flu fully funcitonal

Author: dsweber2

R/utils.R

@@ -172,7 +172,8 @@ data_substitutions <- function(dataset, disease, forecast_generation_date) {
 }
 
 parse_prod_weights <- function(filename = here::here("covid_geo_exclusions.csv"),
-                               forecast_date) {
+                               forecast_date_int, forecaster_fns) {
+  forecast_date <- as.Date(forecast_date_int)
   all_states <- c(
     unique(readr::read_csv("https://raw.githubusercontent.com/cmu-delphi/covidcast-indicators/refs/heads/main/_delphi_utils_python/delphi_utils/data/2020/state_pop.csv", show_col_types = FALSE)$state_id),
     "usa", "us"
@@ -196,7 +197,7 @@ parse_prod_weights <- function(filename = here::here("covid_geo_exclusions.csv")
     unnest_longer(forecaster) %>%
     group_by(forecast_date, forecaster, geo_value) %>%
     summarize(weight = min(weight), .groups = "drop") %>%
-    mutate(forecast_date = as.Date(forecast_date)) %>%
+    mutate(forecast_date = as.Date(forecast_date_int)) %>%
     group_by(forecast_date, geo_value) %>%
     mutate(weight = ifelse(near(weight, 0), 0, weight / sum(weight)))
 }

scripts/covid_hosp_prod.R

@@ -78,8 +78,8 @@ rlang::list2(
     tar_target(
       name = geo_forecasters_weights,
       command = {
-        geo_forecasters_weights <- parse_prod_weights(here::here("covid_geo_exclusions.csv"), forecast_date_int)
-        if (nrow(geo_forecasters_weights %>% filter(forecast_date == forecast_date_int)) == 0) {
+        geo_forecasters_weights <- parse_prod_weights(here::here("covid_geo_exclusions.csv"), forecast_date_int, 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}")
         }
         geo_forecasters_weights

scripts/flu_hosp_prod.R

@@ -110,7 +110,8 @@ rlang::list2(
         ) %>%
         filter(version == max(version)) %>%
         select(-version) %>%
-        data_substitutions(disease = "flu")
+        data_substitutions(disease = "flu") %>%
+        as_epi_df(other_keys = "source", as_of = Sys.Date())
     }
   ),
   tar_target(
@@ -129,8 +130,8 @@ rlang::list2(
     tar_target(
       name = geo_forecasters_weights,
       command = {
-        geo_forecasters_weights <- parse_prod_weights(here::here("flu_geo_exclusions.csv"), forecast_date_int)
-        if (nrow(geo_forecasters_weights %>% filter(forecast_date == forecast_date_int)) == 0) {
+        geo_forecasters_weights <- parse_prod_weights(here::here("flu_geo_exclusions.csv"), forecast_date_int, 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}")
         }
         geo_forecasters_weights