: T
#' @param reports_dir_1L_chr Reports directory (a character vector of length one), Default: 'Reports'
#' @param rltv_path_to_data_dir_1L_chr Relative path to data directory (a character vector of length one), Default: '../Output'
#' @param section_type_1L_chr Section type (a character vector of length one), Default: '#'
#' @return Output summary (a list)
#' @rdname write_rprt
#' @export 
#' @importFrom ready4 write_new_dirs write_to_dv_with_wait
#' @importFrom tibble tibble
write_rprt <- function (rprt_type_ls, outp_smry_ls, append_params_ls = NULL, 
    consent_1L_chr = "", consent_indcs_int = 1L, options_chr = c("Y", 
        "N"), output_type_1L_chr = "PDF", nm_of_mkdn_dir_1L_chr = "Markdown", 
    path_to_prjs_dir_1L_chr = "../../../../Data/Project", prj_dir_dir_1L_chr = "My_Project", 
    push_copy_to_dv_1L_lgl = T, reports_dir_1L_chr = "Reports", 
    rltv_path_to_data_dir_1L_chr = "../Output", section_type_1L_chr = "#") 
{
    path_to_outp_dir_1L_chr <- paste0(path_to_prjs_dir_1L_chr, 
        "/", prj_dir_dir_1L_chr)
    path_to_rprt_dir_1L_chr <- paste0(path_to_outp_dir_1L_chr, 
        "/", reports_dir_1L_chr)
    path_to_rprt_dir_1L_chr %>% ready4::write_new_dirs(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    path_to_rprt_dir_1L_chr <- normalizePath(path_to_rprt_dir_1L_chr)
    params_ls <- list(outp_smry_ls = outp_smry_ls, output_type_1L_chr = output_type_1L_chr, 
        rltv_path_to_data_dir_1L_chr = rltv_path_to_data_dir_1L_chr, 
        section_type_1L_chr = section_type_1L_chr)
    if (!is.null(append_params_ls)) {
        params_ls <- append(params_ls, append_params_ls)
    }
    write_rndrd_rprt(consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
        options_chr = options_chr, nm_of_mkdn_dir_1L_chr = nm_of_mkdn_dir_1L_chr, 
        params_ls = params_ls, path_to_rprt_dir_1L_chr = path_to_rprt_dir_1L_chr, 
        path_to_write_dirs_to_1L_chr = normalizePath(path_to_outp_dir_1L_chr), 
        rprt_type_ls = rprt_type_ls)
    if (!is.null(outp_smry_ls$dv_ls) & push_copy_to_dv_1L_lgl) {
        outp_smry_ls$rprt_dss_tb <- tibble::tibble(ds_obj_nm_chr = rprt_type_ls$file_nm_1L_chr, 
            title_chr = rprt_type_ls$title_1L_chr)
        ready4::write_to_dv_with_wait(outp_smry_ls$rprt_dss_tb, 
            consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
            options_chr = options_chr, dv_nm_1L_chr = outp_smry_ls$dv_ls$dv_nm_1L_chr, 
            ds_url_1L_chr = outp_smry_ls$dv_ls$ds_url_1L_chr, 
            parent_dv_dir_1L_chr = outp_smry_ls$dv_ls$parent_dv_dir_1L_chr, 
            paths_to_dirs_chr = paste0(path_to_outp_dir_1L_chr, 
                "/", reports_dir_1L_chr), inc_fl_types_chr = paste0(".", 
                ifelse(output_type_1L_chr == "Word", "docx", 
                  tolower(output_type_1L_chr))))
    }
    return(outp_smry_ls)
}
#' Write report from template
#' @description write_rprt_from_tmpl() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write report from template. The function is called for its side effects and does not return a value.
#' @param rprt_type_ls Report type (a list)
#' @param path_to_prjs_dir_1L_chr Path to projects directory (a character vector of length one)
#' @param abstract_args_ls Abstract arguments (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param header_yaml_args_ls Header yaml arguments (a list), Default: NULL
#' @param nm_of_mkdn_dir_1L_chr Name of markdown directory (a character vector of length one), Default: 'Markdown'
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param output_type_1L_chr Output type (a character vector of length one), Default: 'PDF'
#' @param params_ls Parameters (a list), Default: NULL
#' @param prj_dir_1L_chr Project directory (a character vector of length one), Default: 'Fake'
#' @param reports_dir_1L_chr Reports directory (a character vector of length one), Default: 'Reports'
#' @param rltv_path_to_data_dir_1L_chr Relative path to data directory (a character vector of length one), Default: '../Output'
#' @return No return value, called for side effects.
#' @rdname write_rprt_from_tmpl
#' @export 
#' @importFrom ready4 write_new_dirs
#' @keywords internal
write_rprt_from_tmpl <- function (rprt_type_ls, path_to_prjs_dir_1L_chr, abstract_args_ls = NULL, 
    consent_1L_chr = "", consent_indcs_int = 1L, header_yaml_args_ls = NULL, 
    nm_of_mkdn_dir_1L_chr = "Markdown", options_chr = c("Y", 
        "N"), output_type_1L_chr = "PDF", params_ls = NULL, prj_dir_1L_chr = "Fake", 
    reports_dir_1L_chr = "Reports", rltv_path_to_data_dir_1L_chr = "../Output") 
{
    path_to_outp_dir_1L_chr <- paste0(path_to_prjs_dir_1L_chr, 
        "/", prj_dir_1L_chr)
    path_to_rprt_dir_1L_chr <- paste0(path_to_outp_dir_1L_chr, 
        "/", reports_dir_1L_chr)
    path_to_rprt_dir_1L_chr %>% ready4::write_new_dirs(consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    path_to_rprt_dir_1L_chr <- normalizePath(path_to_rprt_dir_1L_chr)
    write_rndrd_rprt(abstract_args_ls = abstract_args_ls, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, header_yaml_args_ls = header_yaml_args_ls, 
        options_chr = options_chr, nm_of_mkdn_dir_1L_chr = nm_of_mkdn_dir_1L_chr, 
        params_ls = params_ls, path_to_rprt_dir_1L_chr = path_to_rprt_dir_1L_chr, 
        path_to_write_dirs_to_1L_chr = normalizePath(path_to_outp_dir_1L_chr), 
        rprt_type_ls = rprt_type_ls)
}
#' Write report with record
#' @description write_rprt_with_rcrd() is a Write function that writes a file to a specified local directory. Specifically, this function implements an algorithm to write report with record. The function is called for its side effects and does not return a value.
#' @param path_to_outp_fl_1L_chr Path to output file (a character vector of length one)
#' @param paths_ls Paths (a list)
#' @param rprt_lup Report (a lookup table)
#' @param abstract_args_ls Abstract arguments (a list), Default: NULL
#' @param consent_1L_chr Consent (a character vector of length one), Default: ''
#' @param consent_indcs_int Consent indices (an integer vector), Default: 1
#' @param header_yaml_args_ls Header yaml arguments (a list), Default: NULL
#' @param main_rprt_append_ls Main report append (a list), Default: NULL
#' @param nbr_of_digits_1L_int Number of digits (an integer vector of length one), Default: 2
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param output_type_1L_chr Output type (a character vector of length one), Default: 'PDF'
#' @param rcrd_nm_1L_chr Record name (a character vector of length one), Default: 'AAA_RPRT_WRTNG_MTH'
#' @param rcrd_rprt_append_ls Record report append (a list), Default: NULL
#' @param reference_1L_int Reference (an integer vector of length one), Default: NULL
#' @param rprt_nm_1L_chr Report name (a character vector of length one), Default: 'AAA_TTU_MDL_CTG'
#' @param rprt_output_type_1L_chr Report output type (a character vector of length one), Default: 'PDF'
#' @param start_at_int Start at (an integer vector), Default: c(2, 1)
#' @param use_fake_data_1L_lgl Use fake data (a logical vector of length one), Default: F
#' @return No return value, called for side effects.
#' @rdname write_rprt_with_rcrd
#' @export 
#' @importFrom ready4 get_from_lup_obj
#' @keywords internal
write_rprt_with_rcrd <- function (path_to_outp_fl_1L_chr, paths_ls, rprt_lup, abstract_args_ls = NULL, 
    consent_1L_chr = "", consent_indcs_int = 1L, header_yaml_args_ls = NULL, 
    main_rprt_append_ls = NULL, nbr_of_digits_1L_int = 2L, options_chr = c("Y", 
        "N"), output_type_1L_chr = "PDF", rcrd_nm_1L_chr = "AAA_RPRT_WRTNG_MTH", 
    rcrd_rprt_append_ls = NULL, reference_1L_int = NULL, rprt_nm_1L_chr = "AAA_TTU_MDL_CTG", 
    rprt_output_type_1L_chr = "PDF", start_at_int = c(2, 1), 
    use_fake_data_1L_lgl = F) 
{
    params_ls <- list(abstract_args_ls = NULL, eval_1L_lgl = F, 
        header_yaml_args_ls = header_yaml_args_ls, output_type_1L_chr = rprt_output_type_1L_chr, 
        nbr_of_digits_1L_int = nbr_of_digits_1L_int, rprt_lup = rprt_lup, 
        rprt_nm_1L_chr = rprt_nm_1L_chr, rprt_output_type_1L_chr = output_type_1L_chr, 
        rprt_subtitle_1L_chr = ready4::get_from_lup_obj(rprt_lup, 
            match_value_xx = rprt_nm_1L_chr, match_var_nm_1L_chr = "rprt_nms_chr", 
            target_var_nm_1L_chr = "title_chr", evaluate_1L_lgl = F), 
        subtitle_1L_chr = ready4::get_from_lup_obj(rprt_lup, 
            match_value_xx = "AAA_RPRT_WRTNG_MTH", match_var_nm_1L_chr = "rprt_nms_chr", 
            target_var_nm_1L_chr = "title_chr", evaluate_1L_lgl = F), 
        use_fake_data_1L_lgl = use_fake_data_1L_lgl) %>% append(rcrd_rprt_append_ls)
    params_ls %>% write_report(abstract_args_ls = NULL, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, header_yaml_args_ls = header_yaml_args_ls, 
        options_chr = options_chr, paths_ls = paths_ls, rprt_nm_1L_chr = rcrd_nm_1L_chr, 
        rprt_lup = rprt_lup)
    list(outp_smry_ls = append(readRDS(path_to_outp_fl_1L_chr), 
        list(rprt_lup = rprt_lup)), output_type_1L_chr = output_type_1L_chr, 
        subtitle_1L_chr = ready4::get_from_lup_obj(rprt_lup, 
            match_value_xx = rprt_nm_1L_chr, match_var_nm_1L_chr = "rprt_nms_chr", 
            target_var_nm_1L_chr = "title_chr", evaluate_1L_lgl = F)) %>% 
        append(main_rprt_append_ls) %>% write_report(abstract_args_ls = abstract_args_ls, 
        consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
        header_yaml_args_ls = header_yaml_args_ls, options_chr = options_chr, 
        paths_ls = paths_ls, rprt_nm_1L_chr = rprt_nm_1L_chr, 
        rprt_lup = rprt_lup)
}