fix of youthvars fn ref and addition of documented fns@

NAMESPACE

@@ -171,6 +171,7 @@ export(transform_uid_var)
 export(validate_TTU_predictors_lup)
 export(write_analyses)
 export(write_box_cox_tfmn)
+export(write_csp_output)
 export(write_main_oupt_dir)
 export(write_manuscript)
 export(write_mdl_cmprsn)
@@ -185,6 +186,7 @@ export(write_predr_and_covars_cmprsn)
 export(write_predr_and_mdl_tstng_results)
 export(write_predr_cmprsn_outps)
 export(write_report)
+export(write_reporting_dir)
 export(write_rprt_with_rcrd)
 export(write_scndry_analysis)
 export(write_scndry_analysis_dir)
@@ -277,6 +279,7 @@ importFrom(kableExtra,kbl)
 importFrom(knitr,knit_child)
 importFrom(knitr,knit_expand)
 importFrom(knitr,opts_current)
+importFrom(knitr,purl)
 importFrom(lubridate,days)
 importFrom(magrittr,"%>%")
 importFrom(pacman,p_load)

R/fn_get.R

@@ -5,7 +5,6 @@
 #' @rdname get_background_text
 #' @export 
 
-#' @keywords internal
 get_background_text <- function (results_ls) 
 {
  text_1L_chr <- results_ls$study_descs_ls$background_1L_chr
@@ -34,7 +33,6 @@ get_cndts_for_mxd_mdls <- function (mdl_types_lup = NULL)
 #' @rdname get_conclusion_text
 #' @export 
 
-#' @keywords internal
 get_conclusion_text <- function (results_ls) 
 {
  text_1L_chr <- results_ls$study_descs_ls$conclusion_1L_chr
@@ -48,7 +46,6 @@ get_conclusion_text <- function (results_ls)
 #' @rdname get_covar_ctgs
 #' @export 
 #' @importFrom stringi stri_replace_last_fixed
-#' @keywords internal
 get_covar_ctgs <- function (results_ls, collapse_1L_lgl = T) 
 {
  covar_ctgs_chr <- names(results_ls$candidate_covars_ls) %>% 
@@ -70,7 +67,6 @@ get_covar_ctgs <- function (results_ls, collapse_1L_lgl = T)
 #' @importFrom stats setNames
 #' @importFrom stringi stri_replace_last_fixed
 #' @importFrom Hmisc capitalize
-#' @keywords internal
 get_covars_by_ctg <- function (results_ls, collapse_1L_lgl = F) 
 {
  covars_by_ctg_ls <- results_ls$candidate_covars_ls %>% purrr::map(~.x %>% 
@@ -96,7 +92,6 @@ get_covars_by_ctg <- function (results_ls, collapse_1L_lgl = F)
 #' @rdname get_hlth_utl_nm
 #' @export 
 
-#' @keywords internal
 get_hlth_utl_nm <- function (results_ls, short_nm_1L_lgl = T) 
 {
  health_utl_nm_1L_chr <- ifelse(short_nm_1L_lgl, results_ls$study_descs_ls$health_utl_nm_1L_chr, 
@@ -111,7 +106,6 @@ get_hlth_utl_nm <- function (results_ls, short_nm_1L_lgl = T)
 #' @rdname get_hlth_utl_stat
 #' @export 
 
-#' @keywords internal
 get_hlth_utl_stat <- function (results_ls, stat_1L_chr = "bl_mean") 
 {
  hlth_utl_stat_1L_chr <- switch(stat_1L_chr, bl_mean = results_ls$hlth_utl_and_predrs_ls$bl_hu_mean_1L_dbl, 
@@ -128,7 +122,6 @@ get_hlth_utl_stat <- function (results_ls, stat_1L_chr = "bl_mean")
 #' @rdname get_link_from_tfmn
 #' @export 
 
-#' @keywords internal
 get_link_from_tfmn <- function (tfmn_1L_chr, is_OLS_1L_lgl = F) 
 {
  link_1L_chr <- ifelse(is_OLS_1L_lgl, "identity", ifelse(tfmn_1L_chr == 
@@ -147,7 +140,6 @@ get_link_from_tfmn <- function (tfmn_1L_chr, is_OLS_1L_lgl = F)
 #' @rdname get_lngl_ttu_types
 #' @export 
 #' @importFrom stringi stri_replace_last
-#' @keywords internal
 get_lngl_ttu_types <- function (results_ls, collapse_1L_lgl = T) 
 {
  mdl_types_chr <- results_ls$ttu_lngl_ls$best_mdls_tb$model_type
@@ -169,7 +161,6 @@ get_lngl_ttu_types <- function (results_ls, collapse_1L_lgl = T)
 #' @importFrom purrr map map_chr
 #' @importFrom stats setNames
 #' @importFrom stringi stri_replace_last_fixed
-#' @keywords internal
 get_mdl_cmprsns <- function (results_ls, describe_1L_lgl = T, mixed_1L_lgl = F, 
  as_list_1L_lgl = F) 
 {
@@ -227,7 +218,6 @@ get_mdl_cmprsns <- function (results_ls, describe_1L_lgl = T, mixed_1L_lgl = F,
 #' @importFrom utils data
 #' @importFrom dplyr pull
 #' @importFrom purrr map_lgl
-#' @keywords internal
 get_mdl_type_from_nm <- function (mdl_nm_1L_chr, mdl_types_lup = NULL) 
 {
  if (is.null(mdl_types_lup)) 
@@ -247,7 +237,6 @@ get_mdl_type_from_nm <- function (mdl_nm_1L_chr, mdl_types_lup = NULL)
 #' @importFrom purrr map flatten map_lgl
 #' @importFrom dplyr filter pull
 #' @importFrom stats setNames
-#' @keywords internal
 get_mdls_with_signft_covars <- function (outp_smry_ls, params_ls_ls) 
 {
  signft_covars_chr <- outp_smry_ls$mdls_with_covars_smry_tb %>% 
@@ -272,7 +261,6 @@ get_mdls_with_signft_covars <- function (outp_smry_ls, params_ls_ls)
 #' @export 
 #' @importFrom purrr map_int
 #' @importFrom xfun numbers_to_words
-#' @keywords internal
 get_nbr_of_predrs <- function (results_ls, as_words_1L_lgl = T) 
 {
  nbr_of_predrs_xx <- results_ls$study_descs_ls$predr_ctgs_ls %>% 
@@ -291,7 +279,6 @@ get_nbr_of_predrs <- function (results_ls, as_words_1L_lgl = T)
 #' @importFrom purrr map_lgl map2_chr
 #' @importFrom xfun numbers_to_words
 #' @importFrom stringi stri_replace_last_fixed
-#' @keywords internal
 get_nbr_of_predrs_by_ctg <- function (results_ls) 
 {
  multiple_1L_lgl <- length(get_predr_ctgs(results_ls, collapse_1L_lgl = F) > 
@@ -317,7 +304,6 @@ get_nbr_of_predrs_by_ctg <- function (results_ls)
 #' @export 
 #' @importFrom xfun numbers_to_words
 #' @importFrom Hmisc capitalize
-#' @keywords internal
 get_nbr_of_scndry_analyses <- function (results_ls, as_words_1L_lgl = T, capitalise_1L_lgl = T) 
 {
  nbr_of_scndry_analyses_1L_xx <- names(results_ls$mdl_ingredients_ls) %>% 
@@ -341,7 +327,6 @@ get_nbr_of_scndry_analyses <- function (results_ls, as_words_1L_lgl = T, capital
 #' @rdname get_ordered_sngl_csnl_mdls
 #' @export 
 #' @importFrom stringi stri_replace_last
-#' @keywords internal
 get_ordered_sngl_csnl_mdls <- function (results_ls, select_int = NULL, collapse_1L_lgl = F) 
 {
  ordered_sngl_csnl_mdls_chr <- results_ls$ttu_cs_ls$cs_mdls_predrs_seq_dscdng_chr
@@ -362,7 +347,6 @@ get_ordered_sngl_csnl_mdls <- function (results_ls, select_int = NULL, collapse_
 #' @rdname get_popl_descvs
 #' @export 
 #' @importFrom stringi stri_replace_last_fixed
-#' @keywords internal
 get_popl_descvs <- function (results_ls) 
 {
  popl_descvs_1L_chr <- results_ls$tables_ls$participant_descs$variable %>% 
@@ -379,7 +363,6 @@ get_popl_descvs <- function (results_ls)
 #' @export 
 #' @importFrom purrr map_int
 #' @importFrom stringi stri_replace_last_fixed
-#' @keywords internal
 get_predr_ctgs <- function (results_ls, collapse_1L_lgl = T) 
 {
  predr_ctgs_chr <- (results_ls$study_descs_ls$predr_ctgs_ls %>% 
@@ -406,7 +389,6 @@ get_predr_ctgs <- function (results_ls, collapse_1L_lgl = T)
 #' @importFrom Hmisc capitalize
 #' @importFrom ready4fun get_from_lup_obj
 #' @importFrom stringi stri_replace_last_fixed stri_replace_last
-#' @keywords internal
 get_predrs_by_ctg <- function (results_ls, long_desc_1L_lgl = F, transform_1L_lgl = F, 
  collapse_1L_lgl = F) 
 {
@@ -453,7 +435,6 @@ get_predrs_by_ctg <- function (results_ls, long_desc_1L_lgl = F, transform_1L_lg
 #' @rdname get_prefd_mdl_predrs
 #' @export 
 #' @importFrom stringi stri_replace_last
-#' @keywords internal
 get_prefd_mdl_predrs <- function (results_ls) 
 {
  predrs_1L_chr <- results_ls$predr_var_nms_chr %>% paste0(collapse = ", ") %>% 
@@ -492,7 +473,6 @@ get_random_intercept <- function (mdls_smry_tb, mdl_nm_1L_chr, deterministic_1L_
 #' @importFrom ready4fun get_from_lup_obj
 #' @importFrom ready4use remove_labels_from_ds
 #' @importFrom stringi stri_replace_last_fixed
-#' @keywords internal
 get_scndry_anlys_descs <- function (results_ls) 
 {
  nbr_of_scndry_analyses_1L_int <- get_nbr_of_scndry_analyses(results_ls, 
@@ -529,7 +509,6 @@ get_scndry_anlys_descs <- function (results_ls)
 #' @export 
 #' @importFrom purrr pmap_chr
 #' @importFrom stringi stri_replace_last
-#' @keywords internal
 get_selected_mixed_mdls <- function (results_ls, collapse_1L_lgl = T) 
 {
  mixed_mdls_xx <- results_ls$ttu_lngl_ls$best_mdls_tb %>%