From 987b7ccf99612a8f02a222745e96f957d6f8fc13 Mon Sep 17 00:00:00 2001
From: Duncan Gillespie <duncan.gillespie@sheffield.ac.uk>
Date: Thu, 26 Oct 2023 14:02:41 +0100
Subject: [PATCH] review PAF calculations

---
 R/PAFcalc.R         | 8 ++++++--
 R/subgroupRisk.R    | 2 +-
 man/PAFcalc.Rd      | 6 +++++-
 man/subgroupRisk.Rd | 2 +-
 4 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/R/PAFcalc.R b/R/PAFcalc.R
index 05f24ad..be899ac 100644
--- a/R/PAFcalc.R
+++ b/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)
diff --git a/R/subgroupRisk.R b/R/subgroupRisk.R
index 8b45101..02cab1e 100644
--- a/R/subgroupRisk.R
+++ b/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.
 #' 
diff --git a/man/PAFcalc.Rd b/man/PAFcalc.Rd
index e4b011c..706a1a4 100644
--- a/man/PAFcalc.Rd
+++ b/man/PAFcalc.Rd
@@ -21,7 +21,8 @@ PAFcalc(
   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
 )
 }
 \arguments{
@@ -79,6 +80,9 @@ should refer to mortality or morbidity. Values could be "mort" or "morb". Defaul
 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.}
+
+\item{oesoph_subtypes}{Logical - should the attributable fractions for oesophageal cancer 
+be multiplied by the proportions of each subtype. Defaults to FALSE.}
 }
 \value{
 Returns a data.table containing the estimated PAFs.
diff --git a/man/subgroupRisk.Rd b/man/subgroupRisk.Rd
index 41cf3b8..d9ab8f9 100644
--- a/man/subgroupRisk.Rd
+++ b/man/subgroupRisk.Rd
@@ -55,7 +55,7 @@ just tobacco ("tob") or joint risks for tobacco and alcohol ("tobalc").}
 For use only if average risk is stratified by single years of age. Defaults to FALSE}
 
 \item{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.}
 }
 \value{
 Returns a data table containing the subgroup specific summaries for each disease.