review PAF calculations

R/PAFcalc.R

@@ -33,6 +33,8 @@
 #' that are not categorised as CVD, COPD, or Cancer. Options: c("Cancers", "CVD", "COPD", "immediate"). 
 #' The default is "Cancers", which gives the most conservative (i.e. slowest) estimate of the rate of decline in 
 #' the risk of disease after quitting smoking.
+#' @param oesoph_subtypes Logical - should the attributable fractions for oesophageal cancer 
+#' be multiplied by the proportions of each subtype. Defaults to FALSE.
 #' 
 #' @return Returns a data.table containing the estimated PAFs.
 #' 
@@ -72,7 +74,8 @@ PAFcalc <- function(
     within_model = FALSE,
     mort_or_morb = c("mort", "morb")[1],
     country = c("England", "Scotland")[1],
-    other_lag_function = "Cancers"
+    other_lag_function = "Cancers",
+    oesoph_subtypes = FALSE
 ) {
 
 
@@ -163,7 +166,8 @@ PAFcalc <- function(
     disease_names = disease_names,
     use_weights = use_weights,
     pool = pool,
-    subgroups = subgroups)
+    subgroups = subgroups,
+    oesoph_subtypes = oesoph_subtypes)
 
 
   return(paf_data)

R/subgroupRisk.R

@@ -28,7 +28,7 @@
 #' @param smooth Logical - should the age patterns in average risk be smoothed with a moving average. 
 #' For use only if average risk is stratified by single years of age. Defaults to FALSE
 #' @param oesoph_subtypes Logical - should the attributable fractions for oesophageal cancer 
-#' be multiplied by the proportions of each subtype. In development. Defaults to FALSE.
+#' be multiplied by the proportions of each subtype. Defaults to FALSE.
 #'
 #' @return Returns a data table containing the subgroup specific summaries for each disease.
 #'