Add use_percentage flag to EpiAutoGPInput and output logic

Introduces a use_percentage boolean field to EpiAutoGPInput to distinguish between raw counts and percentage-based input for ED visits. Updates output logic to set the variable name and convert values to proportions when use_percentage is true for nssp targets. Test cases and input construction are updated accordingly.

EpiAutoGP/src/input.jl

@@ -23,6 +23,7 @@ struct EpiAutoGPInput
     pathogen::String
     location::String
     target::String
+    use_percentage::Bool
     forecast_date::Date
     nowcast_dates::Vector{Date}
     nowcast_reports::Vector{Vector{Real}}

EpiAutoGP/src/output.jl

@@ -205,11 +205,20 @@ function create_forecast_output(
     # Create basic forecast DataFrame with date, .draw, .value
     forecast_df = create_forecast_df(results, output_type)
 
-    # Determine variable name based on target
+    # Determine variable name based on target and whether using percentages
     variable_name = if input.target == "nhsn"
         "observed_hospital_admissions"
     else  # nssp
-        "observed_ed_visits"
+        if input.use_percentage
+            "prop_disease_ed_visits"
+        else
+            "observed_ed_visits"
+        end
+    end
+
+    # Convert percentage to proportion if needed (R expects proportions for prop_ variables)
+    if input.use_percentage && input.target == "nssp"
+        forecast_df[!, Symbol(".value")] = forecast_df[!, Symbol(".value")] ./ 100.0
     end
 
     # Add .variable and resolution columns

EpiAutoGP/test/test_input.jl

@@ -11,7 +11,7 @@ function create_sample_input(output_path::String; n_weeks::Int = 30,
                        for _ in 1:10]  # 10 realizations, each with 3 values
 
     input_data = EpiAutoGPInput(
-        dates, reports, pathogen, location, "nhsn",
+        dates, reports, pathogen, location, "nhsn", false,
         forecast_date, nowcast_dates, nowcast_reports
     )
 
@@ -31,7 +31,7 @@ end
         nowcast_reports = [[50.0, 36.0], [52.0, 38.0]]
 
         input_data = EpiAutoGPInput(
-            dates, reports, "COVID-19", "CA", "nhsn",
+            dates, reports, "COVID-19", "CA", "nhsn", false,
             Date("2024-01-03"), dates[2:3], nowcast_reports
         )
 
@@ -50,7 +50,7 @@ end
         valid_data = EpiAutoGPInput(
             [Date("2024-01-01"), Date("2024-01-02")],
             [45.0, 52.0],
-            "COVID-19", "CA", "nhsn",
+            "COVID-19", "CA", "nhsn", false,
             Date("2024-01-02"),
             [Date("2024-01-02")],
             [[50.0], [52.0]]
@@ -59,7 +59,7 @@ end
 
         # Test without nowcasts
         no_nowcast = EpiAutoGPInput(
-            [Date("2024-01-01")], [10.0], "COVID-19", "TX", "nhsn",
+            [Date("2024-01-01")], [10.0], "COVID-19", "TX", "nhsn", false,
             Date("2024-01-01"), Date[], Vector{Real}[]
         )
         @test validate_input(no_nowcast) == true
@@ -69,29 +69,29 @@ end
         # Mismatched lengths
         @test_throws ArgumentError validate_input(EpiAutoGPInput(
             [Date("2024-01-01"), Date("2024-01-02")], [45.0],
-            "COVID-19", "CA", "nhsn", Date("2024-01-01"), Date[], Vector{Real}[]
+            "COVID-19", "CA", "nhsn", false, Date("2024-01-01"), Date[], Vector{Real}[]
         ))
 
         # Empty data
         @test_throws ArgumentError validate_input(EpiAutoGPInput(
-            Date[], Real[], "COVID-19", "CA", "nhsn", Date("2024-01-01"), Date[], Vector{Real}[]
+            Date[], Real[], "COVID-19", "CA", "nhsn", false, Date("2024-01-01"), Date[], Vector{Real}[]
         ))
 
         # Unsorted dates
         @test_throws ArgumentError validate_input(EpiAutoGPInput(
             [Date("2024-01-02"), Date("2024-01-01")], [45.0, 52.0],
-            "COVID-19", "CA", "nhsn", Date("2024-01-02"), Date[], Vector{Real}[]
+            "COVID-19", "CA", "nhsn", false, Date("2024-01-02"), Date[], Vector{Real}[]
         ))
 
         # Invalid nowcast structure
         @test_throws ArgumentError validate_input(EpiAutoGPInput(
-            [Date("2024-01-01")], [45.0], "COVID-19", "CA", "nhsn", Date("2024-01-01"),
+            [Date("2024-01-01")], [45.0], "COVID-19", "CA", "nhsn", false, Date("2024-01-01"),
             [Date("2024-01-01")], [[50.0, 55.0]]  # Wrong length
         ))
 
         # Negative values
         @test_throws ArgumentError validate_input(EpiAutoGPInput(
-            [Date("2024-01-01")], [-5.0], "COVID-19", "CA", "nhsn", Date("2024-01-01"), Date[], Vector{Real}[]
+            [Date("2024-01-01")], [-5.0], "COVID-19", "CA", "nhsn", false, Date("2024-01-01"), Date[], Vector{Real}[]
         ))
     end
 
@@ -104,6 +104,7 @@ end
                 "pathogen" => "COVID-19",
                 "location" => "CA",
                 "target" => "nhsn",
+                "use_percentage" => false,
                 "forecast_date" => "2024-01-02",
                 "nowcast_dates" => ["2024-01-02"],
                 "nowcast_reports" => [[50.0], [55.0]]

EpiAutoGP/test/test_modelling.jl

@@ -15,7 +15,7 @@
         end
 
         return EpiAutoGPInput(
-            dates, reports, "COVID-19", "US", "nhsn",
+            dates, reports, "COVID-19", "US", "nhsn", false,
             dates[end], nowcast_dates, nowcast_reports
         )
     end

EpiAutoGP/test/test_output.jl

@@ -45,6 +45,7 @@ end
             "COVID-19",
             "CA",
             "nhsn",
+            false,
             Date("2024-01-01"),
             Date[],
             Vector{Real}[]