deprecating here

NAMESPACE

@@ -6,6 +6,7 @@ export("cell_footnotes<-")
 export("clayout<-")
 export("col_counts<-")
 export("col_fnotes_here<-")
+export("col_footnotes<-")
 export("col_info<-")
 export("col_total<-")
 export("colcount_format<-")
@@ -64,6 +65,7 @@ export(clear_indent_mods)
 export(col_counts)
 export(col_exprs)
 export(col_fnotes_here)
+export(col_footnotes)
 export(col_info)
 export(col_paths)
 export(col_paths_summary)
@@ -198,6 +200,7 @@ exportMethods("cell_footnotes<-")
 exportMethods("clayout<-")
 exportMethods("col_counts<-")
 exportMethods("col_fnotes_here<-")
+exportMethods("col_footnotes<-")
 exportMethods("col_info<-")
 exportMethods("col_total<-")
 exportMethods("colcount_format<-")
@@ -228,6 +231,7 @@ exportMethods(clayout)
 exportMethods(clear_indent_mods)
 exportMethods(col_counts)
 exportMethods(col_fnotes_here)
+exportMethods(col_footnotes)
 exportMethods(col_info)
 exportMethods(col_total)
 exportMethods(colcount_format)

R/index_footnotes.R

@@ -63,8 +63,8 @@ index_col_refs <- function(tt, cur_idx_fun) {
 
 
 .index_col_refs_inner <- function(ctree, cur_idx_fun) {
-  col_fnotes_here(ctree) <- .reindex_one_pos(
-    col_fnotes_here(ctree),
+  col_footnotes(ctree) <- .reindex_one_pos(
+    col_footnotes(ctree),
     cur_idx_fun
   )
 
@@ -75,9 +75,9 @@ index_col_refs <- function(tt, cur_idx_fun) {
     )
   }
   ctree
-  ## cfs <- col_fnotes_here(ctree)
+  ## cfs <- col_footnotes(ctree)
   ## if(length(unlist(cfs)) > 0) {
-  ##     col_fnotes_here(ctree) <- .reindex_one_pos(lapply(cfs,
+  ##     col_footnotes(ctree) <- .reindex_one_pos(lapply(cfs,
   ##                                      function(refs) lapply(refs, function(refi) {
 }
 
@@ -95,7 +95,7 @@ index_col_refs <- function(tt, cur_idx_fun) {
 #' manually.
 #' @export
 update_ref_indexing <- function(tt) {
-  col_fnotes <- c(list(row_fnotes = list()), col_fnotes_here(tt))
+  col_fnotes <- c(list(row_fnotes = list()), col_footnotes(tt))
   row_fnotes <- row_footnotes(tt)
   cell_fnotes <- cell_footnotes(tt)
   all_fns <- rbind(col_fnotes, cbind(row_fnotes, cell_fnotes))

R/tree_accessors.R

@@ -2877,45 +2877,65 @@ setMethod("cell_footnotes<-", "ContentRow",
   definition = .cfn_set_helper
 )
 
+# Deprecated methods
 #' @export
 #' @rdname ref_fnotes
 setGeneric("col_fnotes_here", function(obj) standardGeneric("col_fnotes_here"))
 #' @export
+#' @rdname ref_fnotes
+setMethod("col_fnotes_here", "ANY", function(obj) {
+  warning("col_fnotes_here is deprecated since {rtables} version 0.6.5.9011. Please use col_footnotes instead.")
+  col_footnotes(obj)
+})
+#' @export
+#' @rdname ref_fnotes
+setGeneric("col_fnotes_here<-", function(obj, value) standardGeneric("col_fnotes_here<-"))
+#' @export
 #' @rdname int_methods
-setMethod("col_fnotes_here", c("LayoutColTree"), function(obj) obj@col_footnotes)
+setMethod("col_fnotes_here<-", "ANY", function(obj, value) {
+  warning("col_fnotes_here<- is deprecated since {rtables} version 0.6.5.9011. Please use col_footnotes<- instead.")
+  col_footnotes(obj) <- value
+})
+
+#' @export
+#' @rdname ref_fnotes
+setGeneric("col_footnotes", function(obj) standardGeneric("col_footnotes"))
 #' @export
 #' @rdname int_methods
-setMethod("col_fnotes_here", c("LayoutColLeaf"), function(obj) obj@col_footnotes)
+setMethod("col_footnotes", "LayoutColTree", function(obj) obj@col_footnotes)
+#' @export
+#' @rdname int_methods
+setMethod("col_footnotes", "LayoutColLeaf", function(obj) obj@col_footnotes)
 
 #' @export
 #' @rdname ref_fnotes
-setGeneric("col_fnotes_here<-", function(obj, value) standardGeneric("col_fnotes_here<-"))
+setGeneric("col_footnotes<-", function(obj, value) standardGeneric("col_footnotes<-"))
 #' @export
 #' @rdname int_methods
-setMethod("col_fnotes_here<-", "LayoutColTree", function(obj, value) {
+setMethod("col_footnotes<-", "LayoutColTree", function(obj, value) {
   obj@col_footnotes <- make_ref_value(value)
   obj
 })
 
 #' @export
 #' @rdname int_methods
-setMethod("col_fnotes_here<-", "LayoutColLeaf", function(obj, value) {
+setMethod("col_footnotes<-", "LayoutColLeaf", function(obj, value) {
   obj@col_footnotes <- make_ref_value(value)
   obj
 })
 
 #' @export
 #' @rdname int_methods
 setMethod(
-  "col_fnotes_here", "VTableTree",
+  "col_footnotes", "VTableTree",
   function(obj) {
     ctree <- coltree(obj)
     cols <- tree_children(ctree)
     while (all(sapply(cols, is, "LayoutColTree"))) {
       cols <- lapply(cols, tree_children)
       cols <- unlist(cols, recursive = FALSE)
     }
-    all_col_fnotes <- lapply(cols, col_fnotes_here)
+    all_col_fnotes <- lapply(cols, col_footnotes)
     if (is.null(unlist(all_col_fnotes))) return(NULL)
 
     return(all_col_fnotes)

R/tt_paginate.R

@@ -444,7 +444,7 @@ setMethod(
       sibpos = sibpos,
       nsibs = nsibs,
       leaf_indices = colnum,
-      col_fnotes = col_fnotes_here(ct)
+      col_fnotes = col_footnotes(ct)
     ))
   }
 )
@@ -484,7 +484,7 @@ setMethod(
           sibpos = sibpos,
           nsibs = nsibs,
           pth = thispth,
-          col_fnotes = col_fnotes_here(ct)
+          col_fnotes = col_footnotes(ct)
         ))
         ret <- c(thisone, ret)
       }

R/tt_pos_and_access.R

@@ -96,7 +96,7 @@ coltree_split <- function(ctree) ctree@split
 
 col_fnotes_at_path <- function(ctree, path, fnotes) {
   if (length(path) == 0) {
-    col_fnotes_here(ctree) <- fnotes
+    col_footnotes(ctree) <- fnotes
     return(ctree)
   }