Use clinelist rather than truncated_linelist

R/observe.R

@@ -24,19 +24,19 @@ observe_process <- function(linelist) {
   return(clinelist)
 }
 
-#' Filter observations based on a observation time of secondary events
+#' Filter observations based on the observation time of secondary events
 #' 
 #' @family observe
 #' @export
 filter_obs_by_obs_time <- function(linelist, obs_time) {
-  truncated_linelist <- data.table::copy(linelist)
-  truncated_linelist[, obs_at := obs_time]
-  truncated_linelist[, obs_time := obs_time - ptime]
-  truncated_linelist[, censored_obs_time := obs_at - ptime_lwr]
-  truncated_linelist[, censored := "interval"]
-  truncated_linelist <- truncated_linelist[stime_upr <= obs_at]
+  clinelist <- data.table::copy(linelist)
+  clinelist[, obs_at := obs_time]
+  clinelist[, obs_time := obs_time - ptime]
+  clinelist[, censored_obs_time := obs_at - ptime_lwr]
+  clinelist[, censored := "interval"]
+  clinelist <- clinelist[stime_upr <= obs_at]
 
-  return(truncated_linelist)
+  return(clinelist)
 }
 
 #' Filter observations based on the observation time of primary events
@@ -48,28 +48,29 @@ filter_obs_by_ptime <- function(linelist, obs_time,
   obs_at <- match.arg(obs_at)
 
   pfilt_t <- obs_time
-  truncated_linelist <- data.table::copy(linelist)
+  clinelist <- data.table::copy(linelist)
 
-  truncated_linelist[, censored := "interval"]
-  truncated_linelist <- truncated_linelist[ptime_upr <= pfilt_t]
+  clinelist[, censored := "interval"]
+  clinelist <- clinelist[ptime_upr <= pfilt_t]
 
   if (obs_at == "obs_secondary") {
     # Update observation time to be the same as the maximum secondary time
-    truncated_linelist[, obs_at := stime_upr]
+    clinelist[, obs_at := stime_upr]
   } else if (obs_at == "max_secondary") {
-    truncated_linelist[, obs_at := stime_upr |> max() |> ceiling()] 
+    clinelist[, obs_at := stime_upr |> max() |> ceiling()] 
   }
 
   # make observation time as specified
-  truncated_linelist[, obs_time := obs_at - ptime]
+  clinelist[, obs_time := obs_at - ptime]
   # Assuming truncation at the beginning of the censoring window
-  truncated_linelist[, censored_obs_time := obs_at - ptime_lwr]
+  clinelist[, censored_obs_time := obs_at - ptime_lwr]
 
   # set observation time to artifial observation time
   if (obs_at == "obs_secondary") {
-    truncated_linelist[, obs_at := pfilt_t]
+    clinelist[, obs_at := pfilt_t]
   }
-  return(truncated_linelist)
+
+  return(clinelist)
 }
 
 #' Pad zero observations as unstable in a lognormal distribution