fix: port @examples, add archive_cases_dv_subset_2

NAMESPACE

@@ -49,6 +49,7 @@ S3method(ungroup,grouped_epi_archive2)
 S3method(unnest,epi_df)
 export("%>%")
 export(archive_cases_dv_subset)
+export(archive_cases_dv_subset_2)
 export(arrange)
 export(as_epi_archive)
 export(as_epi_archive2)

R/archive_new.R

@@ -197,7 +197,7 @@ next_after.Date <- function(x) x + 1L
 #'   value = rnorm(10, mean = 2, sd = 1)
 #' )
 #'
-#' toy_epi_archive <- tib %>% epi_archive$new(
+#' toy_epi_archive <- tib %>% new_epi_archive2(
 #'   geo_type = "state",
 #'   time_type = "day"
 #' )
@@ -743,16 +743,16 @@ merge_epi_archive2 <- function(
 #'
 #' @examples
 #'
-#' grouped_archive <- archive_cases_dv_subset %>% group_by(geo_value)
+#' grouped_archive <- archive_cases_dv_subset_2 %>% group_by(geo_value)
 #'
 #' # `print` for metadata and method listing:
 #' grouped_archive %>% print()
 #'
 #' # The primary use for grouping is to perform a grouped `epix_slide`:
 #'
-#' archive_cases_dv_subset %>%
+#' archive_cases_dv_subset_2 %>%
 #'   group_by(geo_value) %>%
-#'   epix_slide(
+#'   epix_slide2(
 #'     f = ~ mean(.x$case_rate_7d_av),
 #'     before = 2,
 #'     ref_time_values = as.Date("2020-06-11") + 0:2,
@@ -778,7 +778,7 @@ merge_epi_archive2 <- function(
 #'     time_value = as.Date(time_value),
 #'     version = as.Date(version)
 #'   ) %>%
-#'   as_epi_archive(other_keys = "age_group")
+#'   as_epi_archive2(other_keys = "age_group")
 #'
 #' # The following are equivalent:
 #' toy_archive %>% group_by(geo_value, age_group)
@@ -801,7 +801,7 @@ merge_epi_archive2 <- function(
 #'
 #' toy_archive %>%
 #'   group_by(geo_value, age_group, .drop = FALSE) %>%
-#'   epix_slide(f = ~ sum(.x$value), before = 20) %>%
+#'   epix_slide2(f = ~ sum(.x$value), before = 20) %>%
 #'   ungroup()
 #'
 #' @importFrom dplyr group_by
@@ -1030,7 +1030,7 @@ slide.epi_archive2 <- function(epi_archive, f, ..., before, ref_time_values,
 #'   value = rnorm(10, mean = 2, sd = 1)
 #' )
 #'
-#' toy_epi_archive <- tib %>% as_epi_archive(
+#' toy_epi_archive <- tib %>% as_epi_archive2(
 #'   geo_type = "state",
 #'   time_type = "day"
 #' )
@@ -1056,7 +1056,7 @@ slide.epi_archive2 <- function(epi_archive, f, ..., before, ref_time_values,
 #'   cases_rate = c(0.01, 0.02, 0.01, 0.05)
 #' )
 #'
-#' x <- df %>% as_epi_archive(
+#' x <- df %>% as_epi_archive2(
 #'   geo_type = "state",
 #'   time_type = "day",
 #'   other_keys = "county"
@@ -1081,15 +1081,15 @@ as_epi_archive2 <- function(x, geo_type, time_type, other_keys,
 #'
 #' @export
 #' @examples
-#' is_epi_archive(jhu_csse_daily_subset) # FALSE (this is an epi_df, not epi_archive)
-#' is_epi_archive(archive_cases_dv_subset) # TRUE
+#' is_epi_archive2(jhu_csse_daily_subset) # FALSE (this is an epi_df, not epi_archive)
+#' is_epi_archive2(archive_cases_dv_subset_2) # TRUE
 #'
 #' # By default, grouped_epi_archives don't count as epi_archives, as they may
 #' # support a different set of operations from regular `epi_archives`. This
 #' # behavior can be controlled by `grouped_okay`.
-#' grouped_archive <- archive_cases_dv_subset$group_by(geo_value)
-#' is_epi_archive(grouped_archive) # FALSE
-#' is_epi_archive(grouped_archive, grouped_okay = TRUE) # TRUE
+#' grouped_archive <- archive_cases_dv_subset_2 %>% group_by(geo_value)
+#' is_epi_archive2(grouped_archive) # FALSE
+#' is_epi_archive2(grouped_archive, grouped_okay = TRUE) # TRUE
 #'
 #' @seealso [`is_grouped_epi_archive`]
 is_epi_archive2 <- function(x, grouped_okay = FALSE) {

R/data.R

@@ -289,3 +289,11 @@ delayed_assign_with_unregister_awareness(
 #' * Furthermore, the data has been limited to a very small number of rows, the
 #'   signal names slightly altered, and formatted into a tibble.
 "jhu_csse_county_level_subset"
+
+#' @export
+"archive_cases_dv_subset_2"
+
+delayed_assign_with_unregister_awareness(
+  "archive_cases_dv_subset_2",
+  as_epi_archive2(archive_cases_dv_subset_dt, compactify = FALSE)
+)

R/methods-epi_archive_new.R

@@ -41,17 +41,15 @@
 #'
 #' @examples
 #' # warning message of data latency shown
-#' epix_as_of(
-#'   x = archive_cases_dv_subset,
-#'   max_version = max(archive_cases_dv_subset$DT$version)
+#' epix_as_of2(
+#'   archive_cases_dv_subset_2,
+#'   max_version = max(archive_cases_dv_subset_2$DT$version)
 #' )
 #'
-#' @examples
-#'
-#' range(archive_cases_dv_subset$DT$version) # 2020-06-02 -- 2021-12-01
+#' range(archive_cases_dv_subset_2$DT$version) # 2020-06-02 -- 2021-12-01
 #'
-#' epix_as_of(
-#'   x = archive_cases_dv_subset,
+#' epix_as_of2(
+#'   archive_cases_dv_subset_2,
 #'   max_version = as.Date("2020-06-12")
 #' )
 #'
@@ -65,9 +63,9 @@
 #' # muffle such warnings with the following pattern:
 #' withCallingHandlers(
 #'   {
-#'     epix_as_of(
-#'       x = archive_cases_dv_subset,
-#'       max_version = max(archive_cases_dv_subset$DT$version)
+#'     epix_as_of2(
+#'       archive_cases_dv_subset_2,
+#'       max_version = max(archive_cases_dv_subset_2$DT$version)
 #'     )
 #'   },
 #'   epiprocess__snapshot_as_of_clobberable_version = function(wrn) invokeRestart("muffleWarning")
@@ -164,16 +162,14 @@ epix_fill_through_version2 <- function(epi_archive, fill_versions_end,
 #'
 #' @examples
 #' # create two example epi_archive datasets
-#' x <- archive_cases_dv_subset$DT %>%
+#' x <- archive_cases_dv_subset_2$DT %>%
 #'   dplyr::select(geo_value, time_value, version, case_rate_7d_av) %>%
-#'   as_epi_archive(compactify = TRUE)
-#' y <- archive_cases_dv_subset$DT %>%
+#'   as_epi_archive2(compactify = TRUE)
+#' y <- archive_cases_dv_subset_2$DT %>%
 #'   dplyr::select(geo_value, time_value, version, percent_cli) %>%
-#'   as_epi_archive(compactify = TRUE)
+#'   as_epi_archive2(compactify = TRUE)
 #' # merge results stored in a third object:
-#' xy <- epix_merge(x, y)
-#' # vs. mutating x to hold the merge result:
-#' x$merge(y)
+#' xy <- epix_merge2(x, y)
 #'
 #' @importFrom data.table key set setkeyv
 #' @export
@@ -703,9 +699,9 @@ epix_detailed_restricted_mutate2 <- function(.data, ...) {
 #'
 #' # A simple (but not very useful) example (see the archive vignette for a more
 #' # realistic one):
-#' archive_cases_dv_subset %>%
+#' archive_cases_dv_subset_2 %>%
 #'   group_by(geo_value) %>%
-#'   epix_slide(
+#'   epix_slide2(
 #'     f = ~ mean(.x$case_rate_7d_av),
 #'     before = 2,
 #'     ref_time_values = ref_time_values,
@@ -727,9 +723,9 @@ epix_detailed_restricted_mutate2 <- function(.data, ...) {
 #'
 #' # Examining characteristics of the data passed to each computation with
 #' # `all_versions=FALSE`.
-#' archive_cases_dv_subset %>%
+#' archive_cases_dv_subset_2 %>%
 #'   group_by(geo_value) %>%
-#'   epix_slide(
+#'   epix_slide2(
 #'     function(x, gk, rtv) {
 #'       tibble(
 #'         time_range = if (nrow(x) == 0L) {
@@ -756,9 +752,9 @@ epix_detailed_restricted_mutate2 <- function(.data, ...) {
 #' # to each computation. In this case, each computation should expect an
 #' # `epi_archive` containing the relevant version data:
 #'
-#' archive_cases_dv_subset %>%
+#' archive_cases_dv_subset_2 %>%
 #'   group_by(geo_value) %>%
-#'   epix_slide(
+#'   epix_slide2(
 #'     function(x, gk, rtv) {
 #'       tibble(
 #'         versions_start = if (nrow(x$DT) == 0L) {

tests/testthat/test-archive_new.R

@@ -6,7 +6,7 @@ test_that("first input must be a data.frame", {
   )
 })
 
-dt <- archive_cases_dv_subset$DT
+dt <- archive_cases_dv_subset_2$DT
 
 test_that("data.frame must contain geo_value, time_value and version columns", {
   expect_error(as_epi_archive2(select(dt, -geo_value), compactify = FALSE),

tests/testthat/test-compactify.R

@@ -2,7 +2,7 @@ library(epiprocess)
 library(data.table)
 library(dplyr)
 
-dt <- archive_cases_dv_subset$DT
+dt <- archive_cases_dv_subset_2$DT
 dt <- filter(dt, geo_value == "ca") %>%
   filter(version <= "2020-06-15") %>%
   select(-case_rate_7d_av)