Add docs for xportr()

NAMESPACE

@@ -5,6 +5,7 @@ export(length_log)
 export(type_log)
 export(var_names_log)
 export(var_ord_msg)
+export(xportr)
 export(xportr_df_label)
 export(xportr_format)
 export(xportr_label)

R/xportr.R

@@ -0,0 +1,75 @@
+#' Wrapper to apply all core xportr functions and write xpt
+#'
+#' @param .df A data frame of CDISC standard.
+#' @param var_metadata A data frame containing variable level metadata
+#' @param domain Appropriate CDSIC dataset name, e.g. ADAE, DM. Used to subset
+#'   the metadata object. If none is passed, then name of the dataset passed as
+#'   .df will be used.
+#' @param verbose The action this function takes when an action is taken on the
+#'   dataset or function validation finds an issue. See 'Messaging' section for
+#'   details. Options are 'stop', 'warn', 'message', and 'none'
+#' @param df_metadata A data frame containing dataset level metadata.
+#' @param path Path where transport file will be written. File name sans will be
+#'   used as `xpt` name.
+#' @param strict_checks If TRUE, xpt validation will report errors and not write
+#'   out the dataset. If FALSE, xpt validation will report warnings and continue
+#'   with writing out the dataset. Defaults to FALSE
+#'
+#' @return Returns the input dataframe invisibly
+#' @export
+#'
+#' @examples
+#'
+#' has_pkgs <- require(admiral, quietly = TRUE) &&
+#'   require(dplyr, quietly = TRUE) &&
+#'   require(readxl, quietly = TRUE) &&
+#'   require(rlang, quietly = TRUE)
+#'
+#' if (has_pkgs) {
+#'   adsl <- admiral::admiral_adsl
+#'
+#'   spec_path <- system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr")
+#'
+#'   var_spec <- readxl::read_xlsx(spec_path, sheet = "Variables") %>%
+#'     dplyr::rename(type = "Data Type") %>%
+#'     rlang::set_names(tolower)
+#'   dataset_spec <- readxl::read_xlsx(spec_path, sheet = "Datasets") %>%
+#'     dplyr::rename(label = "Description") %>%
+#'     rlang::set_names(tolower)
+#'
+#'   adsl %>%
+#'     xportr_metadata(var_spec, "ADSL", verbose = "warn") %>%
+#'     xportr_type() %>%
+#'     xportr_length() %>%
+#'     xportr_label() %>%
+#'     xportr_order() %>%
+#'     xportr_format() %>%
+#'     xportr_df_label(dataset_spec) %>%
+#'     xportr_write("adsl.xpt")
+#'
+#'   # `xportr()` can be used to apply a whole pipeline at once
+#'   xportr(adsl,
+#'     var_metadata = var_spec,
+#'     df_metadata = dataset_spec,
+#'     domain = "ADSL",
+#'     verbose = "warn",
+#'     path = "adsl.xpt"
+#'   )
+#' }
+xportr <- function(.df,
+                   var_metadata = NULL,
+                   df_metadata = NULL,
+                   domain = NULL,
+                   verbose = NULL,
+                   path,
+                   strict_checks = FALSE) {
+  .df %>%
+    xportr_metadata(var_metadata, domain, verbose) %>%
+    xportr_type() %>%
+    xportr_length() %>%
+    xportr_label() %>%
+    xportr_order() %>%
+    xportr_format() %>%
+    xportr_df_label(dataset_spec) %>%
+    xportr_write(path)
+}