Update NL deaths

- NL deaths no longer reported at HR-level after 2023-06-21
- NL death data after this date is from PHAC dataset
- Start PHAC data on 2023-07-01 rather than 2023-06-24, because the cumulative data on 2023-06-24 would imply negative deaths since 2023-06-21
- ccodwg/CovidTimelineCanada#113

R/assemble_final_datasets.R

@@ -265,8 +265,19 @@ assemble_final_datasets <- function() {
       convert_hr_names(),
     read_d("raw_data/static/nl/nl_deaths_hr_ts_2.csv") %>%
       convert_hr_names(),
-    read_d("raw_data/active_cumul/nl/nl_deaths_hr_ts.csv")
+    read_d("raw_data/static/nl/nl_deaths_hr_ts_3.csv")
   )
+  nl1 <- get_phac_d("deaths", "NL", keep_up_to_date = TRUE) %>%
+    dplyr::filter(.data$date >= as.Date("2023-07-01")) %>%
+    add_hr_col("Unknown")
+  deaths_hr <- deaths_nl |>
+    dplyr::filter(.data$date == max(.data$date)) |>
+    dplyr::pull(.data$value) |>
+    sum()
+  nl1$value <- nl1$value - deaths_hr # subtract deaths assigned to a health region
+  # started with 2023-07-01 instead of 2023-06-24 to avoid negative values for deaths
+  deaths_nl <- dplyr::bind_rows(deaths_nl, nl1)
+  rm(nl1, deaths_hr) # clean up
 
   ## ns
   tryCatch(

R/update_raw_datasets.R

@@ -260,18 +260,6 @@ update_active_cumul <- function(ds) {
       as_of_date = max(as.Date(read_d("raw_data/active_ts/ab/ab_cases_hr_ts.csv")[["date"]]), na.rm = TRUE))
   upload_active_cumul(ac_deaths_hr_ab, files, "covid19_cumul", "deaths_hr_ab")
   sync_active_cumul("deaths_hr_ab", "deaths", "AB", as_of_date = TRUE)
-
-  # active_cumul - death data - nl
-  ac_deaths_hr_nl <- Covid19CanadaDataProcess::process_dataset(
-    uuid = "34f45670-34ed-415c-86a6-e14d77fcf6db",
-    val = "mortality",
-    fmt = "hr_cum_current",
-    ds = load_ds(ds, "34f45670-34ed-415c-86a6-e14d77fcf6db")) %>%
-    convert_hr_names() %>%
-    add_as_of_date(
-      as_of_date = lubridate::date(lubridate::with_tz(as.POSIXct(load_ds(ds, "34f45670-34ed-415c-86a6-e14d77fcf6db")$features$attributes$EditDate / 1000, origin = "1970-01-01")[1], tz = "America/St_Johns")))
-  upload_active_cumul(ac_deaths_hr_nl, files, "covid19_cumul", "deaths_hr_nl")
-  sync_active_cumul("deaths_hr_nl", "deaths", "NL", as_of_date = TRUE)
 }
 
 #' Update raw datasets for CovidTimelineCanada