R/mthd_authorReport.R

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

#' 
#' Author and save a report
#' @name authorReport-Ready4showSynopsis
#' @description authorReport method applied to Ready4showSynopsis
#' @param x An object of class Ready4showSynopsis
#' @param args_ls 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 fl_nm_1L_chr File name (a character vector of length one), Default: 'NA'
#' @param options_chr Options (a character vector), Default: c("Y", "N")
#' @param rmd_fl_nms_ls R Markdown file names (a list), Default: NULL
#' @param what_1L_chr What (a character vector of length one), Default: 'NA'
#' @param ... Additional arguments
#' @return No return value, called for side effects.
#' @rdname authorReport-methods
#' @aliases authorReport,Ready4showSynopsis-method
#' @export 
#' @importFrom purrr flatten_chr
#' @importFrom ready4 write_with_consent authorReport
#' @seealso [rmarkdown::render()]
methods::setMethod("authorReport", "Ready4showSynopsis", function (x, args_ls = NULL, consent_1L_chr = "", consent_indcs_int = 1L, 
    fl_nm_1L_chr = NA_character_, options_chr = c("Y", "N"), 
    rmd_fl_nms_ls = NULL, what_1L_chr = NA_character_, ...) 
{
    if (!is.na(what_1L_chr)) {
        x@a_Ready4showPaths@ms_mkdn_dir_1L_chr <- what_1L_chr
        x@a_Ready4showPaths@ms_dir_1L_chr <- what_1L_chr
    }
    if (is.na(fl_nm_1L_chr)) {
        if (is.na(x@fl_nm_1L_chr)) {
            fl_nm_1L_chr <- "Manuscript"
        }
        else {
            fl_nm_1L_chr <- x@fl_nm_1L_chr
        }
    }
    x@fl_nm_1L_chr <- fl_nm_1L_chr
    if (!is.null(rmd_fl_nms_ls)) {
        x@rmd_fl_nms_ls <- rmd_fl_nms_ls
    }
    paths_ls <- manufacture(x, what_1L_chr = "paths_ls")
    write_new_dirs(paths_ls %>% purrr::flatten_chr(), consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    header_yaml_args_ls <- make_header_yaml_args_ls(x@authors_r3, 
        institutes_tb = x@institutes_r3, keywords_chr = x@keywords_chr, 
        title_1L_chr = x@title_1L_chr)
    if (identical(x@abstract_args_ls, list())) {
        x@abstract_args_ls <- NULL
    }
    write_header_fls(path_to_header_dir_1L_chr = paste0(paths_ls$path_to_ms_mkdn_dir_1L_chr, 
        "/Header"), header_yaml_args_ls = header_yaml_args_ls, 
        abstract_args_ls = x@abstract_args_ls, consent_1L_chr = consent_1L_chr, 
        consent_indcs_int = consent_indcs_int, options_chr = options_chr)
    write_custom_authors(paths_ls, rmd_fl_nms_ls = x@rmd_fl_nms_ls, 
        consent_1L_chr = consent_1L_chr, consent_indcs_int = consent_indcs_int, 
        options_chr = options_chr)
    params_ls <- append(list(X = x), args_ls)
    output_fl_1L_chr <- paste0(x@fl_nm_1L_chr, ifelse(x@outp_formats_chr[1] == 
        "Word", ".docx", paste0(".", tolower(x@outp_formats_chr[1]))))
    file_to_render_1L_chr <- paste0(paths_ls$path_to_ms_mkdn_dir_1L_chr, 
        "/Parent_", x@outp_formats_chr[1], "/", x@rmd_fl_nms_ls[names(x@rmd_fl_nms_ls) == 
            x@outp_formats_chr[1]][[1]], ".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 = output_fl_1L_chr, 
            output_dir = paths_ls$path_to_ms_outp_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)
})