r cmd check updates, fix example

Author: multimeric

R/query.R

@@ -450,28 +450,33 @@ get_metadata <- function(
 }
 
 #' Returns unharmonised metadata for selected datasets.
-#' 
-#' Various metadata fields are *not* common between datasets, so it does not make
-#' sense for these to live in the main metadata table. This function is a 
+#'
+#' Various metadata fields are *not* common between datasets, so it does not
+#' make sense for these to live in the main metadata table. This function is a
 #' utility that allows easy fetching of this data if necessary.
 #'
 #' @param dataset_ids A character vector, where each entry is a dataset ID
-#'  obtained from the `$dataset_id` column of the table returned from
-#'  [get_metadata()]
+#'   obtained from the `$dataset_id` column of the table returned from
+#'   [get_metadata()]
+#' @param remote_url Optional character vector of length 1. An HTTP URL pointing
+#'   to the root URL under which all the unharmonised dataset files are located.
+#' @param cache_directory Optional character vector of length 1. A file path on
+#'   your local system to a directory (not a file) that will be used to store
+#'   the unharmonised metadata files.
 #' @importFrom purrr map set_names
 #' @importFrom glue glue
 #' @importFrom DBI dbConnect
 #' @importFrom duckdb duckdb
 #' @importFrom dplyr tbl
-#' @return A named list, where each name is a dataset ID, and each value is
-#'  a "lazy data frame", ie a `tbl`.
+#' @return A named list, where each name is a dataset ID, and each value is a
+#'   "lazy data frame", ie a `tbl`.
 #' @export
 #' @examples
-#' dataset_id = "838ea006-2369-4e2c-b426-b2a744a2b02b"
-#' harmonised_meta = get_metadata() |> dplyr::filter(dataset_id = dataset_id)
-#' unharmonised_meta = get_unharmonised_metadata(dataset_id)
-#' unharmonised_tbl = unharmonised_meta[[dataset_id]]
-#' dplyr::join(harmonised_meta, unharmonised_tbl, by=c("dataset_id", "cell_"))
+#' dataset = "838ea006-2369-4e2c-b426-b2a744a2b02b"
+#' harmonised_meta = get_metadata() |> dplyr::filter(file_id == dataset) |> dplyr::collect()
+#' unharmonised_meta = get_unharmonised_metadata(dataset)
+#' unharmonised_tbl = dplyr::collect(unharmonised_meta[[dataset]])
+#' dplyr::left_join(harmonised_meta, unharmonised_tbl, by=c("file_id", "cell_"))
 get_unharmonised_metadata = function(
         dataset_ids,
         remote_url = "https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/unharmonised_metadata",