Add AB, ON hospital/ICU admissions and PT-level deaths

- hosp_admissions and icu_admissions (ccodwg/CovidTimelineCanada#111) - PT-level deaths time series for later use (ccodwg/CovidTimelineCanada#120)
ccodwg · Oct 11, 2023 · 5df287a · 5df287a
1 parent c2dc865
commit 5df287a
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diff --git a/R/assemble_final_datasets.R b/R/assemble_final_datasets.R
@@ -630,6 +630,14 @@ assemble_final_datasets <- function() {
 
   # hosp_admissions dataset
 
+  ## ab
+  hosp_admissions_ab <- read_d("raw_data/active_ts/ab/ab_hosp_admissions_pt_ts.csv") |>
+    dplyr::transmute(
+      .data$name,
+      .data$region,
+      .data$date,
+      value = cumsum(.data$value_daily))
+
   ## mb
   mb1 <- read_d("raw_data/static/mb/mb_hosp_admissions_pt_ts.csv") # up to 2022-03-19
   mb2 <- read_d("raw_data/reports/mb/mb_weekly_report.csv") %>%
@@ -640,6 +648,16 @@ assemble_final_datasets <- function() {
   hosp_admissions_mb <- append_daily_d(hosp_admissions_mb, mb3)
   rm(mb1, mb2, mb3) # clean up
 
+  ## on
+  hosp_admissions_on <- read_d("raw_data/reports/on/on_pho_outcomes.csv") |>
+    dplyr::filter(.data$outcome_weekly_type == "COVID-19 hospitalizations" & is.na(.data$sub_region_1)) |>
+    report_pluck("hosp_admissions", "outcome_weekly_value", "value_daily", "pt") |>
+    dplyr::transmute(
+      .data$name,
+      .data$region,
+      .data$date,
+      value = cumsum(.data$value_daily))
+
   ## qc
   hosp_admissions_qc <- read_d("raw_data/active_ts/qc/qc_hosp_admissions_pt_ts.csv") |>
     date_shift(1)
@@ -656,6 +674,14 @@ assemble_final_datasets <- function() {
 
   # icu_admissions dataset
 
+  ## ab
+  icu_admissions_ab <- read_d("raw_data/active_ts/ab/ab_icu_admissions_pt_ts.csv") |>
+    dplyr::transmute(
+      .data$name,
+      .data$region,
+      .data$date,
+      value = cumsum(.data$value_daily))
+
   ## mb
   mb1 <- read_d("raw_data/static/mb/mb_icu_admissions_pt_ts.csv") # up to 2022-03-19
   mb2 <- read_d("raw_data/reports/mb/mb_weekly_report.csv") %>%

diff --git a/R/dl_datasets.R b/R/dl_datasets.R
@@ -22,6 +22,7 @@ dl_datasets <- function() {
       # ab
       "3e4fd9ff-48f9-4de1-a48a-97fd33b68337", NA, NA, # c
       "2a11bbcc-7b43-47d1-952d-437cdc9b2ffb", NA, NA, # c, d
+      "e477791b-bced-4b20-b40b-f8d7629c9b69", NA, NA, # h_a, i_a
       # bc
       # can
       "314c507d-7e48-476e-937b-965499f51e8e", NA, NA, # c, d
@@ -37,6 +38,7 @@ dl_datasets <- function() {
       # nt
       # nu
       # on
+      "75dd0545-f728-4af5-8185-4269596785ef", NA, NA, # d (pt)
       "4b214c24-8542-4d26-a850-b58fc4ef6a30", NA, NA, # h, i
       # pe
       # qc

diff --git a/R/update_raw_datasets.R b/R/update_raw_datasets.R
@@ -84,6 +84,15 @@ update_active_ts <- function(ds) {
   # active_ts - death data
   cat("Updating active_ts: death data", fill = TRUE)
 
+  ## ab
+  Covid19CanadaDataProcess::process_dataset(
+    uuid = "e477791b-bced-4b20-b40b-f8d7629c9b69",
+    val = "mortality",
+    fmt = "prov_ts",
+    ds = load_ds(ds, "e477791b-bced-4b20-b40b-f8d7629c9b69")) %>%
+    add_name_col("deaths") %>%
+    write_ts("active_ts", "ab", "deaths")
+
   ## can
   Covid19CanadaDataProcess::process_dataset(
     uuid = "314c507d-7e48-476e-937b-965499f51e8e",
@@ -93,6 +102,15 @@ update_active_ts <- function(ds) {
     add_name_col("deaths")  %>%
     write_ts("active_ts", "can", "deaths")
 
+  ## on
+  Covid19CanadaDataProcess::process_dataset(
+    uuid = "75dd0545-f728-4af5-8185-4269596785ef",
+    val = "mortality",
+    fmt = "prov_ts",
+    ds = load_ds(ds, "75dd0545-f728-4af5-8185-4269596785ef")) %>%
+    add_name_col("deaths") %>%
+    write_ts("active_ts", "on", "deaths")
+
   ## qc
   Covid19CanadaDataProcess::process_dataset(
     uuid = "3b93b663-4b3f-43b4-a23d-cbf6d149d2c5",
@@ -159,6 +177,14 @@ update_active_ts <- function(ds) {
   # active_ts - hosp_admissions data
   cat("Updating active_ts: hosp admissions data", fill = TRUE)
 
+  ## ab
+  Covid19CanadaDataProcess::process_dataset(
+    uuid = "e477791b-bced-4b20-b40b-f8d7629c9b69",
+    val = "hosp_admissions",
+    fmt = "prov_ts",
+    ds = load_ds(ds, "e477791b-bced-4b20-b40b-f8d7629c9b69")) %>%
+    write_ts("active_ts", "ab", "hosp_admissions")
+
   ## qc
   Covid19CanadaDataProcess::process_dataset(
     uuid = "3b93b663-4b3f-43b4-a23d-cbf6d149d2c5",
@@ -170,6 +196,14 @@ update_active_ts <- function(ds) {
   # active_ts - icu_admissions data
   cat("Updating active_ts: icu admissions data", fill = TRUE)
 
+  ## ab
+  Covid19CanadaDataProcess::process_dataset(
+    uuid = "e477791b-bced-4b20-b40b-f8d7629c9b69",
+    val = "icu_admissions",
+    fmt = "prov_ts",
+    ds = load_ds(ds, "e477791b-bced-4b20-b40b-f8d7629c9b69")) %>%
+    write_ts("active_ts", "ab", "icu_admissions")
+
   ## qc
   Covid19CanadaDataProcess::process_dataset(
     uuid = "3b93b663-4b3f-43b4-a23d-cbf6d149d2c5",