fix bug linked to dev status labels

STAPM · Nov 28, 2020 · db9e878 · db9e878
1 parent 46102ca
commit db9e878
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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: 1.3.0
+Version: 1.3.1
 Authors@R: 
     c(
     person(given = "Duncan",

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,14 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
-export("\\lifecycle{experimental}")
-export("\\lifecycle{maturing}")
-export("\\lifecycle{stable}")
+export(AlcBinge)
+export(AlcBinge_stapm)
+export(AlcLags)
+export(ExpandCodes)
+export(PArisk)
 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,":=")
 importFrom(data.table,copy)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
 importFrom(data.table,setnames)
+importFrom(lifecycle,deprecate_soft)
diff --git a/R/AlcBinge.R b/R/AlcBinge.R
@@ -1,5 +1,7 @@
 
 #' Calculate variables to inform alcohol binge model
+#' 
+#' \lifecycle{superseded}
 #'
 #' 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
@@ -19,7 +21,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{stable}
 #'
 #' @examples
 #'

diff --git a/R/AlcBinge_stapm.R b/R/AlcBinge_stapm.R
@@ -1,5 +1,7 @@
 
 #' Calculate variables to inform alcohol binge model - STAPM version
+#' 
+#' \lifecycle{maturing}
 #'
 #' Designed to work with simulated individual trajectories of alcohol consumption - stratified by 
 #' age category, sex and IMD quintile. Assigns coefficients stratified by age category, sex and IMD quintile to 
@@ -28,7 +30,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{maturing}
 #'
 #' @examples
 #'

diff --git a/R/AlcLags.R b/R/AlcLags.R
@@ -1,6 +1,8 @@
 
 #' Alcohol lag times
 #'
+#' \lifecycle{stable}
+#'
 #' Prepare the disease specific functions that describe how a change in alcohol consumption
 #' gradually has an effect on the relative risk of disease incidence over time (up to 20 years)
 #' since alcohol consumption changed.
@@ -18,7 +20,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{stable}
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/ExpandCodes.R b/R/ExpandCodes.R
@@ -1,6 +1,8 @@
 
 
 #' Convert groups of ICD-10 codes to single codes
+#' 
+#' \lifecycle{stable}
 #'
 #' Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol.
 #'
@@ -14,7 +16,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
-#' \lifecycle{stable}
 #'
 #' @examples
 #'

diff --git a/R/PArisk.R b/R/PArisk.R
@@ -1,6 +1,8 @@
 
 
 #' Relative risks for alcohol-related injuries
+#' 
+#' \lifecycle{stable}
 #'
 #' Uses the 'new' binge model methods to calculate a relative risk
 #' for each individual for experiencing each cause during one year.
@@ -37,7 +39,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
-#' \lifecycle{stable}
 #'
 #' @examples
 #' 

diff --git a/R/RRAlc.R b/R/RRAlc.R
@@ -1,6 +1,8 @@
 
 
 #' Relative risks for alcohol related diseases
+#' 
+#' \lifecycle{stable}
 #'
 #' Computes the relative risks for each alcohol related disease based on the published risk curves.
 #'
@@ -38,7 +40,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{stable}
 #'
 #' @examples
 #'

diff --git a/R/RRFunc.R b/R/RRFunc.R
@@ -1,5 +1,7 @@
 
 #' Individual relative risks of disease
+#' 
+#' \lifecycle{maturing}
 #'
 #' @description 
 #' This function takes a sample of individuals and computes each individual's relative risk
@@ -111,7 +113,6 @@
 #' @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{

diff --git a/R/RRTobDR.R b/R/RRTobDR.R
@@ -1,4 +1,6 @@
 #' Dose-response relative risks for tobacco-related cancers
+#' 
+#' \lifecycle{experimental}
 #'
 #' Computes the relative risks for each tobacco-related cancer based on the published risk curves.
 #'
@@ -17,7 +19,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
-#' \lifecycle{experimental}
 #'
 #'
 #' @examples

diff --git a/R/RRtob.R b/R/RRtob.R
@@ -1,5 +1,7 @@
 
 #' Tobacco relative risks
+#' 
+#' \lifecycle{maturing}
 #'
 #' Relative risks for current vs. never cigarette smokers.
 #'
@@ -38,7 +40,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{maturing}
 #'
 #' @examples
 #'\dontrun{

diff --git a/R/TobAlcInt.R b/R/TobAlcInt.R
@@ -1,6 +1,8 @@
 
 
 #' Risk interaction between tobacco and alcohol
+#' 
+#' \lifecycle{maturing}
 #'
 #' Assigns the disease-specific interaction term (synergy index) appropriate to each
 #' individual's tobacco and alcohol consumption.
@@ -33,7 +35,6 @@
 #' 
 #' \insertRef{Prabhu2014}{tobalcepi}  
 #' 
-#' \lifecycle{maturing}
 #' 
 #' @examples 
 #' 

diff --git a/R/TobLags.R b/R/TobLags.R
@@ -1,5 +1,7 @@
 
 #' Tobacco lag times
+#' 
+#' \lifecycle{stable}
 #'
 #' Prepare the disease specific functions that describe how a change in tobacco consumption
 #' gradually has an effect on the relative risk of disease incidence over time (up to 40 years)
@@ -38,7 +40,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #'
-#' \lifecycle{stable}
 #'
 #' @examples
 #'

diff --git a/R/WArisk_acute.R b/R/WArisk_acute.R
@@ -1,5 +1,7 @@
 
 #' Risk of acute conditions wholly-attributable to alcohol
+#' 
+#' \lifecycle{stable}
 #'
 #' Uses the 'new' binge model methods to calculate the risk
 #' that each individual experiences each acute consequence of drinking during one year 
@@ -42,7 +44,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{stable}
 #'
 #' @examples
 #' 

diff --git a/R/subgroupRisk.R b/R/subgroupRisk.R
@@ -1,5 +1,7 @@
 
 #' Summarise relative risk
+#' 
+#' \lifecycle{stable}
 #'
 #' Calculate the sum of the relative risk for all individuals in a subgroup,
 #' or calculate the subgroup specific attributable fraction based on the current relative risks.
@@ -22,7 +24,6 @@
 #' @importFrom data.table := setDT setnames
 #' @export
 #' 
-#' \lifecycle{stable}
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/tobalcepi-package.R b/R/tobalcepi-package.R
@@ -0,0 +1,9 @@
+#' @keywords internal
+"_PACKAGE"
+
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
+## usethis namespace: start
+#' @importFrom lifecycle deprecate_soft
+## usethis namespace: end
+NULL
diff --git a/man/AlcBinge.Rd b/man/AlcBinge.Rd
diff --git a/man/AlcBinge_stapm.Rd b/man/AlcBinge_stapm.Rd
diff --git a/man/AlcLags.Rd b/man/AlcLags.Rd
diff --git a/man/ExpandCodes.Rd b/man/ExpandCodes.Rd
diff --git a/man/PArisk.Rd b/man/PArisk.Rd
diff --git a/man/RRFunc.Rd b/man/RRFunc.Rd
diff --git a/man/RRTobDR.Rd b/man/RRTobDR.Rd
diff --git a/man/RRalc.Rd b/man/RRalc.Rd
diff --git a/man/RRtob.Rd b/man/RRtob.Rd