add new option to functions

R/PAFcalc.R

@@ -29,6 +29,10 @@
 #' @param mort_or_morb Character string - whether the risk functions for conditions with separate mortality and morbidity risk functions 
 #' should refer to mortality or morbidity. Values could be "mort" or "morb". Default is "mort".
 #' @param country Character string - "England" or "Scotland"
+#' @param other_lag_function Character - the name of the lag function to use for tobacco related conditions 
+#' 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.
 #' 
 #' @return Returns a data.table containing the estimated PAFs.
 #' 
@@ -67,7 +71,8 @@ PAFcalc <- function(
     tobalc_include_int = FALSE,
     within_model = FALSE,
     mort_or_morb = c("mort", "morb")[1],
-    country = c("England", "Scotland")[1]
+    country = c("England", "Scotland")[1],
+    other_lag_function = "Cancers"
 ) {
 
 
@@ -113,7 +118,8 @@ PAFcalc <- function(
         show_progress = TRUE,
         within_model = within_model,
         tobalc_include_int = tobalc_include_int,
-        country = country)
+        country = country,
+        other_lag_function = other_lag_function)
 
       if(y == years[1]) {
 

R/RRFunc.R

@@ -102,6 +102,10 @@
 #' there is a version that suits the STAPM model by using only the age, sex and IMD quintile variables 
 #' that are tracked within the STAPM model simulation.
 #' @param country Character string - "England" or "Scotland"
+#' @param other_lag_function Character - the name of the lag function to use for tobacco related conditions 
+#' 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.
 #' 
 #' @return Two data tables are returned:
 #' \itemize{
@@ -224,7 +228,9 @@
 #'   data = data,
 #'   substance = "tob",
 #'   tob_diseases = tob_disease_names,
-#'   show_progress = TRUE
+#'   show_progress = TRUE,
+#'   other_lag_function = "Cancers"
+#'   
 #' )
 #'
 #'
@@ -250,7 +256,8 @@ RRFunc <- function(
     tobalc_int_data = tobalcepi::tob_alc_risk_int,
     show_progress = FALSE,
     within_model = TRUE,
-    country = c("England", "Scotland")[1]
+    country = c("England", "Scotland")[1],
+    other_lag_function = "Cancers"
 ) {
 
 
@@ -712,7 +719,7 @@ RRFunc <- function(
       # Matching on the time since quit
       data <- merge(
         data,
-        tobalcepi::TobLags(d),
+        tobalcepi::TobLags(d, other_lag_function = other_lag_function),
         by = "time_since_quit", all.x = T, all.y = F, sort = F)
 
       data[is.na(prop_risk_reduction), prop_risk_reduction := 0L]

R/TobLags.R

@@ -51,9 +51,13 @@
 #' 
 #'
 #' @examples
-#'
+#' \dontrun{
 #' TobLags("Pharynx")
-#'
+#' 
+#' TobLags("Low_back_pain", other_lag_function = "immediate")
+#' TobLags("Low_back_pain", other_lag_function = "CVD")
+#' TobLags("Low_back_pain", other_lag_function = "Cancers")
+#'}
 TobLags <- function(
     disease_name = c("Pharynx", "Oral_cavity"),
     n_years = 40,