add icd10lookups + dev status

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tobalcepi
 Type: Package
 Title: Risk Functions and Attributable Fractions for Tobacco and Alcohol
-Version: 1.2.2
+Version: 1.3.0
 Authors@R: 
     c(
     person(given = "Duncan",
@@ -42,9 +42,10 @@ Imports:
     testthat,
     dplyr,
     data.table,
-    Rdpack
-RdMacros: Rdpack
+    Rdpack,
+    lifecycle
+RdMacros: Rdpack, lifecycle
 VignetteBuilder: knitr
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Depends: 
     R (>= 2.10)

NAMESPACE

@@ -1,18 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
-export(AlcBinge)
-export(AlcBinge_stapm)
-export(AlcLags)
-export(ExpandCodes)
-export(PArisk)
+export("\\lifecycle{experimental}")
+export("\\lifecycle{maturing}")
+export("\\lifecycle{stable}")
 export(RRFunc)
-export(RRTobDR)
-export(RRalc)
-export(RRtob)
 export(TobAlcInt)
-export(TobLags)
-export(WArisk_acute)
-export(subgroupRisk)
 import(data.table)
 importFrom(Rdpack,reprompt)
 importFrom(data.table,":=")

R/AlcBinge.R

@@ -18,6 +18,8 @@
 #' @return Returns data plus the estimated variables.
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{stable}
 #'
 #' @examples
 #'

R/AlcBinge_stapm.R

@@ -27,6 +27,8 @@
 #' @return Returns data plus the estimated variables.
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{maturing}
 #'
 #' @examples
 #'

R/AlcLags.R

@@ -17,6 +17,8 @@
 #' on an individual's relative risk of disease has so far emerged.
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{stable}
 #'
 #' @examples
 #' \dontrun{

R/ExpandCodes.R

@@ -14,6 +14,8 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
+#' \lifecycle{stable}
+#'
 #' @examples
 #'
 #' \dontrun{

R/PArisk.R

@@ -37,6 +37,8 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
+#' \lifecycle{stable}
+#'
 #' @examples
 #' 
 #' \dontrun{

R/RRAlc.R

@@ -37,6 +37,8 @@
 #' @return Returns a numeric vector of each individual's relative risks for the alcohol related disease specified by "disease".
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{stable}
 #'
 #' @examples
 #'

R/RRFunc.R

@@ -111,6 +111,7 @@
 #' @seealso \code{\link{RRalc}} for alcohol-specific risks, \code{\link{RRtob}} for tobacco-specific risks, 
 #' \code{\link{AlcLags}} for alcohol-specific lag times, and \code{\link{TobLags}} for tobacco-specific lag times.
 #' 
+#' \lifecycle{maturing}
 #'
 #' @examples
 #' \dontrun{

R/RRTobDR.R

@@ -17,6 +17,9 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
+#' \lifecycle{experimental}
+#'
+#'
 #' @examples
 #'
 #' \dontrun{

R/RRtob.R

@@ -37,6 +37,8 @@
 #' specified by "disease".
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{maturing}
 #'
 #' @examples
 #'\dontrun{

R/TobAlcInt.R

@@ -33,6 +33,8 @@
 #' 
 #' \insertRef{Prabhu2014}{tobalcepi}  
 #' 
+#' \lifecycle{maturing}
+#' 
 #' @examples 
 #' 
 #' \dontrun{

R/TobLags.R

@@ -38,6 +38,8 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
+#' \lifecycle{stable}
+#'
 #' @examples
 #'
 #' TobLags("Pharynx")

R/WArisk_acute.R

@@ -41,6 +41,8 @@
 #' @return Returns a numeric vector of each individual's relative risk of the acute consequences of drinking.
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{stable}
 #'
 #' @examples
 #' 

R/alc_icd10_lookups.R

@@ -0,0 +1,18 @@
+
+#' Diseases related to alcohol and their ICD-10 defintions
+#'
+#' Deaths in the mortality data are assigned a single ICD-10 code e.g. C00,
+#' but for our analysis we need to group these into cause-groups according to groups e.g. C00-C06.
+#' To do this, we define each group by its consituent ICD-10 codes e.g. C00, C01, C02, C03, C04, C05, C06.
+#'
+#' @docType data
+#'
+#' @format A data table
+#'
+#' @source Our alcohol disease list in the folder PR_Disease_Risk_TA
+#'
+#'
+#'
+#'
+#'
+"alc_icd10_lookups"

R/subgroupRisk.R

@@ -21,6 +21,8 @@
 #' @return Returns a data table containing the subgroup specific summaries for each disease.
 #' @importFrom data.table := setDT setnames
 #' @export
+#' 
+#' \lifecycle{stable}
 #'
 #' @examples
 #' \dontrun{

R/tob_icd10_lookups.R

@@ -0,0 +1,18 @@
+
+#' Diseases related to tobacco and their ICD-10 defintions
+#'
+#' Deaths in the mortality data are assigned a single ICD-10 code e.g. C00,
+#' but for our analysis we need to group these into cause-groups according to groups e.g. C00-C06.
+#' To do this, we define each group by its consituent ICD-10 codes e.g. C00, C01, C02, C03, C04, C05, C06.
+#'
+#' @docType data
+#'
+#' @format A data table
+#'
+#' @source Our tobacco disease list in the folder PR_Disease_Risk_TA
+#'
+#'
+#'
+#'
+#'
+"tob_icd10_lookups"

R/tobalc_icd10_lookups.R

@@ -0,0 +1,18 @@
+
+#' Diseases related to both tobacco and alcohol and their ICD-10 defintions
+#'
+#' Deaths in the mortality data are assigned a single ICD-10 code e.g. C00,
+#' but for our analysis we need to group these into cause-groups according to groups e.g. C00-C06.
+#' To do this, we define each group by its consituent ICD-10 codes e.g. C00, C01, C02, C03, C04, C05, C06.
+#'
+#' @docType data
+#'
+#' @format A data table
+#'
+#' @source Our joint tobacco and alcohol disease list in the folder PR_Disease_Risk_TA
+#'
+#'
+#'
+#'
+#'
+"tobalc_icd10_lookups"

README.Rmd

@@ -19,9 +19,11 @@ knitr::opts_chunk$set(
 ```
 # tobalcepi <img src="tools/tobalcepi_hex.png" align="right" style="padding-left:10px;background-color:white;" width="100" height="100" />
 
+<!-- badges: start -->
+[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)  
+  <!-- badges: end -->
 
-**DRAFT WORKING VERSION** - Some code and documentation is still incomplete or in need of being refined. The code and documentation are still undergoing internal review by the analyst team.   
 
 ## Motivation
 The motivation for `tobalcepi` was to organise how we store, process and use the information on the risks of disease that stem from tobacco and/or alcohol consumption, including to provide functions to easily use these risk estimates in modelling.     

README.md

@@ -3,13 +3,14 @@
 
 # tobalcepi <img src="tools/tobalcepi_hex.png" align="right" style="padding-left:10px;background-color:white;" width="100" height="100" />
 
+<!-- badges: start -->
+
+[![Lifecycle:
+maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
-developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-
-**DRAFT WORKING VERSION** - Some code and documentation is still
-incomplete or in need of being refined. The code and documentation are
-still undergoing internal review by the analyst team.
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)  
+<!-- badges: end -->
 
 ## Motivation
 
@@ -217,8 +218,8 @@ Tobacco and Alcohol. R package version x.x.x.
 
 Angus, Colin, M Henney, L Webster, and Duncan Gillespie. 2018.
 “Alcohol-Attributable Diseases and Dose-Response Curves for the
-Sheffield Alcohol Policy Model Version 4.0.”
-<https://doi.org/10.15131/shef.data.6819689.v1>.
+Sheffield Alcohol Policy Model Version 4.0.” The University of
+Sheffield. <https://doi.org/10.15131/shef.data.6819689.v2>.
 
 </div>
 

_pkgdown.yml

@@ -29,6 +29,7 @@ reference:
 - subtitle: Disease definitions and relative risks
   contents:
   - tob_disease_names
+  - tob_icd10_lookups
   - tobacco_relative_risks
   - RRtob
   - RRTobDR
@@ -41,6 +42,7 @@ reference:
 - subtitle: Disease definitions and relative risks
   contents:
   - alc_disease_names
+  - alc_icd10_lookups
   - RRalc
 - subtitle: Disease risk linked to intoxication
   contents:  
@@ -58,6 +60,7 @@ reference:
   contents:
   - TobAlcInt
   - tob_alc_risk_int
+  - tobalc_icd10_lookups
 
 - title: Misc
   contents:

data-raw/alcohol_disease_names.R

@@ -0,0 +1,58 @@
+
+# This code stores the list of the names of diseases that are attributable to tobacco and alcohol
+
+# doing this helps to keep the formatting of disease names consistent
+
+library(data.table)
+library(readxl)
+
+# Set the file path to point to the University of Sheffield X drive
+root_dir <- "/Volumes/"
+
+
+##########################################
+
+# Load the data 
+
+
+AlcList <- readxl::read_excel(paste0(root_dir, 
+  "ScHARR/PR_Disease_Risk_TA/Code/tables/16102018tobaccoandalcoholDiseaseListandRiskFunctions.xlsx"), 
+  sheet = "Alcohol")
+
+# Set it as a data table
+data.table::setDT(AlcList)
+
+# Columns names to consistent lower case
+setnames(AlcList, colnames(AlcList), tolower(colnames(AlcList)))
+
+##########################################
+
+# Save disease names
+
+alc_disease_names <- as.character(c(unique(AlcList$condition)))
+
+
+usethis::use_data(alc_disease_names, overwrite = T)
+
+##########################################
+
+# Save ICD-10 lookups
+
+# The aim of this code is to prepare lists of tobacco and alcohol related diseases
+# with their corresponding ICD-10 codes
+
+# These data are used to search for the relevant conditions 
+# in the process of preparing the mortality and hospitalisation rates
+# for use in the modelling
+
+
+alc_icd10_lookups <- AlcList[ , c("condition", "icd10_lookups")]
+
+alc_icd10_lookups[stringr::str_detect(condition, "Oesoph"), condition := "Oesophageal"]
+
+alc_icd10_lookups <- unique(alc_icd10_lookups, by = "icd10_lookups")
+
+usethis::use_data(alc_icd10_lookups, overwrite = T)
+
+
+