Merge pull request #502 from cmu-delphi/ds/fix-doc

fix+doc: ?epi_df works again

Author: dshemetov

R/epi_df.R

@@ -81,10 +81,7 @@
 #'
 #' An unrecognizable time type is labeled "custom".
 #'
-#' @template epi_df-params
-#' @rdname epi_df
-#'
-#' @export
+#' @name epi_df
 #' @examples
 #' # Convert a `tsibble` that has county code as an extra key
 #' # Notice that county code should be a character string to preserve any leading zeroes
@@ -154,6 +151,30 @@
 #'   as_epi_df(additional_metadata = list(other_keys = c("state", "pol")))
 #'
 #' attr(ex3, "metadata")
+NULL
+
+#' Create an `epi_df` object
+#'
+#' @rdname epi_df
+#' @param geo_type DEPRECATED Has no effect. Geo value type is inferred from the
+#' location column and set to "custom" if not recognized.
+#' @param time_type DEPRECATED Has no effect. Time value type inferred from the time
+#' column and set to "custom" if not recognized. Unpredictable behavior may result
+#' if the time type is not recognized.
+#' @param as_of Time value representing the time at which the given data were
+#'   available. For example, if `as_of` is January 31, 2022, then the `epi_df`
+#'   object that is created would represent the most up-to-date version of the
+#'   data available as of January 31, 2022. If the `as_of` argument is missing,
+#'   then the current day-time will be used.
+#' @param additional_metadata List of additional metadata to attach to the
+#'   `epi_df` object. The metadata will have `geo_type`, `time_type`, and
+#'   `as_of` fields; named entries from the passed list will be included as
+#'   well. If your tibble has additional keys, be sure to specify them as a
+#'   character vector in the `other_keys` component of `additional_metadata`.
+#' @param ... Additional arguments passed to methods.
+#' @return An `epi_df` object.
+#'
+#' @export
 new_epi_df <- function(x = tibble::tibble(), geo_type, time_type, as_of,
                        additional_metadata = list()) {
   # Define metadata fields
@@ -180,22 +201,24 @@ new_epi_df <- function(x = tibble::tibble(), geo_type, time_type, as_of,
 }
 
 #' @rdname epi_df
+#' @param x An `epi_df`, `data.frame`, [tibble::tibble], or [tsibble::tsibble]
+#'   to be converted
 #' @param ... used for specifying column names, as in [`dplyr::rename`]. For
 #'   example, `geo_value = STATEFP, time_value = end_date`.
 #' @export
 as_epi_df <- function(x, ...) {
   UseMethod("as_epi_df")
 }
 
-#' @method as_epi_df epi_df
 #' @rdname epi_df
+#' @method as_epi_df epi_df
 #' @export
 as_epi_df.epi_df <- function(x, ...) {
   return(x)
 }
 
-#' @method as_epi_df tbl_df
 #' @rdname epi_df
+#' @method as_epi_df tbl_df
 #' @importFrom rlang .data
 #' @importFrom tidyselect any_of
 #' @importFrom cli cli_inform