Closes 120 - Replace metacore with metadata

DESCRIPTION

@@ -58,7 +58,8 @@ Imports:
     readr,
     janitor,
     tm,
-    haven (>= 2.5.0)
+    haven (>= 2.5.0),
+    lifecycle
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -43,6 +43,7 @@ importFrom(glue,glue)
 importFrom(glue,glue_collapse)
 importFrom(graphics,stem)
 importFrom(janitor,make_clean_names)
+importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,extract2)
 importFrom(purrr,map)

NEWS.md

@@ -13,6 +13,9 @@
 
 * Moved `{pkgdown}` site to bootswatch. Enabled search and linked slack icon (#122).
 
+## Deprecation and Breaking Changes
+
+* The `metacore` argument has been renamed to `metadata` in the following six xportr functions: `xportr_df_label()`, `xportr_format()`, `xportr_label()`, `xportr_length()`, `xportr_order()`, and `xportr_type()`. Please update your code to use the new `metadata` argument in place of `metacore`.
 # xportr 0.2.0
 * Added a new validation test that errors when users pass invalid formats (#60 #64). Thanks to @zdz2101!
 * Fixed an issue where xportr_format could pass invalid formats to haven::write_xpt.

R/df_label.R

@@ -3,9 +3,10 @@
 #' Assigns dataset label from a dataset level metadata to a given data frame.
 #'
 #' @param .df A data frame of CDISC standard.
-#' @param metacore A data frame containing dataset level metadata.
+#' @param metadata A data frame containing dataset level metadata.
 #' @param domain A character value to subset the `.df`. If `NULL`(default), uses
 #'   `.df` value as a subset condition.
+#' @param metacore `r lifecycle::badge("deprecated")` Previously used to pass metadata now renamed with `metadata`
 #'
 #' @return Data frame with label attributes.
 #' @family metadata functions
@@ -26,7 +27,15 @@
 #' )
 #'
 #' adsl <- xportr_df_label(adsl, metadata)
-xportr_df_label <- function(.df, metacore = NULL, domain = NULL) {
+xportr_df_label <- function(.df, metadata = NULL, domain = NULL, metacore = deprecated()) {
+  if (!missing(metacore)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.0",
+      what = "xportr_format(metacore = )",
+      with = "xportr_format(metadata = )"
+    )
+    metadata <- metacore
+  }
   domain_name <- getOption("xportr.df_domain_name")
   label_name <- getOption("xportr.df_label")
 
@@ -39,15 +48,15 @@ xportr_df_label <- function(.df, metacore = NULL, domain = NULL) {
   ## End of common section
 
   ## Pull out correct metadata
-  metacore <- metacore %||%
+  metadata <- metadata %||%
     attr(.df, "_xportr.df_metadata_") %||%
-    rlang::abort("Metadata must be set with `metacore` or `xportr_metadata()`")
+    rlang::abort("Metadata must be set with `metadata` or `xportr_metadata()`")
 
-  if (inherits(metacore, "Metacore")) {
-    metacore <- metacore$ds_spec
+  if (inherits(metadata, "Metacore")) {
+    metadata <- metadata$ds_spec
   }
 
-  label <- metacore %>%
+  label <- metadata %>%
     filter(!!sym(domain_name) == domain) %>%
     select(!!sym(label_name)) %>%
     # If a dataframe is used this will also be a dataframe, change to character.

R/format.R

@@ -3,11 +3,12 @@
 #' Assigns a SAS format from a variable level metadata to a given data frame.
 #'
 #' @param .df A data frame of CDISC standard.
-#' @param metacore A data frame containing variable level metadata.
+#' @param metadata A data frame containing variable level metadata.
 #' @param domain A character value to subset the `.df`. If `NULL`(default), uses
 #'   `.df` value as a subset condition.
 #' @param verbose The action the function takes when a variable label isn't.
 #'   found. Options are 'stop', 'warn', 'message', and 'none'
+#' @param metacore `r lifecycle::badge("deprecated")` Previously used to pass metadata now renamed with `metadata`
 #'
 #' @return Data frame with `SASformat` attributes for each variable.
 #' @family metadata functions
@@ -27,7 +28,20 @@
 #' )
 #'
 #' adsl <- xportr_format(adsl, metadata)
-xportr_format <- function(.df, metacore = NULL, domain = NULL, verbose = getOption("xportr.format_verbose", "none")) {
+xportr_format <- function(
+    .df,
+    metadata = NULL,
+    domain = NULL,
+    verbose = getOption("xportr.length_verbose", "none"),
+    metacore = deprecated()) {
+  if (!missing(metacore)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.0",
+      what = "xportr_format(metacore = )",
+      with = "xportr_format(metadata = )"
+    )
+    metadata <- metacore
+  }
   domain_name <- getOption("xportr.domain_name")
   format_name <- getOption("xportr.format_name")
   variable_name <- getOption("xportr.variable_name")
@@ -40,19 +54,19 @@ xportr_format <- function(.df, metacore = NULL, domain = NULL, verbose = getOpti
 
   ## End of common section
 
-  metacore <- metacore %||%
+  metadata <- metadata %||%
     attr(.df, "_xportr.df_metadata_") %||%
-    rlang::abort("Metadata must be set with `metacore` or `xportr_metadata()`")
+    rlang::abort("Metadata must be set with `metadata` or `xportr_metadata()`")
 
-  if (inherits(metacore, "Metacore")) {
-    metacore <- metacore$var_spec
+  if (inherits(metadata, "Metacore")) {
+    metadata <- metadata$var_spec
   }
 
-  if (domain_name %in% names(metacore)) {
-    metadata <- metacore %>%
+  if (domain_name %in% names(metadata)) {
+    metadata <- metadata %>%
       dplyr::filter(!!sym(domain_name) == domain & !is.na(!!sym(format_name)))
   } else {
-    metadata <- metacore
+    metadata <- metadata
   }
 
   filtered_metadata <- metadata %>%

R/label.R

@@ -3,11 +3,12 @@
 #' Assigns variable label from a variable level metadata to a given data frame.
 #'
 #' @param .df A data frame of CDISC standard.
-#' @param metacore A data frame containing variable level metadata.
+#' @param metadata A data frame containing variable level metadata.
 #' @param domain A character value to subset the `.df`. If `NULL`(default), uses
 #'   `.df` value as a subset condition.
 #' @param verbose The action the function takes when a variable length isn't
 #'   Found. Options are 'stop', 'warn', 'message', and 'none'
+#' @param metacore `r lifecycle::badge("deprecated")` Previously used to pass metadata now renamed with `metadata`
 #'
 #' @return Data frame with label attributes for each variable.
 #' @family metadata functions
@@ -29,8 +30,20 @@
 #' )
 #'
 #' adsl <- xportr_label(adsl, metadata)
-xportr_label <- function(.df, metacore = NULL, domain = NULL,
-                         verbose = getOption("xportr.label_verbose", "none")) {
+xportr_label <- function(
+    .df,
+    metadata = NULL,
+    domain = NULL,
+    verbose = getOption("xportr.length_verbose", "none"),
+    metacore = deprecated()) {
+  if (!missing(metacore)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.0",
+      what = "xportr_format(metacore = )",
+      with = "xportr_format(metadata = )"
+    )
+    metadata <- metacore
+  }
   domain_name <- getOption("xportr.domain_name")
   variable_name <- getOption("xportr.variable_name")
   variable_label <- getOption("xportr.label")
@@ -43,19 +56,19 @@ xportr_label <- function(.df, metacore = NULL, domain = NULL,
 
   ## End of common section
 
-  metacore <- metacore %||%
+  metadata <- metadata %||%
     attr(.df, "_xportr.df_metadata_") %||%
-    rlang::abort("Metadata must be set with `metacore` or `xportr_metadata()`")
+    rlang::abort("Metadata must be set with `metadata` or `xportr_metadata()`")
 
-  if (inherits(metacore, "Metacore")) {
-    metacore <- metacore$var_spec
+  if (inherits(metadata, "Metacore")) {
+    metadata <- metadata$var_spec
   }
 
-  if (domain_name %in% names(metacore)) {
-    metadata <- metacore %>%
+  if (domain_name %in% names(metadata)) {
+    metadata <- metadata %>%
       dplyr::filter(!!sym(domain_name) == domain)
   } else {
-    metadata <- metacore
+    metadata <- metadata
   }
 
 

R/length.R

@@ -3,11 +3,12 @@
 #' Assigns SAS length from a variable level metadata to a given data frame.
 #'
 #' @param .df A data frame of CDISC standard.
-#' @param metacore A data frame containing variable level metadata.
+#' @param metadata A data frame containing variable level metadata.
 #' @param domain A character value to subset the `.df`. If `NULL`(default), uses
 #'   `.df` value as a subset condition.
 #' @param verbose The action the function takes when a length isn't found in
 #'   metadata. Options are 'stop', 'warn', 'message', and 'none'
+#' @param metacore `r lifecycle::badge("deprecated")` Previously used to pass metadata now renamed with `metadata`
 #'
 #' @return Data frame with `SASlength` attributes for each variable.
 #' @family metadata functions
@@ -27,8 +28,20 @@
 #' )
 #'
 #' adsl <- xportr_length(adsl, metadata)
-xportr_length <- function(.df, metacore = NULL, domain = NULL,
-                          verbose = getOption("xportr.length_verbose", "none")) {
+xportr_length <- function(
+    .df,
+    metadata = NULL,
+    domain = NULL,
+    verbose = getOption("xportr.length_verbose", "none"),
+    metacore = deprecated()) {
+  if (!missing(metacore)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.0",
+      what = "xportr_format(metacore = )",
+      with = "xportr_format(metadata = )"
+    )
+    metadata <- metacore
+  }
   domain_name <- getOption("xportr.domain_name")
   variable_length <- getOption("xportr.length")
   variable_name <- getOption("xportr.variable_name")
@@ -41,19 +54,19 @@ xportr_length <- function(.df, metacore = NULL, domain = NULL,
 
   ## End of common section
 
-  metacore <- metacore %||%
+  metadata <- metadata %||%
     attr(.df, "_xportr.df_metadata_") %||%
-    rlang::abort("Metadata must be set with `metacore` or `xportr_metadata()`")
+    rlang::abort("Metadata must be set with `metadata` or `xportr_metadata()`")
 
-  if (inherits(metacore, "Metacore")) {
-    metacore <- metacore$var_spec
+  if (inherits(metadata, "Metacore")) {
+    metadata <- metadata$var_spec
   }
 
-  if (domain_name %in% names(metacore)) {
-    metadata <- metacore %>%
+  if (domain_name %in% names(metadata)) {
+    metadata <- metadata %>%
       filter(!!sym(domain_name) == domain)
   } else {
-    metadata <- metacore
+    metadata <- metadata
   }
 
 

R/order.R

@@ -1,10 +1,11 @@
 #' Order variables of a dataset according to Spec
 #'
 #' @param .df A data frame of CDISC standard.
-#' @param metacore A data frame containing variable level metadata.
+#' @param metadata A data frame containing variable level metadata.
 #' @param domain A character value to subset the `.df`. If `NULL`(default), uses
 #'   `.df` value as a subset condition.
 #' @param verbose Option for messaging order results
+#' @param metacore `r lifecycle::badge("deprecated")` Previously used to pass metadata now renamed with `metadata`
 #'
 #' @export
 #' @return Dataframe that has been re-ordered according to spec
@@ -24,7 +25,20 @@
 #' )
 #'
 #' adsl <- xportr_order(adsl, metadata)
-xportr_order <- function(.df, metacore = NULL, domain = NULL, verbose = getOption("xportr.order_verbose", "none")) {
+xportr_order <- function(
+    .df,
+    metadata = NULL,
+    domain = NULL,
+    verbose = getOption("xportr.length_verbose", "none"),
+    metacore = deprecated()) {
+  if (!missing(metacore)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.0",
+      what = "xportr_format(metacore = )",
+      with = "xportr_format(metadata = )"
+    )
+    metadata <- metacore
+  }
   domain_name <- getOption("xportr.domain_name")
   order_name <- getOption("xportr.order_name")
   variable_name <- getOption("xportr.variable_name")
@@ -37,19 +51,19 @@ xportr_order <- function(.df, metacore = NULL, domain = NULL, verbose = getOptio
 
   ## End of common section
 
-  metacore <- metacore %||%
+  metadata <- metadata %||%
     attr(.df, "_xportr.df_metadata_") %||%
-    rlang::abort("Metadata must be set with `metacore` or `xportr_metadata()`")
+    rlang::abort("Metadata must be set with `metadata` or `xportr_metadata()`")
 
-  if (inherits(metacore, "Metacore")) {
-    metacore <- metacore$ds_vars
+  if (inherits(metadata, "Metacore")) {
+    metadata <- metadata$ds_vars
   }
 
-  if (domain_name %in% names(metacore)) {
-    metadata <- metacore %>%
+  if (domain_name %in% names(metadata)) {
+    metadata <- metadata %>%
       dplyr::filter(!!sym(domain_name) == domain & !is.na(!!sym(order_name)))
   } else {
-    metadata <- metacore %>%
+    metadata <- metadata %>%
       dplyr::filter(!is.na(!!sym(order_name)))
   }