fix

Author: dsweber2

scripts/flu_hosp_prod.R

@@ -16,15 +16,15 @@ end_date <- Sys.Date()
 # today, which is a Wednesday. Sometimes, if we're doing a delayed forecast,
 # it's a Thursday. It's used for stamping the data and for determining the
 # appropriate as_of when creating the forecast.
-forecast_generation_date <- Sys.Date()
+forecast_generation_dates <- Sys.Date()
 # Usually, the forecast_date is the same as the generation date, but you can
 # override this. It should be a Wednesday.
-forecast_date <- round_date(forecast_generation_date, "weeks", week_start = 3)
+forecast_dates <- round_date(forecast_generation_dates, "weeks", week_start = 3)
 # If doing backfill, you can set the forecast_date to a sequence of dates.
-# forecast_date <- seq.Date(as.Date("2024-11-20"), Sys.Date(), by = 7L)
+# forecast_dates <- seq.Date(as.Date("2024-11-20"), Sys.Date(), by = 7L)
 # forecast_generation_date needs to follow suit, but it's more complicated
 # because sometimes we forecast on Thursday.
-# forecast_generation_date <- c(as.Date(c("2024-11-21", "2024-11-27", "2024-12-04", "2024-12-11", "2024-12-18", "2024-12-26", "2025-01-02")), seq.Date(as.Date("2025-01-08"), Sys.Date(), by = 7L))
+# forecast_generation_dates <- c(as.Date(c("2024-11-21", "2024-11-27", "2024-12-04", "2024-12-11", "2024-12-18", "2024-12-26", "2025-01-02")), seq.Date(as.Date("2025-01-08"), Sys.Date(), by = 7L))
 
 # Whether we're running in backtest mode.
 # If TRUE, we don't run the report notebook, which is (a) slow and (b) should be
@@ -167,15 +167,15 @@ rlang::list2(
   tar_map(
     # Because targets relies on R metaprogramming, it loses the Date class.
     values = tibble(
-      forecast_date_int = forecast_date,
-      forecast_generation_date_int = forecast_generation_date,
-      forecast_date_chr = as.character(forecast_date_int)
+      forecast_date_int = forecast_dates,
+      forecast_generation_date_int = forecast_generation_dates,
+      forecast_date_chr = as.character(forecast_dates)
     ),
     names = "forecast_date_chr",
     tar_change(
       name = geo_forecasters_weights,
       command = {
-        geo_forecasters_weights <- parse_prod_weights(here::here("flu_geo_exclusions.csv"), forecast_date_int, forecaster_fns)
+        geo_forecasters_weights <- parse_prod_weights(here::here("flu_geo_exclusions.csv"), forecast_date_int, names(forecaster_fns))
         if (nrow(geo_forecasters_weights %>% filter(forecast_date == as.Date(forecast_date_int))) == 0) {
           cli_abort("there are no weights  for the forecast date {forecast_date}")
         }
@@ -342,25 +342,27 @@ rlang::list2(
     tar_target(
       name = make_submission_csv,
       command = {
-        if (!backtest_mode) {
+        if (!backtest_mode && submission_directory != "cache") {
           combo_ens_climate_linear_window_season %>%
             format_flusight(disease = "flu") %>%
             write_submission_file(
               get_forecast_reference_date(forecast_date_int),
               file.path(submission_directory, "model-output/CMU-TimeSeries")
             )
+        } else {
+          cli_alert_info("Not making submission csv because we're in backtest mode or submission directory is cache")
         }
       }
     ),
     tar_target(
       name = make_climate_submission_csv,
       command = {
-        if (!backtest_mode) {
+        if (!backtest_mode && submission_directory != "cache") {
           forecasts <- forecast_res
           forecasts %>%
             filter(forecaster %in% c("climate_base", "climate_geo_agged")) %>%
             group_by(geo_value, target_end_date, quantile) %>%
-            summarize(forecast_date = first(forecast_date), value = mean(value, na.rm = TRUE), .groups = "drop") %>%
+            summarize(forecast_date = as.Date(forecast_date_int), value = mean(value, na.rm = TRUE), .groups = "drop") %>%
             ungroup() %>%
             filter(!(geo_value %in% excluded_geos)) %>%
             format_flusight(disease = "flu") %>%
@@ -370,6 +372,8 @@ rlang::list2(
               submission_directory = file.path(submission_directory, "model-output/CMU-climate_baseline"),
               file_name = "CMU-climate_baseline"
             )
+        } else {
+          cli_alert_info("Not making climate submission csv because we're in backtest mode or submission directory is cache")
         }
       },
       priority = 0.99
@@ -468,10 +472,11 @@ rlang::list2(
       cue = tar_cue(mode = "always")
     )
   ),
-  tar_target(
-    new_data_notebook,
-    command = {
-      rmarkdown::render("scripts/reports/new_data.Rmd", output_file = here::here("reports", "new_data.html"))
-    }
-  )
+  # TODO
+  # tar_target(
+  #   new_data_notebook,
+  #   command = {
+  #     rmarkdown::render("scripts/reports/new_data.Rmd", output_file = here::here("reports", "new_data.html"))
+  #   }
+  # )
 )