Update to packages needed

R/3_test_spatial_models.R

@@ -46,13 +46,13 @@ test_model_date_shuffle(
   raw_hospital_counts = hospital_counts,             #Raw hospital data
   raw_ww_data = ww_data,                             #Raw wastewater data
   pop_data,                                          #Population by catchment
-  sites = "1;7;22",                                  #If listing individual sites, combine with ; (i.e. 2;3;4)
+  sites = "all",                                     #If listing individual sites, combine with ; (i.e. 2;3;4)
   WA_population = 7786000,                           #WA population
   forecast_horizon = 28,                             #Number of days you are going to predict to
   spatial = facility_distance,                       #Spatial data values
   calibration_time = 90,                             #How long we want to calibrate for
   repeats = 10,                                      #How many shuffles of data we want to repeat this on
-  savename = "rapid_test",                           #Savename modifier for file output
+  savename = "full_run",                             #Savename modifier for file output
   fit_options = fit_this
 )
 

figs/date_shuffle/full_run/key.csv

@@ -0,0 +1,11 @@
+"sites","forecast_horizon","calibration_time","repeats","savename","random_dates"
+"all",28,90,10,"full_run",2022-12-14
+"all",28,90,10,"full_run",2022-11-27
+"all",28,90,10,"full_run",2023-03-24
+"all",28,90,10,"full_run",2022-11-30
+"all",28,90,10,"full_run",2023-04-02
+"all",28,90,10,"full_run",2022-12-19
+"all",28,90,10,"full_run",2022-12-10
+"all",28,90,10,"full_run",2022-11-25
+"all",28,90,10,"full_run",2022-12-11
+"all",28,90,10,"full_run",2023-01-23

figs/date_shuffle/rapid_test/key.csv

@@ -1,11 +1,11 @@
 "sites","forecast_horizon","calibration_time","repeats","savename","random_dates"
-"1;7;22",28,90,10,"rapid_test",2023-01-08
-"1;7;22",28,90,10,"rapid_test",2023-04-17
-"1;7;22",28,90,10,"rapid_test",2023-03-10
-"1;7;22",28,90,10,"rapid_test",2023-04-12
-"1;7;22",28,90,10,"rapid_test",2022-12-14
-"1;7;22",28,90,10,"rapid_test",2022-11-15
-"1;7;22",28,90,10,"rapid_test",2022-12-22
-"1;7;22",28,90,10,"rapid_test",2023-01-25
-"1;7;22",28,90,10,"rapid_test",2022-11-22
-"1;7;22",28,90,10,"rapid_test",2023-02-15
+"all",28,90,10,"rapid_test",2023-01-08
+"all",28,90,10,"rapid_test",2023-04-17
+"all",28,90,10,"rapid_test",2023-03-10
+"all",28,90,10,"rapid_test",2023-04-12
+"all",28,90,10,"rapid_test",2022-12-14
+"all",28,90,10,"rapid_test",2022-11-15
+"all",28,90,10,"rapid_test",2022-12-22
+"all",28,90,10,"rapid_test",2023-01-25
+"all",28,90,10,"rapid_test",2022-11-22
+"all",28,90,10,"rapid_test",2023-02-15