fix: tweaks for prod

dshemetov · dshemetov · commit 995be7b39fc5 · 2025-03-05T15:41:20.000-08:00
* update exclusions and subs
* fix geo_values == c() bug
* fix timezone issues
diff --git a/covid_data_substitutions.csv b/covid_data_substitutions.csv
@@ -2,3 +2,4 @@ geo_value, forecast_date, time_value, value
 nh, 2025-01-15, 2025-01-11, 150
 dc, 2025-02-19, 2025-02-15, 18
 ga, 2025-02-19, 2025-02-15, 210
+sd, 2025-03-05, 2025-02-26, 35
diff --git a/covid_geo_exclusions.csv b/covid_geo_exclusions.csv
@@ -3,15 +3,27 @@ forecast_date,forecaster,geo_value,weight
 # defaults
 ##################
 2024-10-01, all, mp, 0
-2024-10-01, windowed_seasonal, all, 0
+2024-10-01, windowed_seasonal, all, 0.0001
 2024-10-01, windowed_seasonal_extra_sources, all, 3
-2024-10-01, climate_linear, all, 3
+2024-10-01, climate_linear, all, 0.0001
 2024-10-01, linear, all, 3
 2024-10-01, linearlog, all, 0
 2024-10-01, climate_base, all, 2
 2024-10-01, climate_geo_agged, all, 0.5
 2024-10-01, climate_quantile_extrapolated, all, 0
 ##################
+# March 5th
+##################
+2025-03-05, all, mp, 0
+2025-03-05, windowed_seasonal, all,  0.0001
+2025-03-05, windowed_seasonal_extra_sources, all, 3
+2025-03-05, climate_linear, all, 0.0001
+2025-03-05, linear, all, 3
+2025-03-05, linearlog, all, 0
+2025-03-05, climate_base, all, 2
+2025-03-05, climate_geo_agged, all, 0.5
+2025-03-05, climate_quantile_extrapolated, all, 0
+##################
 # Feb 26
 ##################
 2025-02-26, all, mp, 0
diff --git a/flu_data_substitutions.csv b/flu_data_substitutions.csv
@@ -14,3 +14,6 @@ nm, 2025-02-19, 2025-02-12, 170
 ok, 2025-02-19, 2025-02-12, 600
 dc, 2025-02-26, 2025-02-12, 160
 dc, 2025-02-26, 2025-02-19, 130
+dc, 2025-03-05, 2025-02-12, 160
+dc, 2025-03-05, 2025-02-19, 130
+hi, 2025-03-05, 2025-02-26, 70
diff --git a/flu_geo_exclusions.csv b/flu_geo_exclusions.csv
@@ -12,6 +12,18 @@ forecast_date,forecaster,geo_value,weight
 2024-10-01, climate_geo_agged, all, 0.25
 2024-10-01, climate_quantile_extrapolated, all, 0
 ##################
+# March 5th
+##################
+2025-03-05, all, mp, 0
+2025-03-05, windowed_seasonal, all, 3
+2025-03-05, windowed_seasonal_extra_sources, all, 3
+2025-03-05, climate_linear, all, 3
+2025-03-05, linear, all, 2
+2025-03-05, linearlog, all, 0
+2025-03-05, climate_base, all, 0.5
+2025-03-05, climate_geo_agged, all, 0.25
+2025-03-05, climate_quantile_extrapolated, all, 0
+##################
 # Feb 26
 ##################
 2025-02-26, all, mp, 0
diff --git a/reports/template.md b/reports/template.md
@@ -27,7 +27,14 @@ Simplistic/low data methods:
 - [Flu flatline](flu-notebook-flatline.html)
 - [Flu climate](flu-notebook-climate_linear.html)
 
-### Covid
+### Covid (new)
+
+- [Covid AR with population scaling](covid-notebook-scaled_pop_main.html)
+- [Covid AR with population scaling and seasonal features](covid-notebook-scaled_pop_season.html)
+- [Covid AR with population scaling, and exogenous features](covid-notebook-scaled_pop_exogenous.html)
+- [Covid Flatline](covid-notebook-flatline_forecaster.html)
+
+### Covid (old)
 
 - [Covid AR with population scaling](covid-notebook-1.html)
 - [Covid AR with population scaling and smoothed features](covid-notebook-2.html)
diff --git a/scripts/build_nhsn_archive.R b/scripts/build_nhsn_archive.R
@@ -37,7 +37,7 @@ options(readr.show_col_types = FALSE)
 
 # Script run time
 run_time <- with_tz(Sys.time(), tzone = "UTC")
-run_time_local <- with_tz(run_time, tzone = "America/New_York")
+run_time_local <- with_tz(run_time)
 
 # Configuration
 config <- list(
diff --git a/scripts/covid_hosp_prod.R b/scripts/covid_hosp_prod.R
@@ -86,7 +86,7 @@ forecaster_fns <- list2(
       ) %>%
       mutate(target_end_date = target_end_date + 3) %>%
       # Wyoming has no data for NSSP since July 2024
-      filter(geo_value != c("mo", "usa", "wy"))
+      filter(geo_value %nin% c("mo", "usa", "wy"))
     fcst
   }
 )
diff --git a/scripts/flu_hosp_prod.R b/scripts/flu_hosp_prod.R
@@ -98,7 +98,7 @@ forecaster_fns <- list2(
       ) %>%
       select(-source) %>%
       mutate(target_end_date = target_end_date + 3) %>%
-      filter(geo_value != c("mo", "us", "wy"))
+      filter(geo_value %nin% c("mo", "us", "wy"))
     fcst
   }
 )

Original file line number	Diff line number	Diff line change
`@@ -86,7 +86,7 @@ forecaster_fns <- list2(`
`86`	`86`	`) %>%`
`87`	`87`	`mutate(target_end_date = target_end_date + 3) %>%`
`88`	`88`	`# Wyoming has no data for NSSP since July 2024`
`89`		`- filter(geo_value != c("mo", "usa", "wy"))`
	`89`	`+ filter(geo_value %nin% c("mo", "usa", "wy"))`
`90`	`90`	`fcst`
`91`	`91`	`}`
`92`	`92`	`)`
Original file line number	Diff line number	Diff line change
`@@ -98,7 +98,7 @@ forecaster_fns <- list2(`
`98`	`98`	`) %>%`
`99`	`99`	`select(-source) %>%`
`100`	`100`	`mutate(target_end_date = target_end_date + 3) %>%`
`101`		`- filter(geo_value != c("mo", "us", "wy"))`
	`101`	`+ filter(geo_value %nin% c("mo", "us", "wy"))`
`102`	`102`	`fcst`
`103`	`103`	`}`
`104`	`104`	`)`