merge remote

Merge branch 'revision-summary-printing' of https://github.com/cmu-delphi/epiprocess into revision-summary-printing

# Conflicts:
#	R/revision_analysis.R

Author: dajmcdon

NAMESPACE

@@ -53,7 +53,7 @@ S3method(print,epi_archive)
 S3method(print,epi_df)
 S3method(print,grouped_epi_archive)
 S3method(print,growth_rate_params)
-S3method(print,revision_behavior)
+S3method(print,revision_analysis)
 S3method(summary,epi_df)
 S3method(ungroup,epi_df)
 S3method(ungroup,grouped_epi_archive)

R/revision_analysis.R

@@ -61,10 +61,10 @@
 #'   Using a `time_type` of `"integer"` with week numbers like 202501 will
 #'   produce incorrect results for some calculations, since week numbering
 #'   contains jumps at year boundaries.
-#' 
+#'
 #' @return An S3 object with class `revision_behavior`. This function is typically
 #'   called for the purposes of inspecting the printed output. The
-#'   results of the computations are available in 
+#'   results of the computations are available in
 #'   `revision_analysis(...)$revision_behavior`. If you only want to access
 #'   the internal computations, use `return_only_tibble = TRUE`.
 #'
@@ -186,7 +186,7 @@ revision_analysis <- function(epi_arch,
   if (!return_only_tibble) {
     revision_behavior <- structure(list(
       revision_behavior = revision_behavior,
-      range_time_values = range(epi_arch$DT$time_value), 
+      range_time_values = range(epi_arch$DT$time_value),
       signal_variable = arg,
       drop_nas = drop_nas,
       time_type = time_type,
@@ -227,35 +227,34 @@ print.revision_analysis <- function(x,
                                     abs_spread_threshold = NULL,
                                     rel_spread_threshold = 0.1,
                                     ...) {
-  cli::cli_h2("An epi_archive spanning {.val {x$range_time_values[1]}} to {.val {x$range_time_values[1]}}.")
+  rev_beh <- x$revision_behavior
+  cli::cli_h2("An epi_archive spanning {.val {rev_beh$range_time_values[1]}} to {.val {rev_beh$range_time_values[1]}}.")
   cli::cli_h3("Min lag (time to first version):")
-  time_delta_summary(x$revision_behavior$min_lag, x$time_type) %>% print()
+  time_delta_summary(rev_beh$min_lag, x$time_type) %>% print()
   if (!x$drop_nas) {
     cli_inform("Fraction of all versions that are `NA`:")
     cli_li(num_percent(x$total_na, x$n_obs, ""))
     cli_inform("")
   }
   cli::cli_h3("Fraction of epi_key + time_values with")
-  total_num <- nrow(x$revision_behavior) # nolint: object_usage_linter
-  total_num_unrevised <- sum(x$n_revisions == 0) # nolint: object_usage_linter
+  total_num <- nrow(rev_beh) # nolint: object_usage_linter
+  total_num_unrevised <- sum(rev_beh$n_revisions == 0) # nolint: object_usage_linter
   cli_inform("No revisions:")
   cli_li(num_percent(total_num_unrevised, total_num, ""))
   total_quickly_revised <- sum( # nolint: object_usage_linter
-    time_delta_to_n_steps(x$revision_behavior$max_lag, x$time_type) <=
+    time_delta_to_n_steps(rev_beh$max_lag, x$time_type) <=
       time_delta_to_n_steps(quick_revision, x$time_type)
   )
   cli_inform("Quick revisions (last revision within {format_time_delta(quick_revision, x$time_type)}
                 of the `time_value`):")
   cli_li(num_percent(total_quickly_revised, total_num, ""))
-  total_barely_revised <- sum( # nolint: object_usage_linter
-    x$n_revisions <= few_revisions
-  )
+  total_barely_revised <- sum(x$n_revisions <= few_revisions)
   cli_inform("Few revisions (At most {few_revisions} revisions for that `time_value`):")
   cli_li(num_percent(total_barely_revised, total_num, ""))
-  
+
   cli::cli_h3("Fraction of revised epi_key + time_values which have:")
-  
-  real_revisions <- x$revision_behavior %>% filter(n_revisions > 0) # nolint: object_usage_linter
+
+  real_revisions <- rev_beh %>% filter(n_revisions > 0) # nolint: object_usage_linter
   n_real_revised <- nrow(real_revisions) # nolint: object_usage_linter
   rel_spread <- sum( # nolint: object_usage_linter
     real_revisions$rel_spread < rel_spread_threshold,
@@ -268,12 +267,12 @@ print.revision_analysis <- function(x,
   ) # nolint: object_usage_linter
   cli_inform("Spread of more than {abs_spread_threshold} in actual value (when revised):")
   cli_li(num_percent(abs_spread, n_real_revised, ""))
-  
+
   # time_type_unit_pluralizer[[time_type]] is a format string controlled by us
   # and/or downstream devs, so we can paste it onto our format string safely:
   units_plural <- pluralize(paste0("{qty(2)}", time_type_unit_pluralizer[[x$time_type]])) # nolint: object_usage_linter
   cli::cli_h3("{toTitleCase(units_plural)} until within {x$within_latest*100}% of the latest value:")
-  time_delta_summary(x$revision_behavior[["lag_near_latest"]], x$time_type) %>% print()
+  time_delta_summary(rev_beh[["lag_near_latest"]], x$time_type) %>% print()
 }
 
 #' @export

man/revision_analysis.Rd

@@ -14,11 +14,11 @@
       
       -- Fraction of epi_key + time_values with 
       No revisions:
-      * 0 out of 7 (0%)
+      * 3 out of 7 (42.86%)
       Quick revisions (last revision within 3 days of the `time_value`):
       * 4 out of 7 (57.14%)
       Few revisions (At most 3 revisions for that `time_value`):
-      * 0 out of 7 (0%)
+      * 6 out of 7 (85.71%)
       
       -- Fraction of revised epi_key + time_values which have: 
       Less than 0.1 spread in relative value:
@@ -74,11 +74,11 @@
       
       -- Fraction of epi_key + time_values with 
       No revisions:
-      * 0 out of 7 (0%)
+      * 2 out of 7 (28.57%)
       Quick revisions (last revision within 3 days of the `time_value`):
       * 4 out of 7 (57.14%)
       Few revisions (At most 3 revisions for that `time_value`):
-      * 0 out of 7 (0%)
+      * 6 out of 7 (85.71%)
       
       -- Fraction of revised epi_key + time_values which have: 
       Less than 0.1 spread in relative value:
@@ -134,11 +134,11 @@
       
       -- Fraction of epi_key + time_values with 
       No revisions:
-      * 0 out of 7 (0%)
+      * 2 out of 7 (28.57%)
       Quick revisions (last revision within 1 week of the `time_value`):
       * 2 out of 7 (28.57%)
       Few revisions (At most 3 revisions for that `time_value`):
-      * 0 out of 7 (0%)
+      * 6 out of 7 (85.71%)
       
       -- Fraction of revised epi_key + time_values which have: 
       Less than 0.1 spread in relative value:
@@ -194,11 +194,11 @@
       
       -- Fraction of epi_key + time_values with 
       No revisions:
-      * 0 out of 7 (0%)
+      * 2 out of 7 (28.57%)
       Quick revisions (last revision within 1 month of the `time_value`):
       * 2 out of 7 (28.57%)
       Few revisions (At most 3 revisions for that `time_value`):
-      * 0 out of 7 (0%)
+      * 6 out of 7 (85.71%)
       
       -- Fraction of revised epi_key + time_values which have: 
       Less than 0.1 spread in relative value:
@@ -254,11 +254,11 @@
       
       -- Fraction of epi_key + time_values with 
       No revisions:
-      * 0 out of 7 (0%)
+      * 2 out of 7 (28.57%)
       Quick revisions (last revision within 3 time steps of the `time_value`):
       * 4 out of 7 (57.14%)
       Few revisions (At most 3 revisions for that `time_value`):
-      * 0 out of 7 (0%)
+      * 6 out of 7 (85.71%)
       
       -- Fraction of revised epi_key + time_values which have: 
       Less than 0.1 spread in relative value:

tests/testthat/_snaps/revision-latency-functions.md

@@ -78,7 +78,7 @@ test_that("revision_summary works for dummy datasets", {
   # Yearmonthly has the same story. It would have been close to encountering
   # min_waiting_period-based filtering but we actually set its versions_end to
   # sometime in 2080 rather than 2022:
-  rs4 <- dummy_ex_yearmonthly %>% revision_summary(drop_nas = FALSE) 
+  rs4 <- dummy_ex_yearmonthly %>% revision_summary(drop_nas = FALSE)
   expect_snapshot(rs4)
   expect_snapshot(rs4$revision_behavior %>% print(n = 10, width = 300))
   # Integer is very much like daily. We have to provide some of the
@@ -91,7 +91,7 @@ test_that("revision_summary works for dummy datasets", {
     revision_summary(
       min_waiting_period = 60, quick_revision = 3,
       drop_nas = FALSE
-    ) 
+    )
   expect_snapshot(rs5)
   expect_snapshot(rs5$revision_behavior %>% print(n = 10, width = 300))
 })