diff --git a/R/assemble_final_datasets.R b/R/assemble_final_datasets.R index e85e826..cfcaf3f 100644 --- a/R/assemble_final_datasets.R +++ b/R/assemble_final_datasets.R @@ -687,9 +687,17 @@ assemble_final_datasets <- function() { ## ns ns1 <- read_d("raw_data/static/ns/ns_hosp_admissions_pt_ts.csv") |> dplyr::mutate(value = cumsum(value_daily)) |> - dplyr::select(-.data$value_daily) - hosp_admissions_ns <- ns1 - rm(ns1) # clean up + dplyr::select(-.data$value_daily) |> + # overlaps with beginning of report + dplyr::filter(date <= as.Date("2022-05-16")) + ns2 <- read_d("raw_data/reports/ns/ns_weekly_report.csv") |> + report_pluck("hosp_admissions", "new_hospitalizations", "value_daily", "pt") |> + dplyr::filter(date >= as.Date("2022-05-23")) + ns3 <- read_d("raw_data/reports/ns/ns_monthly_report.csv") |> + report_pluck("hosp_admissions", "new_hospitalizations", "value_daily", "pt") + hosp_admissions_ns <- append_daily_d(ns1, ns2) + hosp_admissions_ns <- append_daily_d(hosp_admissions_ns, ns3) + rm(ns1, ns2, ns3) # clean up ## on hosp_admissions_on <- read_d("raw_data/reports/on/on_pho_outcomes.csv") |> @@ -759,7 +767,7 @@ assemble_final_datasets <- function() { ## remove regions with extra/alternate data tests_completed_pt <- tests_completed_pt %>% dplyr::filter(!.data$region %in% c( - "AB", "BC", "MB", "NS", "ON", "QC", "SK", "YT")) + "AB", "BC", "MB", "NB", "NS", "ON", "QC", "SK", "YT")) ## add data for provinces where RVDSS data are representative of all tests (MB, NS, SK) tests_completed_pt <- dplyr::bind_rows( @@ -809,6 +817,20 @@ assemble_final_datasets <- function() { tests_completed_pt <- dplyr::bind_rows(tests_completed_pt, bc3) rm(bc1, bc2, bc3) # clean up + ## add NB data + nb1 <- get_phac_d("tests_completed", "NB", keep_up_to_date = TRUE) |> + # avoid overlap with new dataset + dplyr::filter(.data$date <= as.Date("2022-11-19")) + nb2 <- read_d("raw_data/reports/nb/nb_weekly_report.csv") |> + report_pluck("tests_completed", "new_tests_completed", "value_daily", "pt") |> + dplyr::filter(.data$date >= as.Date("2022-11-26")) + nb3 <- read_d("raw_data/reports/nb/nb_weekly_report_2.csv") |> + report_pluck("tests_completed", "tests_completed", "value_daily", "pt") + nb4 <- append_daily_d(nb1, nb2) + nb4 <- append_daily_d(nb4, nb3) + tests_completed_pt <- dplyr::bind_rows(tests_completed_pt, nb4) + rm(nb1, nb2, nb3, nb4) # clean up + ## add ON data on1 <- read_d("raw_data/static/on/on_tests_completed_pt_ts.csv") |> dplyr::filter(.data$date <= as.Date("2023-04-01"))