Add lifecycle deprecation badges/warnings

.pre-commit-config.yaml

@@ -15,6 +15,7 @@ repos:
           - methods
           - checkmate
           - htmltools
+          - lifecycle
           - stats
           - stringi
       - id: use-tidy-description

DESCRIPTION

@@ -36,6 +36,7 @@ Depends:
 Imports:
     checkmate (>= 2.1.0),
     htmltools (>= 0.5.4),
+    lifecycle (>= 0.2.0),
     stats,
     stringi (>= 1.6)
 Suggests:
@@ -44,7 +45,6 @@ Suggests:
     dplyr (>= 1.0.5),
     flextable (>= 0.8.4),
     knitr (>= 1.42),
-    lifecycle (>= 0.2.0),
     officer (>= 0.5.0),
     r2rtf (>= 0.3.2),
     rmarkdown (>= 2.19),

NAMESPACE

@@ -288,6 +288,7 @@ importFrom(formatters,export_as_pdf)
 importFrom(formatters,export_as_txt)
 importFrom(htmltools,tagList)
 importFrom(htmltools,tags)
+importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(stats,binom.test)
 importFrom(stats,na.omit)

NEWS.md

@@ -15,6 +15,8 @@
 
 ### Miscellaneous
  * Removed deprecated functions `add_analyzed_var` and `trim_zero_rows`.
+ * Added `lifecycle` badge files for documentation.
+ * Deprecated the `gap` and `check_headers` arguments to `rbindl_rtables` using `lifecycle`.
 
 ## rtables 0.6.6
 ### New Features

R/colby_constructors.R

@@ -46,7 +46,12 @@ setGeneric(
 
 #' @rdname int_methods
 setMethod("split_rows", "NULL", function(lyt, spl, pos, cmpnd_fun = AnalyzeMultiVars) {
-  .Deprecated(msg = "Initializing layouts via NULL is deprecated, please use basic_table() instead")
+  lifecycle::deprecate_warn(
+    when = "0.3.8",
+    what = I("split_rows(NULL)"),
+    with = "basic_table()",
+    details = "Initializing layouts via `NULL` is no longer supported."
+  )
   rl <- PreDataRowLayout(SplitVector(spl))
   cl <- PreDataColLayout()
   PreDataTableLayouts(rlayout = rl, clayout = cl)
@@ -208,10 +213,12 @@ setGeneric(
 
 #' @rdname int_methods
 setMethod("split_cols", "NULL", function(lyt, spl, pos) {
-  .Deprecated(msg = paste(
-    "Initializing layouts via NULL is deprecated,",
-    "please use basic_table() instead"
-  ))
+  lifecycle::deprecate_warn(
+    when = "0.3.8",
+    what = I("split_cols(NULL)"),
+    with = "basic_table()",
+    details = "Initializing layouts via `NULL` is no longer supported."
+  )
   cl <- PreDataColLayout(SplitVector(spl))
   rl <- PreDataRowLayout()
   PreDataTableLayouts(rlayout = rl, clayout = cl)

R/package.R

@@ -4,6 +4,7 @@
 #' @importFrom utils head head.matrix tail tail.matrix
 #' @importFrom stats setNames na.omit prop.test binom.test relevel quantile
 #' @importFrom htmltools tags tagList
+#' @importFrom lifecycle deprecated
 #' @importFrom magrittr %>%
 #' @import methods
 NULL

R/tree_accessors.R

@@ -3001,10 +3001,10 @@ setGeneric("col_fnotes_here", function(obj) standardGeneric("col_fnotes_here"))
 #' @export
 #' @rdname ref_fnotes
 setMethod("col_fnotes_here", "ANY", function(obj) {
-  .Deprecated(
-    new = "col_footnotes",
-    old = "col_fnotes_here",
-    msg = "col_fnotes_here was deprecated in {rtables} version 0.6.5.9011. Please use col_footnotes instead."
+  lifecycle::deprecate_warn(
+    when = "0.6.6",
+    what = "col_fnotes_here()",
+    with = "col_footnotes()"
   )
   col_footnotes(obj)
 })
@@ -3016,10 +3016,10 @@ setGeneric("col_fnotes_here<-", function(obj, value) standardGeneric("col_fnotes
 #' @export
 #' @rdname int_methods
 setMethod("col_fnotes_here<-", "ANY", function(obj, value) {
-  .Deprecated(
-    new = "col_footnotes<-",
-    old = "col_fnotes_here<-",
-    msg = "col_fnotes_here<- was deprecated in {rtables} version 0.6.5.9011. Please use col_footnotes<- instead."
+  lifecycle::deprecate_warn(
+    when = "0.6.6",
+    what = I("col_fnotes_here()<-"),
+    with = I("col_footnotes()<-")
   )
   col_footnotes(obj) <- value
 })

R/tt_compatibility.R

@@ -383,9 +383,18 @@ only_first_annot <- function(all_annots) {
 #' @rdname rbind
 #' @aliases rbind
 #' @export
-rbindl_rtables <- function(x, gap = 0, check_headers = TRUE) {
-  if (!check_headers) {
-    warning("check_headers = FALSE is no longer supported, ignoring.")
+rbindl_rtables <- function(x, gap = lifecycle::deprecated(), check_headers = lifecycle::deprecated()) {
+  if (lifecycle::is_present(gap)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.2",
+      what = "rbindl_rtables(gap)"
+    )
+  }
+  if (lifecycle::is_present(check_headers)) {
+    lifecycle::deprecate_warn(
+      when = "0.3.2",
+      what = "rbindl_rtables(check_headers)"
+    )
   }
 
   firstcols <- col_info(x[[1]])
@@ -507,7 +516,7 @@ rbindl_rtables <- function(x, gap = 0, check_headers = TRUE) {
 setMethod(
   "rbind", "VTableNodeInfo",
   function(..., deparse.level = 1) {
-    rbindl_rtables(list(...), check_headers = TRUE)
+    rbindl_rtables(list(...))
   }
 )
 
@@ -530,7 +539,7 @@ setMethod(
 setMethod(
   "rbind2", "VTableNodeInfo",
   function(x, y) {
-    rbindl_rtables(list(x, y), check_headers = TRUE)
+    rbindl_rtables(list(x, y))
   }
 )
 
@@ -926,7 +935,9 @@ chk_compat_cinfos <- function(tt1, tt2) {
 }
 
 
-#' **Deprecated:** Insert `rrow`s at (before) a specific location
+#' Insert `rrow`s at (before) a specific location
+#'
+#' `r lifecycle::badge("deprecated")`
 #'
 #' This function is deprecated and will be removed in a future release of `rtables`. Please use
 #' [insert_row_at_path()] or [label_at_path()] instead.
@@ -973,7 +984,11 @@ chk_compat_cinfos <- function(tt1, tt2) {
 #' @export
 insert_rrow <- function(tbl, rrow, at = 1,
                         ascontent = FALSE) {
-  .Deprecated("insert_row_at_path or label_at_path(tab)<-", old = "insert_rrow")
+  lifecycle::deprecate_warn(
+    when = "0.4.0",
+    what = "insert_rrow()",
+    with = I("insert_row_at_path() or label_at_path()")
+  )
   stopifnot(
     is(tbl, "VTableTree"),
     is(rrow, "TableRow"),
@@ -985,9 +1000,7 @@ insert_rrow <- function(tbl, rrow, at = 1,
   }
 
   if (at == 1) {
-    return(rbindl_rtables(list(rrow, tbl),
-      check_headers = TRUE
-    ))
+    return(rbindl_rtables(list(rrow, tbl)))
   } else if (at == nrow(tbl) + 1) {
     return(rbind2(tbl, rrow))
   }

R/tt_dotabulation.R

@@ -1132,7 +1132,7 @@ recursive_applysplit <- function(df,
 #'
 #' @inheritParams gen_args
 #' @inheritParams lyt_args
-#' @param col_counts (`numeric` or `NULL`)\cr `r lifecycle::badge("deprecated")` if non-`NULL`, column counts
+#' @param col_counts (`numeric` or `NULL`)\cr if non-`NULL`, column counts
 #'   which override those calculated automatically during tabulation. Must specify "counts" for *all*
 #'   resulting columns if non-`NULL`. `NA` elements will be replaced with the automatically calculated counts.
 #' @param col_total (`integer(1)`)\cr the total observations across all columns. Defaults to `nrow(df)`.