separate variables in code for clarity

R/create.R

@@ -144,20 +144,20 @@ create_shifted_cases <- function(reported_cases, shift,
                                  smoothing_window, horizon) {
   shifted_reported_cases <- data.table::copy(reported_cases)[
     ,
-    confirm := data.table::shift(confirm,
+    shifted := data.table::shift(confirm,
       n = shift,
       type = "lead", fill = NA
     )
   ][
     ,
-    confirm := runner::mean_run(
-      confirm, k = smoothing_window, lag = -floor(smoothing_window / 2)
+    smoothed := runner::mean_run(
+      shifted, k = smoothing_window, lag = -floor(smoothing_window / 2)
     )
   ]
 
   ## Forecast trend on reported cases using the last week of data
   final_week <- data.table::data.table(
-  confirm = shifted_reported_cases[1:(.N - horizon - shift)][
+  confirm = shifted_reported_cases[1:(.N - horizon)][
       max(1, .N - 6):.N]$confirm)[,
     t := seq_len(.N)
   ][
@@ -180,7 +180,7 @@ create_shifted_cases <- function(reported_cases, shift,
     confirm := data.table::fifelse(
       t >= 7,
       exp(lm_model$coefficients[1] + lm_model$coefficients[2] * t),
-      confirm
+      smoothed
     )
   ][, t := NULL]
 
@@ -189,7 +189,11 @@ create_shifted_cases <- function(reported_cases, shift,
    confirm := ceiling(confirm)
   ]
   shifted_reported_cases <- shifted_reported_cases[-(1:smoothing_window)]
-  return(shifted_reported_cases)
+  shifted_reported_cases <- shifted_reported_cases[,
+    shifted := NULL][,
+    smoothed := NULL
+  ]
+  return(shifted_reported_cases[])
 }
 
 #' Construct the Required Future Rt assumption