Provide additional aliases for S4 subsetting methods (#117)

R/Config.R

@@ -51,7 +51,10 @@ tiledb_config <- function(config = NA_character_) {
 #' cfg <- tiledb_config()
 #' cfg["sm.tile_cache_size"]
 #' cfg["does_not_exist"]
-#'
+#' @aliases [,tiledb_config
+#' @aliases [,tiledb_config-method
+#' @aliases [,tiledb_config,ANY,tiledb_config-method
+#' @aliases [,tiledb_config,ANY,ANY,tiledb_config-method
 setMethod("[", "tiledb_config",
           function(x, i, j, ..., drop=FALSE) {
             if (!is.character(i)) {
@@ -79,6 +82,10 @@ setMethod("[", "tiledb_config",
 #' cfg["sm.tile_cache_size"] <- 100
 #' cfg["sm.tile_cache_size"]
 #'
+#' @aliases [<-,tiledb_config
+#' @aliases [<-,tiledb_config-method
+#' @aliases [<-,tiledb_config,ANY,tiledb_config-method
+#' @aliases [<-,tiledb_config,ANY,ANY,tiledb_config-method
 setMethod("[<-", "tiledb_config",
           function(x, i, j, value) {
             if (!is.character(i)) {

R/DenseArray.R

@@ -234,6 +234,10 @@ attribute_buffers <- function(array, sch, dom, sub, selected) {
 #' @param ... Extra parameter for method signature, currently unused.
 #' @param drop Optional logical switch to drop dimensions, default FALSE, currently unused.
 #' @return An element from a dense array
+#' @aliases [,tiledb_dense
+#' @aliases [,tiledb_dense-method
+#' @aliases [,tiledb_dense,ANY,tiledb_dense-method
+#' @aliases [,tiledb_dense,ANY,ANY,tiledb_dense-method
 setMethod("[", "tiledb_dense",
           function(x, i, j, ..., drop = FALSE) {
             ## helper function to deal with i and/or j missing
@@ -356,6 +360,10 @@ setMethod("[", "tiledb_dense",
 #' @param value The value being assigned
 #' @return The modified object
 #' @importFrom utils head
+#' @aliases [<-,tiledb_dense
+#' @aliases [<-,tiledb_dense-method
+#' @aliases [<-,tiledb_dense,ANY,tiledb_dense-method
+#' @aliases [<-,tiledb_dense,ANY,ANY,tiledb_dense-method
 setMethod("[<-", "tiledb_dense",
           function(x, i, j, ..., value) {
             if (!is.list(value)) {

R/FilterList.R

@@ -117,6 +117,10 @@ setMethod("nfilters", signature(object = "tiledb_filter_list"),
 #' filter_list[0]
 #'
 #' @export
+#' @aliases [,tiledb_filter_list
+#' @aliases [,tiledb_filter_list-method
+#' @aliases [,tiledb_filter_list,ANY,tiledb_filter_list-method
+#' @aliases [,tiledb_filter_list,ANY,ANY,tiledb_filter_list-method
 setMethod("[", "tiledb_filter_list",
           function(x, i, j, ..., drop = FALSE) {
             tiledb_filter.from_ptr(libtiledb_filter_list_get_filter_from_index(x@ptr, i))

R/SparseArray.R

@@ -148,6 +148,10 @@ as_data_frame <- function(dom, data, extended=FALSE) {
 #' @param ... Extra parameter for method signature, currently unused.
 #' @param drop Optional logical switch to drop dimensions, default FALSE, currently unused.
 #' @return An element from the sparse array
+#' @aliases [,tiledb_sparse
+#' @aliases [,tiledb_sparse-method
+#' @aliases [,tiledb_sparse,ANY,tiledb_sparse-method
+#' @aliases [,tiledb_sparse,ANY,ANY,tiledb_sparse-method
 setMethod("[", "tiledb_sparse",
           function(x, i, j, ..., drop = FALSE) {
             ## helper function to deal with i and/or j missing
@@ -265,6 +269,10 @@ setMethod("[", "tiledb_sparse",
 #' @param ... Extra parameter for method signature, currently unused.
 #' @param value The value being assigned
 #' @return The modified object
+#' @aliases [<-,tiledb_sparse
+#' @aliases [<-,tiledb_sparse-method
+#' @aliases [<-,tiledb_sparse,ANY,tiledb_sparse-method
+#' @aliases [<-,tiledb_sparse,ANY,ANY,tiledb_sparse-method
 setMethod("[<-", "tiledb_sparse",
           function(x, i, j, ..., value) {
             if (!is.list(value)) {

R/tiledb_array.R

@@ -112,6 +112,10 @@ setMethod("show",
 #' @param drop Optional logical switch to drop dimensions, default FALSE, currently unused.
 #' @return An element from the sparse array
 #' @import nanotime
+#' @aliases [,tiledb_array
+#' @aliases [,tiledb_array-method
+#' @aliases [,tiledb_array,ANY,tiledb_array-method
+#' @aliases [,tiledb_array,ANY,ANY,tiledb_array-method
 setMethod("[", "tiledb_array",
           function(x, i, j, ..., drop = FALSE) {
   ## add defaults
@@ -279,6 +283,10 @@ setMethod("[", "tiledb_array",
 #' arr[c(1,2), c(1,3)] <- c(42,43) ## two values
 #' arr[2, 4] <- 88                 ## or just one
 #' }
+#' @aliases [<-,tiledb_array
+#' @aliases [<-,tiledb_array-method
+#' @aliases [<-,tiledb_array,ANY,tiledb_array-method
+#' @aliases [<-,tiledb_array,ANY,ANY,tiledb_array-method
 setMethod("[<-", "tiledb_array",
           function(x, i, j, ..., value) {
   if (!is.data.frame(value)) {

inst/NEWS.md

@@ -1,9 +1,14 @@
+# Ongoing
+
+* This release of the R package supports [TileDB 1.7.7](https://github.com/TileDB-Inc/TileDB/releases/tag/1.7.7) and [TileDB 2.0.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.0.0)
+
+## Improvements
+
+- All S4 classes are now consistently documented or aliased
 
 # 0.6.0
 
-* This release of the R package supports [TileDB
-  1.7.7](https://github.com/TileDB-Inc/TileDB/releases/tag/1.7.7) and
-  [TileDB 2.0.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.0.0)
+* This release of the R package supports [TileDB 1.7.7](https://github.com/TileDB-Inc/TileDB/releases/tag/1.7.7) and [TileDB 2.0.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.0.0)
 
 ## Improvements