Minor documentation fixes

R/ArraySchema.R

@@ -95,7 +95,7 @@ tiledb_array_schema <- function(
     } # make it a list so that lapply works below
     stopifnot(
       "length of 'attrs' cannot be zero" = length(attrs) > 0,
-      "'attrs' must be a list of one or tiled_attr objects" = all(vapply(attrs, is_attr, logical(1)))
+      "'attrs' must be a list of one or tiledb_attr objects" = all(vapply(attrs, is_attr, logical(1)))
     )
   } else {
     attrs <- NULL

R/Ctx.R

@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2017-2023 TileDB Inc.
+#  Copyright (c) 2017-2025 TileDB Inc.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
@@ -55,7 +55,7 @@ getContext <- function() tiledb_get_context()
 #'
 #' @param ctx A TileDB context object
 #' @return NULL, invisibly. The function is invoked for the side-effect of
-#' storing the VFS object.
+#' storing the Ctx object.
 #' @export
 tiledb_set_context <- function(ctx) {
   stopifnot(`The 'ctx' argument must be a tiledb_ctx object` = is(ctx, "tiledb_ctx"))

R/Group.R

@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2022-2024 TileDB Inc.
+#  Copyright (c) 2022-2025 TileDB Inc.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
@@ -37,8 +37,8 @@ setClass("tiledb_group",
 #' \dQuote{READ} or \dQuote{WRITE}
 #' @param ctx (optional) A TileDB Context object; if not supplied the default
 #' context object is retrieved
-#' @param cfg (optional) A TileConfig object
-#' @return A 'group' object
+#' @param cfg (optional) A TileDB Config object
+#' @return A TileDB Group object
 #' @export
 tiledb_group <- function(
   uri,
@@ -262,7 +262,8 @@ tiledb_group_get_metadata <- function(grp, key) {
 ##' \code{tiledb_group()}
 ##' @param key A character value with they index under which the
 ##' data will be written
-##' @return A boolean value indicating with the object is present
+##' @return A logical value indicating if the given key exists in the
+##'  metadata of the given group
 ##' @export
 tiledb_group_has_metadata <- function(grp, key) {
   stopifnot(

R/Metadata.R

@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2017-2023 TileDB Inc.
+#  Copyright (c) 2017-2025 TileDB Inc.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
@@ -25,7 +25,7 @@
 ##' @param arr A TileDB Array object
 ##' @param key A character value describing a metadata key
 ##' @return A logical value indicating if the given key exists in the
-##'   metdata of the given array
+##'   metadata of the given array
 ##' @export
 tiledb_has_metadata <- function(arr, key) {
   stopifnot(

R/Query.R

@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2017-2024 TileDB Inc.
+#  Copyright (c) 2017-2025 TileDB Inc.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
@@ -31,13 +31,13 @@ setClass("tiledb_query",
 ## could add arr of type 'ANY' (using shortcut to not have to deal with collate order)
 ## if array was needed for query object
 
-#' Creates a 'tiledb_query' object
+#' Creates a `tiledb_query` object
 #'
 #' @param array A TileDB Array object
 #' @param type A character value that must be one of 'READ', 'WRITE', or
-#' 'DELETE' (for TileDB >= 2.12.0)
+#' 'DELETE', 'MODIFY_EXCLUSIVE' (for TileDB >= 2.12.0)
 #' @param ctx (optional) A TileDB Ctx object
-#' @return 'tiledb_query' object
+#' @return A `tiledb_query` object
 #' @export tiledb_query
 tiledb_query <- function(
   array,
@@ -59,7 +59,7 @@ tiledb_query <- function(
 #' Return TileDB Query type
 #'
 #' @param query A TileDB Query object
-#' @return A character value, either 'READ' or 'WRITE'
+#' @return A character value, either 'READ', 'WRITE', 'DELETE' or 'MODIFY_EXCLUSIVE'
 #' @export
 tiledb_query_type <- function(query) {
   stopifnot(`Argument 'query' must be a tiledb_query object` = is(query, "tiledb_query"))
@@ -74,7 +74,7 @@ tiledb_query_type <- function(query) {
 #' @return The modified query object, invisibly
 #' @export
 tiledb_query_set_layout <- function(
-  query, 
+  query,
   layout = c(
     "COL_MAJOR", "ROW_MAJOR",
     "GLOBAL_ORDER", "UNORDERED"
@@ -99,7 +99,7 @@ tiledb_query_get_layout <- function(query) {
 #' Set subarray for TileDB Query object
 #'
 #' @param query A TileDB Query object
-#' @param subarray A subarry vector object
+#' @param subarray A subarray vector object
 #' @param type An optional type as a character, if missing type is
 #'   inferred from the vector.
 #' @return The modified query object, invisibly
@@ -123,7 +123,7 @@ tiledb_query_set_subarray <- function(query, subarray, type) {
 #' @param query A TileDB Query object
 #' @param attr A character value containing the attribute
 #' @param buffer A vector providing the query buffer
-#' @return The modified query object, invisisibly
+#' @return The modified query object, invisibly
 #' @export
 tiledb_query_set_buffer <- function(query, attr, buffer) {
   stopifnot(
@@ -165,8 +165,8 @@ tiledb_query_create_buffer_ptr_char <- function(query, varvec) {
 #' @return An external pointer to the allocated buffer object
 #' @export
 tiledb_query_alloc_buffer_ptr_char <- function(
-  sizeoffsets, 
-  sizedata, 
+  sizeoffsets,
+  sizedata,
   nullable = FALSE
 ) {
   stopifnot(
@@ -221,15 +221,15 @@ tiledb_query_set_buffer_ptr_char <- function(query, attr, bufptr) {
 #' @param ncells A number of elements (not bytes)
 #' @param nullable Optional boolean parameter indicating whether missing values
 #' are allowed (for which another column is allocated), default is FALSE
-#' @param varnum Option intgeter parameter for the number of elemements per variable,
+#' @param varnum Optional integer parameter for the number of elements per variable,
 #' default is one
 #' @return An external pointer to the allocated buffer object
 #' @export
 tiledb_query_buffer_alloc_ptr <- function(
-  query, 
-  datatype, 
-  ncells, 
-  nullable = FALSE, 
+  query,
+  datatype,
+  ncells,
+  nullable = FALSE,
   varnum = 1
 ) {
   stopifnot(
@@ -303,7 +303,7 @@ tiledb_query_get_buffer_ptr <- function(bufptr) {
 #' @return An R object as resulting from the query
 #' @export
 tiledb_query_get_buffer_char <- function(
-  bufptr, 
+  bufptr,
   sizeoffsets = 0,
   sizestring = 0
 ) {
@@ -378,7 +378,7 @@ tiledb_query_status <- function(query) {
 #' @param attr A character value containing the attribute
 #' @return A integer with the number of elements in the results buffer
 #' for the given attribute
-#' @seealso tiledb_query_result_buffer_elements_vec
+#' @seealso [tiledb_query_result_buffer_elements_vec]
 #' @export
 tiledb_query_result_buffer_elements <- function(query, attr) {
   stopifnot(
@@ -407,11 +407,11 @@ tiledb_query_result_buffer_elements <- function(query, attr) {
 #' for fixed-size attribute or dimensions), the number elements in the results
 #' buffer for the given attribute, and (if nullable) a third element with the validity
 #' buffer size.
-#' @seealso tiledb_query_result_buffer_elements
+#' @seealso [tiledb_query_result_buffer_elements]
 #' @export
 tiledb_query_result_buffer_elements_vec <- function(
-  query, 
-  attr, 
+  query,
+  attr,
   nullable = FALSE
 ) {
   stopifnot(
@@ -433,10 +433,10 @@ tiledb_query_result_buffer_elements_vec <- function(
 #' @return The query object, invisibly
 #' @export
 tiledb_query_add_range <- function(
-  query, 
-  schema, 
-  attr, lowval, 
-  highval, 
+  query,
+  schema,
+  attr, lowval,
+  highval,
   stride = NULL
 ) {
   stopifnot(
@@ -465,11 +465,11 @@ tiledb_query_add_range <- function(
 #' @return The query object, invisibly
 #' @export
 tiledb_query_add_range_with_type <- function(
-  query, 
-  idx, 
-  datatype, 
-  lowval, 
-  highval, 
+  query,
+  idx,
+  datatype,
+  lowval,
+  highval,
   stride = NULL
 ) {
   stopifnot(
@@ -677,7 +677,7 @@ tiledb_query_ctx <- function(query) {
 #    query@arr
 # }
 
-##' Run an aggregate oprtation on the given query attribute
+##' Run an aggregate operation on the given query attribute
 ##'
 ##' @param query A TileDB Query object
 ##' @param attrname The name of an attribute
@@ -686,7 +686,7 @@ tiledb_query_ctx <- function(query) {
 ##' @return The value of the aggregation
 ##' @export
 tiledb_query_apply_aggregate <- function(
-  query, 
+  query,
   attrname,
   operation = c("Count", "NullCount", "Min", "Max", "Mean",  "Sum"),
   nullable = TRUE

R/TileDBArray.R

@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2017-2024 TileDB Inc.
+#  Copyright (c) 2017-2025 TileDB Inc.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
@@ -28,7 +28,7 @@
 #' based on a refactored implementation utilising newer TileDB features.
 #'
 #' @slot ctx A TileDB context object
-#' @slot uri A character despription with the array URI
+#' @slot uri A character description with the array URI
 #' @slot is.sparse A logical value whether the array is sparse or not
 #' @slot attrs A character vector to select particular column
 #' \sQuote{attributes}; default is an empty character vector implying
@@ -52,7 +52,7 @@
 #' conversion, permitted values are \sQuote{asis} (default, returning a list
 #' of columns), \sQuote{array}, \sQuote{matrix},\sQuote{data.frame},
 #' \sQuote{data.table} \sQuote{tibble}, \sQuote{arrow_table} or \sQuote{arrow}
-#' (where the last two are synomyms); note that \sQuote{data.table},
+#' (where the last two are synonyms); note that \sQuote{data.table},
 #' \sQuote{tibble} and \sQuote{arrow} require the respective packages
 #' to be installed.
 #' @slot query_statistics A logical value, defaults to \sQuote{FALSE}; if
@@ -125,10 +125,10 @@ setClass(
 #' default uninitialized without a condition; this functionality requires
 #' TileDB 2.3.0 or later
 #' @param timestamp_start optional A POSIXct Datetime value determining the
-#' inclusive time point at which the array is to be openened. No fragments
+#' inclusive time point at which the array is to be opened. No fragments
 #' written earlier will be considered.
 #' @param timestamp_end optional A POSIXct Datetime value determining the
-#' inclusive time point until which the array is to be openened. No fragments
+#' inclusive time point until which the array is to be opened. No fragments
 #' written earlier later be considered.
 #' @param return_as optional A character value with the desired
 #' \code{tiledb_array} conversion, permitted values are \sQuote{asis} (default,
@@ -502,9 +502,9 @@ setValidity("tiledb_array", function(object) {
 #'
 #' Heterogenous domains are supported, including timestamps and characters.
 #'
-#' This function may still still change; the current implementation should be
+#' This function may still change; the current implementation should be
 #' considered as an initial draft.
-#' @param x tiledb_array object
+#' @param x A `tiledb_array` object.
 #' @param i optional row index expression which can be a list in which case
 #' minimum and maximum of each list element determine a range; multiple list
 #' elements can be used to supply multiple ranges.
@@ -1253,7 +1253,7 @@ setMethod(
 #' as part of the left-hand side object, or as part of the data.frame
 #' provided appropriate column names.
 #'
-#' This function may still still change; the current implementation should be
+#' This function may still change; the current implementation should be
 #' considered as an initial draft.
 #' @param x sparse or dense TileDB array object
 #' @param i parameter row index
@@ -1803,7 +1803,7 @@ setGeneric(
 #' Retrieve query_layout values for the array
 #'
 #' A \code{tiledb_array} object can have a corresponding query with a given
-#' layout given layout. This methods returns the selection value for
+#' layout. This method returns the selection value for
 #' \sQuote{query_layout} as a character value.
 #' @param object A \code{tiledb_array} object
 #' @return A character value describing the query layout
@@ -1819,7 +1819,7 @@ setMethod("query_layout", signature = "tiledb_array", function(object) object@qu
 #'
 #' @param value A character variable for the query layout. Permitted values
 #' are \dQuote{ROW_MAJOR}, \dQuote{COL_MAJOR}, \dQuote{GLOBAL_ORDER}, or
-#' \dQuote{UNORDERD}.
+#' \dQuote{UNORDERED}.
 #' @return The modified \code{tiledb_array} array object
 #' @export
 setReplaceMethod(