update dev status formatting

STAPM · Nov 28, 2020 · 195e92e · 195e92e
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diff --git a/R/AlcBinge.R b/R/AlcBinge.R
@@ -1,7 +1,5 @@
 
-#' Calculate variables to inform alcohol binge model
-#' 
-#' \lifecycle{superseded}
+#' Calculate variables to inform alcohol binge model \lifecycle{superseded}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

diff --git a/R/AlcBinge_stapm.R b/R/AlcBinge_stapm.R
@@ -1,7 +1,5 @@
 
-#' Calculate variables to inform alcohol binge model - STAPM version
-#' 
-#' \lifecycle{maturing}
+#' 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 

diff --git a/R/AlcLags.R b/R/AlcLags.R
@@ -1,7 +1,5 @@
 
-#' Alcohol lag times
-#'
-#' \lifecycle{stable}
+#' 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)

diff --git a/R/ExpandCodes.R b/R/ExpandCodes.R
@@ -1,8 +1,6 @@
 
 
-#' Convert groups of ICD-10 codes to single codes
-#' 
-#' \lifecycle{stable}
+#' 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.
 #'

diff --git a/R/PArisk.R b/R/PArisk.R
@@ -1,8 +1,6 @@
 
 
-#' Relative risks for alcohol-related injuries
-#' 
-#' \lifecycle{stable}
+#' 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.

diff --git a/R/RRAlc.R b/R/RRAlc.R
@@ -1,8 +1,6 @@
 
 
-#' Relative risks for alcohol related diseases
-#' 
-#' \lifecycle{stable}
+#' Relative risks for alcohol related diseases \lifecycle{stable}
 #'
 #' Computes the relative risks for each alcohol related disease based on the published risk curves.
 #'

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

diff --git a/R/RRTobDR.R b/R/RRTobDR.R
@@ -1,6 +1,4 @@
-#' Dose-response relative risks for tobacco-related cancers
-#' 
-#' \lifecycle{experimental}
+#' 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.
 #'

diff --git a/R/RRtob.R b/R/RRtob.R
@@ -1,7 +1,5 @@
 
-#' Tobacco relative risks
-#' 
-#' \lifecycle{maturing}
+#' Tobacco relative risks \lifecycle{maturing}
 #'
 #' Relative risks for current vs. never cigarette smokers.
 #'

diff --git a/R/TobAlcInt.R b/R/TobAlcInt.R
@@ -1,8 +1,6 @@
 
 
-#' Risk interaction between tobacco and alcohol
-#' 
-#' \lifecycle{maturing}
+#' 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.

diff --git a/R/TobLags.R b/R/TobLags.R
@@ -1,7 +1,5 @@
 
-#' Tobacco lag times
-#' 
-#' \lifecycle{stable}
+#' 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)

diff --git a/R/WArisk_acute.R b/R/WArisk_acute.R
@@ -1,7 +1,5 @@
 
-#' Risk of acute conditions wholly-attributable to alcohol
-#' 
-#' \lifecycle{stable}
+#' 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 

diff --git a/R/subgroupRisk.R b/R/subgroupRisk.R
@@ -1,7 +1,5 @@
 
-#' Summarise relative risk
-#' 
-#' \lifecycle{stable}
+#' 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.

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -28,11 +28,12 @@ reference:
 - title: Tobacco relative risks
 - subtitle: Disease definitions and relative risks
   contents:
+  - RRtob
+  - RRTobDR
   - tob_disease_names
   - tob_icd10_lookups
   - tobacco_relative_risks
-  - RRtob
-  - RRTobDR
+
 - subtitle: Tobacco lag times
   contents:
   - TobLags
@@ -41,9 +42,10 @@ reference:
 - title: Alcohol relative risks
 - subtitle: Disease definitions and relative risks
   contents:
+  - RRalc
   - alc_disease_names
   - alc_icd10_lookups
-  - RRalc
+
 - subtitle: Disease risk linked to intoxication
   contents:  
   - AlcBinge

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
diff --git a/man/TobAlcInt.Rd b/man/TobAlcInt.Rd