Merge pull request #284 from cmu-delphi/ndefries/all-versions/examples

add epix_slide example comparing same computation with all_vers FALSE

Author: brookslogan

R/methods-epi_archive.R

@@ -790,6 +790,8 @@ group_by.epi_archive = function(.data, ..., .add=FALSE, .drop=dplyr::group_by_dr
 #'                        as.Date("2020-06-15"),
 #'                        by = "1 day")
 #'
+#' # A simple (but not very useful) example (see the archive vignette for a more
+#' # realistic one):
 #' archive_cases_dv_subset %>%
 #'   group_by(geo_value) %>%
 #'   epix_slide(f = ~ mean(.x$case_rate_7d_av),
@@ -801,39 +803,71 @@ group_by.epi_archive = function(.data, ..., .add=FALSE, .drop=dplyr::group_by_dr
 #' # values. The actual number of `time_value`s in each computation depends on
 #' # the reporting latency of the signal and `time_value` range covered by the
 #' # archive (2020-06-01 -- 2021-11-30 in this example).  In this case, we have
-#' # 0 `time_value`s, for ref time 2020-06-01 --> the result is automatically discarded
-#' # 1 `time_value`, for ref time 2020-06-02
-#' # 2 `time_value`s, for the rest of the results
-#' # never 3 `time_value`s, due to data latency
-#'
-#'
+#' # * 0 `time_value`s, for ref time 2020-06-01 --> the result is automatically
+#' #                                                discarded
+#' # * 1 `time_value`, for ref time 2020-06-02
+#' # * 2 `time_value`s, for the rest of the results
+#' # * never the 3 `time_value`s we would get from `epi_slide`, since, because
+#' #   of data latency, we'll never have an observation
+#' #   `time_value == ref_time_value` as of `ref_time_value`.
+#' # The example below shows this type of behavior in more detail.
+#'
+#' # Examining characteristics of the data passed to each computation with
+#' # `all_versions=FALSE`.
+#' archive_cases_dv_subset %>%
+#'  group_by(geo_value) %>%
+#'  epix_slide(
+#'    function(x, g) {
+#'      tibble(
+#'        time_range = if(nrow(x) == 0L) {
+#'          "0 `time_value`s"
+#'        } else {
+#'          sprintf("%s -- %s", min(x$time_value), max(x$time_value))
+#'        },
+#'        n = nrow(x),
+#'        class1 = class(x)[[1L]]
+#'      )
+#'    },
+#'    before = 5, all_versions = FALSE,
+#'    ref_time_values = ref_time_values, names_sep=NULL) %>%
+#'  ungroup() %>%
+#'  arrange(geo_value, time_value)
 #'
 #' # --- Advanced: ---
 #'
 #' # `epix_slide` with `all_versions=FALSE` (the default) applies a
 #' # version-unaware computation to several versions of the data. We can also
 #' # use `all_versions=TRUE` to apply a version-*aware* computation to several
-#' # versions of the data. In this case, each computation should expect an
+#' # versions of the data, again looking at characteristics of the data passed
+#' # to each computation. In this case, each computation should expect an
 #' # `epi_archive` containing the relevant version data:
 #'
 #' archive_cases_dv_subset %>%
 #'   group_by(geo_value) %>%
 #'   epix_slide(
 #'     function(x, g) {
 #'       tibble(
-#'         versions_end = max(x$versions_end),
+#'         versions_start = if (nrow(x$DT) == 0L) {
+#'           "NA (0 rows)"
+#'         } else {
+#'           toString(min(x$DT$version))
+#'         },
+#'         versions_end = x$versions_end,
 #'         time_range = if(nrow(x$DT) == 0L) {
 #'           "0 `time_value`s"
 #'         } else {
 #'           sprintf("%s -- %s", min(x$DT$time_value), max(x$DT$time_value))
 #'         },
+#'         n = nrow(x$DT),
 #'         class1 = class(x)[[1L]]
 #'       )
 #'     },
-#'     before = 2, all_versions = TRUE,
+#'     before = 5, all_versions = TRUE,
 #'     ref_time_values = ref_time_values, names_sep=NULL) %>%
 #'   ungroup() %>%
-#'   arrange(geo_value, time_value)
+#'   # Focus on one geo_value so we can better see the columns above:
+#'   filter(geo_value == "ca") %>%
+#'   select(-geo_value)
 #'
 #' @importFrom rlang enquo !!!
 #' @export