hotfix: data subs, make Makefile commands consistent

Author: dshemetov

Makefile

@@ -60,7 +60,7 @@ submit-flu-dry:
 
 submit: submit-covid submit-flu
 
-get_nwss:
+get-nwss:
 	mkdir -p aux_data/nwss_covid_data; \
 	mkdir -p aux_data/nwss_flu_data; \
 	. .venv/bin/activate; \
@@ -90,14 +90,14 @@ upload: push
 dashboard:
 	Rscript scripts/dashboard.R
 
-update_site:
+update-site:
 	Rscript -e "suppressPackageStartupMessages(source(here::here('R', 'load_all.R'))); update_site()" > cache/update_site_log.txt
 
 netlify:
 	netlify deploy --dir=reports --prod
 
-get_flu_prod_errors:
+get-flu-prod-errors:
 	Rscript -e "suppressPackageStartupMessages(source(here::here('R', 'load_all.R'))); get_targets_errors(project = 'flu_hosp_prod')"
 
-get_covid_prod_errors:
+get-covid-prod-errors:
 	Rscript -e "suppressPackageStartupMessages(source(here::here('R', 'load_all.R'))); get_targets_errors(project = 'covid_hosp_prod')"

covid_data_substitutions.csv

@@ -6,4 +6,4 @@ sd, 2025-03-05, 2025-02-26, 35
 ak, 2025-03-26, 2025-03-19, 15
 ar, 2025-03-26, 2025-03-19, 85
 ky, 2025-03-26, 2025-03-19, 130
-nj, 2025-03-26, 2025-03-19, 270
+nj, 2025-03-26, 2025-03-19, 270

covid_geo_exclusions.csv

@@ -12,6 +12,21 @@ forecast_date,forecaster,geo_value,weight
 2024-10-01, climate_geo_agged, all, 0.5
 2024-10-01, climate_quantile_extrapolated, all, 0
 ##################
+# April 2
+##################
+2025-04-02, all, mp, 0
+2025-04-02, windowed_seasonal, all, 0.0001
+2025-04-02, windowed_seasonal_extra_sources, all, 3
+2025-04-02, climate_linear, all, 0.0001
+2025-04-02, linear, all, 3
+2025-04-02, linearlog, all, 0
+2025-04-02, climate_base, all, 2
+2025-04-02, climate_geo_agged, all, 0.5
+2025-04-02, climate_quantile_extrapolated, all, 0
+# Make ar_only the most important for dc
+2025-04-02, windowed_seasonal, dc, 5
+2025-04-02, windowed_seasonal_extra_sources, dc, 5
+##################
 # March 26
 ##################
 2025-03-26, all, mp, 0

flu_data_substitutions.csv

@@ -19,3 +19,4 @@ dc, 2025-03-05, 2025-02-19, 130
 hi, 2025-03-05, 2025-02-26, 70
 nj, 2025-03-26, 2025-03-19, 260
 tn, 2025-03-26, 2025-03-19, 430
+nh, 2025-04-02, 2025-03-22, 80

scripts/build_nhsn_archive.R

@@ -33,6 +33,7 @@ suppressPackageStartupMessages({
 # Suppresses read_csv progress and column type messages
 options(readr.show_progress = FALSE)
 options(readr.show_col_types = FALSE)
+options(cli.width = 120)
 
 # Script run time
 run_time <- with_tz(Sys.time(), tzone = "UTC")
@@ -154,7 +155,7 @@ process_nhsn_data_file <- function(key) {
 #' day. The archive has the columns geo_value, time_value, disease, endpoint
 #' (either basic or prelim), version, version_timestamp (to enable keeping the
 #' most recent value), and value.
-update_nhsn_data_archive <- function(verbose = FALSE) {
+update_nhsn_data_archive <- function() {
   # Get the last timestamp of the archive
   last_timestamp <- get_s3_object_last_modified(config$archive_s3_key, config$s3_bucket)
 
@@ -181,12 +182,11 @@ update_nhsn_data_archive <- function(verbose = FALSE) {
     return(invisible(NULL))
   }
 
-  cli_inform("New datasets available at {run_time_local} (UTC: {run_time}).")
-  cli_inform("Adding {nrow(new_data_files_latest_per_day)} new NHSN datasets to the archive.")
+  cli_inform("New datasets available at, adding {nrow(new_data_files_latest_per_day)} new NHSN datasets to the archive.")
 
   # Process each new dataset snapshot
   new_data <- new_data_files_latest_per_day$Key %>%
-    map(process_nhsn_data_file, .progress = verbose) %>%
+    map(process_nhsn_data_file, .progress = interactive()) %>%
     bind_rows()
 
   # Look through the existing archive to see if there were updates today. If so, replace them with the new data.
@@ -204,12 +204,11 @@ update_nhsn_data_archive <- function(verbose = FALSE) {
 }
 
 update_nhsn_data <- function(verbose = FALSE) {
-  options(cli.width = 120)
   if (verbose) {
     cli_inform(glue("Checking for updates to NHSN data at {run_time_local} (UTC: {run_time})..."))
   }
   update_nhsn_data_raw()
-  update_nhsn_data_archive(verbose = verbose)
+  update_nhsn_data_archive()
 }
 
-update_nhsn_data(verbose = TRUE)
+update_nhsn_data(verbose = TRUE)