fix issue with 54 instead of 52 tob disease names

STAPM · Nov 25, 2020 · bdde600 · bdde600
1 parent f40146b
commit bdde600
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tobalcepi
 Type: Package
 Title: Risk Functions and Attributable Fractions for Tobacco and Alcohol
-Version: 1.2.0
+Version: 1.2.1
 Authors@R: 
     c(
     person(given = "Duncan",
@@ -41,7 +41,9 @@ Imports:
     readxl,
     testthat,
     dplyr,
-    data.table
+    data.table,
+    Rdpack
+RdMacros: Rdpack
 VignetteBuilder: knitr
 RoxygenNote: 7.1.0
 Depends: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,6 +14,7 @@ export(TobLags)
 export(WArisk_acute)
 export(subgroupRisk)
 import(data.table)
+importFrom(Rdpack,reprompt)
 importFrom(data.table,":=")
 importFrom(data.table,setDT)
 importFrom(data.table,setnames)
diff --git a/R/AlcBinge.R b/R/AlcBinge.R
@@ -3,7 +3,7 @@
 #'
 #' Designed to work with cross-sectional survey data with a wide range of individual-level covariates. 
 #' Uses survey data and previously estimated coefficients to describe
-#' the patterns of single occassion drinking.
+#' the patterns of single occasion drinking.
 #'
 #' This is based on a study by Hill-McManus 2014,
 #' who analysed drinking occasions using data from detailed diaries in the National Diet and Nutrition Survey 2000/2001.

diff --git a/R/tob_disease_names.R b/R/tob_disease_names.R
@@ -1,16 +1,14 @@
 
 #' Names of tobacco-related diseases
 #'
-#'
+#' @importFrom Rdpack reprompt
 #'
 #' @docType data
 #'
-#' @format A data table
-#'
-#' @source 
-#'
-#'
-#'
+#' @format A character vector containing the names of the 52 disease categories 
+#' of smoking related diseases \insertCite{webster2018risk;textual}{tobalcepi}.
 #'
+#' @references
+#' \insertRef{webster2018risk}{tobalcepi}
 #'
 "tob_disease_names"
diff --git a/R/tobacco_relative_risks.R b/R/tobacco_relative_risks.R
@@ -1,16 +1,14 @@
 
 #' Tobacco relative risks
 #'
-#'
+#' @importFrom Rdpack reprompt
 #'
 #' @docType data
 #'
-#' @format A data table
-#'
-#' @source 
-#'
-#'
-#'
+#' @format A data table containing the relative risks of 52 disease categories 
+#' for current vs. never smokers \insertCite{webster2018risk;textual}{tobalcepi}.
 #'
+#' @references
+#' \insertRef{webster2018risk}{tobalcepi}
 #'
 "tobacco_relative_risks"
diff --git a/README.Rmd b/README.Rmd
@@ -1,6 +1,6 @@
 ---
 output: github_document
-bibliography: disease-risks.bib
+bibliography: inst/REFERENCES.bib
 link-citations: yes
 citation_package: natbib
 biblio-style: vancouver
@@ -29,7 +29,7 @@ The motivation for `tobalcepi` was to organise how we store, process and use the
 `tobalcepi` was created as part of a programme of work on the health economics of tobacco and alcohol at the School of Health and Related Research (ScHARR), The University of Sheffield. This programme is based around the development of the Sheffield Tobacco and Alcohol Policy Modelling (STAPM), which aims to use comparable methodologies to evaluate the impacts of tobacco and alcohol policies, and investigate the consequences of clustering and interactions between tobacco and alcohol consumption behaviours.    
 
 ## Relative risk data
-The disease lists and risk functions in this package all have published sources, which we have referenced. We store the master files for our tobacco and alcohol disease lists and risk functions sources in the University of Sheffield folder `X:/ScHARR/PR_Disease_Risk_TA/Disease_Lists`. In order to obtain mathematical descriptions of the risk functions for use in modelling, we needed to contact some authors to ask for additional information.     
+The disease lists and risk functions in this package all have published sources, which we have referenced. We store the master files for our tobacco and alcohol disease lists and risk functions sources in the University of Sheffield folder `X:/ScHARR/PR_Disease_Risk_TA/Code/tables`. In order to obtain mathematical descriptions of the risk functions for use in modelling, we needed to contact some authors to ask for additional information.     
 
 ### Alcohol
 The high-level function for alcohol is `tobalcepi::RRalc()`, which calculates individual risks of diseases as follows:  

diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ The disease lists and risk functions in this package all have published
 sources, which we have referenced. We store the master files for our
 tobacco and alcohol disease lists and risk functions sources in the
 University of Sheffield folder
-`X:/ScHARR/PR_Disease_Risk_TA/Disease_Lists`. In order to obtain
+`X:/ScHARR/PR_Disease_Risk_TA/Code/tables`. In order to obtain
 mathematical descriptions of the risk functions for use in modelling, we
 needed to contact some authors to ask for additional information.
 

diff --git a/data-raw/disease_names.R b/data-raw/disease_names.R
@@ -9,12 +9,7 @@ library(readxl)
 # Set the file path to point to the University of Sheffield X drive
 root_dir <- "/Volumes/"
 
-# Load the master spreadsheet containing disease risks
-TobList <- readxl::read_excel(paste0(root_dir, "ScHARR/PR_Disease_Risk_TA/Code/tables/16102018tobaccoandalcoholDiseaseListandRiskFunctions.xlsx"), sheet = "Tobacco")
 
-tob_disease_names <- as.character(c(unique(TobList$condition)))
-
-usethis::use_data(tob_disease_names, overwrite = T)
 
 
 

diff --git a/data-raw/tobacco_relative_risks.R b/data-raw/tobacco_relative_risks.R
@@ -1,6 +1,9 @@
 
 # This code reads and processes the relative risks for tobacco
-# They are stored in X:/ScHARR/PR_Disease_Risk_TA/Code/tables
+# for current vs. never smokers
+
+# They are stored in a master spreadsheet in X:/ScHARR/PR_Disease_Risk_TA/Code/tables
+# `16102018 tobacco and alcohol Disease List and Risk Functions.xlsx`
 
 # This code reads that file and cleans it to prepare the data to be used in the model
 
@@ -10,7 +13,9 @@ library(readxl)
 root_dir <- "/Volumes/"
 
 # Load the master spreadsheet containing disease risks
-tobacco_relative_risks <- readxl::read_excel(paste0(root_dir, "ScHARR/PR_Disease_Risk_TA/Code/tables/16102018tobaccoandalcoholDiseaseListandRiskFunctions.xlsx"), sheet = "Tobacco")
+tobacco_relative_risks <- readxl::read_excel(paste0(root_dir, 
+  "ScHARR/PR_Disease_Risk_TA/Code/tables/16102018tobaccoandalcoholDiseaseListandRiskFunctions.xlsx"), 
+  sheet = "Tobacco")
 
 # Set it as a data table
 data.table::setDT(tobacco_relative_risks)
@@ -25,3 +30,8 @@ data.table::setnames(tobacco_relative_risks, "Current", "relative_risk")
 # Save the result to the package data folder
 usethis::use_data(tobacco_relative_risks, overwrite = T)
 
+# Save a separate list of the disease names
+tob_disease_names <- as.character(c(unique(tobacco_relative_risks$condition)))
+
+usethis::use_data(tob_disease_names, overwrite = T)
+
diff --git a/data/tob_disease_names.rda b/data/tob_disease_names.rda
diff --git a/data/tobacco_relative_risks.rda b/data/tobacco_relative_risks.rda
diff --git a/disease-risks.bib → inst/REFERENCES.bib b/disease-risks.bib → inst/REFERENCES.bib
diff --git a/man/AlcBinge.Rd b/man/AlcBinge.Rd
diff --git a/man/tob_disease_names.Rd b/man/tob_disease_names.Rd
diff --git a/man/tobacco_relative_risks.Rd b/man/tobacco_relative_risks.Rd
diff --git a/public/404.html b/public/404.html
diff --git a/public/LICENSE.html b/public/LICENSE.html
diff --git a/public/articles/alc_partially_attrib_acute.html b/public/articles/alc_partially_attrib_acute.html
diff --git a/public/articles/alc_wholly_attrib_acute.html b/public/articles/alc_wholly_attrib_acute.html
diff --git a/public/articles/alc_wholly_attrib_chronic.html b/public/articles/alc_wholly_attrib_chronic.html
diff --git a/public/articles/index.html b/public/articles/index.html
diff --git a/public/articles/smoking-disease-risks.html b/public/articles/smoking-disease-risks.html
diff --git a/public/authors.html b/public/authors.html
diff --git a/public/index.html b/public/index.html
diff --git a/public/pkgdown.yml b/public/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
   alc_wholly_attrib_acute: alc_wholly_attrib_acute.html
   alc_wholly_attrib_chronic: alc_wholly_attrib_chronic.html
   smoking-disease-risks: smoking-disease-risks.html
-last_built: 2020-11-25T11:12Z
+last_built: 2020-11-25T11:48Z
 urls:
   reference: https://stapm.gitlab.io/tobalcepi/reference
   article: https://stapm.gitlab.io/tobalcepi/articles

diff --git a/public/reference/AlcBinge.html b/public/reference/AlcBinge.html
diff --git a/public/reference/AlcBinge_stapm.html b/public/reference/AlcBinge_stapm.html
diff --git a/public/reference/AlcLags.html b/public/reference/AlcLags.html
diff --git a/public/reference/ExpandCodes.html b/public/reference/ExpandCodes.html
diff --git a/public/reference/PArisk.html b/public/reference/PArisk.html
diff --git a/public/reference/RRFunc.html b/public/reference/RRFunc.html
diff --git a/public/reference/RRTobDR.html b/public/reference/RRTobDR.html
diff --git a/public/reference/RRalc.html b/public/reference/RRalc.html
diff --git a/public/reference/RRtob.html b/public/reference/RRtob.html