fix: .ref_time_values -> .versions in epix_slide and some doc fixes

R/archive.R

@@ -626,7 +626,7 @@ print.epi_archive <- function(x, ..., class = TRUE, methods = TRUE) {
 #'   epix_slide(
 #'     .f = ~ mean(.x$case_rate_7d_av),
 #'     .before = 2,
-#'     .ref_time_values = as.Date("2020-06-11") + 0:2,
+#'     .versions = as.Date("2020-06-11") + 0:2,
 #'     .new_col_name = "case_rate_3d_av"
 #'   ) %>%
 #'   ungroup()

R/grouped_epi_archive.R

@@ -224,13 +224,20 @@ epix_slide.grouped_epi_archive <- function(
   # early development versions and much more likely to be clutter than
   # informative in the signature.
   provided_args <- rlang::call_args_names(rlang::call_match())
-  if (any(provided_args %in% c("x", "f", "before", "ref_time_values", "new_col_name", "all_versions"))) {
+  if (any(provided_args %in% c(
+    "x", "f", "before", "new_col_name", "all_versions",
+  ))) {
     cli::cli_abort(
-      "epix_slide: you are using one of the following old argument names: `x`, `f`, `before`, `ref_time_values`,
-      `new_col_name`, `all_versions`. Please use the new names: `.x`, `.f`, `.before`, `.ref_time_values`,
+      "epix_slide: you are using one of the following old argument names: `x`, `f`, `before`,
+      `new_col_name`, `all_versions`. Please use the new names: `.x`, `.f`, `.before`,
       `.new_col_name`, `.all_versions`."
     )
   }
+  if (any(provided_args %in% c("ref_time_values", ".ref_time_values"))) {
+    cli::cli_abort(
+      "epix_slide: the argument `ref_time_values` is deprecated. Please use `.versions` instead."
+    )
+  }
   if ("group_by" %in% provided_args) {
     cli_abort("
           The `group_by` argument to `slide` has been removed; please use

R/methods-epi_archive.R

@@ -654,7 +654,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'   in the archive is "day", and the `.ref_time_value` is January 8, then the
 #'   smallest time_value in the snapshot will be January 1. If missing, then the
 #'   default is no limit on the time values, so the full snapshot is given.
-#' @param .ref_time_values Reference time values / versions for sliding
+#' @param .versions Reference time values / versions for sliding
 #'   computations; each element of this vector serves both as the anchor point
 #'   for the `time_value` window for the computation and the `max_version`
 #'   `epix_as_of` which we fetch data in this window. If missing, then this will
@@ -712,7 +712,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'   computations are allowed more flexibility in their outputs than in
 #'   `epi_slide`, we can't guess a good representation for missing computations
 #'   for excluded group-`.ref_time_value` pairs.
-#'   76. The `.ref_time_values` default for `epix_slide` is based on making an
+#'   76. The `.versions` default for `epix_slide` is based on making an
 #'   evenly-spaced sequence out of the `version`s in the `DT` plus the
 #'   `versions_end`, rather than the `time_value`s.
 #'
@@ -731,7 +731,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #' library(dplyr)
 #'
 #' # Reference time points for which we want to compute slide values:
-#' ref_time_values <- seq(as.Date("2020-06-01"),
+#' versions <- seq(as.Date("2020-06-01"),
 #'   as.Date("2020-06-15"),
 #'   by = "1 day"
 #' )
@@ -743,7 +743,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'   epix_slide(
 #'     .f = ~ mean(.x$case_rate_7d_av),
 #'     .before = 2,
-#'     .ref_time_values = ref_time_values,
+#'     .versions = versions,
 #'     .new_col_name = "case_rate_7d_av_recent_av"
 #'   ) %>%
 #'   ungroup()
@@ -777,7 +777,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'       )
 #'     },
 #'     .before = 5, .all_versions = FALSE,
-#'     .ref_time_values = ref_time_values
+#'     .versions = versions
 #'   ) %>%
 #'   ungroup() %>%
 #'   arrange(geo_value, time_value)
@@ -812,7 +812,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'       )
 #'     },
 #'     .before = 5, .all_versions = TRUE,
-#'     .ref_time_values = ref_time_values
+#'     .versions = versions
 #'   ) %>%
 #'   ungroup() %>%
 #'   # Focus on one geo_value so we can better see the columns above:

vignettes/advanced.Rmd

@@ -106,7 +106,7 @@ edf %>%
   mutate(version = time_value) %>%
   as_epi_archive() %>%
   group_by(geo_value) %>%
-  epix_slide(x_2dav = mean(x), .before = 1, .ref_time_values = as.Date("2020-06-02")) %>%
+  epix_slide(x_2dav = mean(x), .before = 1, .versions = as.Date("2020-06-02")) %>%
   ungroup()
 
 edf %>%
@@ -429,7 +429,7 @@ k_week_ahead <- function(x, ahead = 7, as_of = TRUE) {
         fc = prob_arx(.data$percent_cli, .data$case_rate_7d_av, .data$geo_value, .data$time_value,
           args = prob_arx_args(ahead = ahead)
         ),
-        .before = 219, .ref_time_values = fc_time_values
+        .before = 219, .versions = fc_time_values
       ) %>%
       mutate(
         target_date = .data$time_value + ahead, as_of = TRUE,

vignettes/archive.Rmd

@@ -346,7 +346,7 @@ z <- x %>%
   group_by(geo_value) %>%
   epix_slide(
     fc = prob_arx(x = percent_cli, y = case_rate_7d_av), .before = 119,
-    .ref_time_values = fc_time_values
+    .versions = fc_time_values
   ) %>%
   ungroup()
 
@@ -383,7 +383,7 @@ k_week_ahead <- function(x, ahead = 7, as_of = TRUE) {
       group_by(.data$geo_value) %>%
       epix_slide(
         fc = prob_arx(.data$percent_cli, .data$case_rate_7d_av, ahead = ahead), .before = 119,
-        .ref_time_values = fc_time_values
+        .versions = fc_time_values
       ) %>%
       mutate(target_date = .data$time_value + ahead, as_of = TRUE) %>%
       ungroup()
@@ -392,7 +392,7 @@ k_week_ahead <- function(x, ahead = 7, as_of = TRUE) {
       group_by(.data$geo_value) %>%
       epi_slide(
         fc = prob_arx(.data$percent_cli, .data$case_rate_7d_av, ahead = ahead), .window_size = 120,
-        .ref_time_values = fc_time_values
+        .versions = fc_time_values
       ) %>%
       mutate(target_date = .data$time_value + ahead, as_of = FALSE) %>%
       ungroup()