update site

DESCRIPTION

@@ -48,7 +48,8 @@ Imports:
     lifecycle,
     crayon,
     TTR,
-    Rfast
+    Rfast,
+    stapmr
 RdMacros: Rdpack, lifecycle
 VignetteBuilder: knitr
 RoxygenNote: 7.1.2

R/AlcBinge_stapm.R

@@ -1,9 +1,9 @@
 
-#' Calculate variables to inform alcohol binge model - STAPM version \lifecycle{maturing}
+#' Calculate variables to inform alcohol binge model - STAPM version
 #'
 #' 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 
-#' the simulated sample of individuals to estimate their characteristics of single occassion drinking 
+#' the simulated sample of individuals to estimate their characteristics of single occasion drinking 
 #' at each time step in the simulation.  
 #'
 #' The coefficients used come originally from a study by Hill-McManus 2014,

R/AlcLags.R

@@ -1,11 +1,11 @@
 
-#' Alcohol lag times \lifecycle{stable}
+#' Alcohol lag times
 #'
 #' 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.
 #'
-#' All lag times are taken from the review by Holmes et al. 2012,
+#' All lag times are taken from the review by \insertCite{holmes2012temporal;textual}{tobalcepi} ,
 #'  and are the numbers used in the current version of SAPM.
 #'
 #' @param disease_name Character - the name of the disease under consideration.
@@ -19,6 +19,9 @@
 #' @importFrom data.table := setDT setnames data.table
 #' @importFrom stapmr %fin%
 #' 
+#' @references
+#' \insertRef{holmes2012temporal}{tobalcepi}  
+#' 
 #' @export
 #' 
 #'

R/ExpandCodes.R

@@ -1,6 +1,6 @@
 
 
-#' Convert groups of ICD-10 codes to single codes \lifecycle{stable}
+#' Convert groups of ICD-10 codes to single codes
 #'
 #' Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol.
 #'

R/PAFcalc.R

@@ -1,12 +1,12 @@
 
 #' Calculate Population Attributable Fractions
 #' 
-#' Uses \code{RRFunc()} and \code{subgroupRisk()} to 
+#' Uses [tobalcepi::RRFunc()] and [tobalcepi::subgroupRisk()] to 
 #' calculate population attributable fractions 
 #' based on the survey data provided.
 #' 
 #' 
-#' @param data Data table of individual characteristics
+#' @param data Data table of individual characteristics. Defaults to NULL.
 #' @param rrdata Optional - data table containing individual tobacco and alcohol consumption characteristics 
 #' with relative risks of disease already assigned. This could be useful for increasing efficiency - saving computer processing time. 
 #' Defaults to NULL.
@@ -51,7 +51,7 @@
 #' }
 #' 
 PAFcalc <- function(
-  data,
+  data = NULL,
   rrdata = NULL,
   substance,
   tob_include_risk_in_former_smokers = TRUE,
@@ -68,10 +68,12 @@ PAFcalc <- function(
   mort_or_morb = c("mort", "morb")[1]
 ) {
 
-  years <- min(data$year):max(data$year)
+
 
   if(is.null(rrdata)) {
 
+    years <- min(data$year):max(data$year)
+
     cat("Assigning relative risks\n")
 
     for(y in years) {

R/RRAlc.R

@@ -1,6 +1,6 @@
 
 
-#' Relative risks for alcohol related diseases \lifecycle{stable}
+#' Relative risks for alcohol related diseases
 #'
 #' Computes the relative risks for each alcohol related disease based on the published risk curves.
 #'
@@ -10,13 +10,13 @@
 #' indicates protective effects of alcohol, there is an option to remove the protective effect by setting all
 #' RR < 1 = 1.   
 #' 
-#' Relative risks for partially attributable acute are computed by the \code{PArisk()} function called from within
+#' Relative risks for partially attributable acute are computed by the [tobalcepi::PArisk()] function called from within
 #'  this function. The characteristics of individual single occasion drinking are also calculated within this function 
-#'  using \code{AlcBinge_stapm()}.     
+#'  using [tobalcepi::AlcBinge_stapm()].     
 #'  
 #'  Relative risks for wholly attributable chronic and wholly attributable acute conditions are calculated
 #'  based on the extent to which either weekly or daily consumption exceeds a pre-specified threshold. The risk 
-#'  for wholly attributable acute conditions is calculated by the function \code{WArisk_acute()}. We developed a new 
+#'  for wholly attributable acute conditions is calculated by the function [tobalcepi::WArisk_acute()]. We developed a new 
 #'  method to model the absolute risk of wholly attributable acute conditions to suit the STAPM modelling. 
 #'  This new method is based on the method used to model the risk of partially attributable acute conditions - 
 #'  the shape of the risk function is determined by the individual variation in the total annual number of units that

R/RRFunc.R

@@ -1,5 +1,5 @@
 
-#' Individual relative risks of disease \lifecycle{maturing}
+#' Individual relative risks of disease
 #'
 #' @description 
 #' This function takes a sample of individuals and computes each individual's relative risk
@@ -10,7 +10,7 @@
 #' @details See below
 #' @section Alcohol risk:
 #' For alcohol, the relative risk for each individual for each disease is calculated based on 
-#' their average weekly alcohol consumption (using \code{RRalc()}). 
+#' their average weekly alcohol consumption (using [tobalcepi::RRalc()]). 
 #' Alcohol consumption is converted to grams of ethanol consumed on average in a day, and 
 #' this is truncated at 150g/day. We assume 8 grams of ethanol per UK standard unit of alcohol. 
 #'  For diseases that have separate mortality and morbidity risk functions, 

R/RRtob.R

@@ -1,5 +1,5 @@
 
-#' Tobacco relative risks \lifecycle{maturing}
+#' Tobacco relative risks
 #'
 #' Relative risks for current vs. never cigarette smokers.
 #'

R/TobAlcInt.R

@@ -1,6 +1,6 @@
 
 
-#' Risk interaction between tobacco and alcohol \lifecycle{maturing}
+#' Risk interaction between tobacco and alcohol
 #'
 #' Assigns the disease-specific interaction term (synergy index) appropriate to each
 #' individual's tobacco and alcohol consumption.

R/TobLags.R

@@ -1,5 +1,5 @@
 
-#' Tobacco lag times \lifecycle{stable}
+#' Tobacco lag times
 #'
 #' 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)

R/WArisk_acute.R

@@ -1,5 +1,5 @@
 
-#' Risk of acute conditions wholly-attributable to alcohol \lifecycle{stable}
+#' Risk of acute conditions wholly-attributable to alcohol
 #'
 #' Uses the 'new' binge model methods to calculate the risk
 #' that each individual experiences each acute consequence of drinking during one year 
@@ -10,7 +10,7 @@
 #' the distribution of characteristics of single occasion drinking described by the 
 #' parameter estimates of Hill-McManus et al 2014.     
 #' 
-#' The function uses the outputs of AlcBinge_stapm() 
+#' The function uses the outputs of [tobalcepi::AlcBinge_stapm()] 
 #' to estimate for each individual: (1) the average amount that each individual is expected to
 #' drink on a single drinking occasion; (2) the standard deviation of the amount that each individual is expected to
 #' drink on a single drinking occasion; (3) the expected number of drinking occasions that

R/binge_params.R

@@ -1,8 +1,8 @@
 
-#' Parameters to estimate amount drunk on single occassions - STAPM version
+#' Parameters to estimate amount drunk on single occasions - STAPM version
 #' 
 #' As our starting point we use the parameter estimates from Hill-McManus et al 2014 - stored within the `tobalcepi` package as the data object `binge_params`. 
-#' The problem with using these parameters directly in STAPM is that STAPM does not model the individual lifecourse trajectories of 
+#' The problem with using these parameters directly in STAPM is that STAPM does not model the individual life-course trajectories of 
 #' some of the covariates investigated by Hill-McManus et al, e.g. income, kids or social status. To get these parameters into a form that can be used in STAPM, 
 #' we matched them to the individual covariates in a sample of Health Survey for England data from 2011-2017, and then averaged the parameter values 
 #' by age category, sex and IMD quintiles. The code that does this is in the `data-raw/binge_params` folder of the `tobalcepi` package. 

R/icd10_lookups.R

@@ -1,9 +1,9 @@
 
-#' Diseases related to tobacco and their ICD-10 defintions
+#' Diseases related to tobacco and their ICD-10 definitions
 #'
 #' 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.
+#' To do this, we define each group by its constituent ICD-10 codes e.g. C00, C01, C02, C03, C04, C05, C06.
 #'
 #' @docType data
 #'
@@ -18,11 +18,11 @@
 "tob_icd10_lookups"
 
 
-#' Diseases related to alcohol and their ICD-10 defintions
+#' Diseases related to alcohol and their ICD-10 definitions
 #'
 #' 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.
+#' To do this, we define each group by its constituent ICD-10 codes e.g. C00, C01, C02, C03, C04, C05, C06.
 #'
 #' @docType data
 #'
@@ -37,11 +37,11 @@
 "alc_icd10_lookups"
 
 
-#' Diseases related to both tobacco and alcohol and their ICD-10 defintions
+#' Diseases related to both tobacco and alcohol and their ICD-10 definitions
 #'
 #' 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.
+#' To do this, we define each group by its constituent ICD-10 codes e.g. C00, C01, C02, C03, C04, C05, C06.
 #'
 #' @docType data
 #'

R/subgroupRisk.R

@@ -1,5 +1,5 @@
 
-#' Summarise relative risk \lifecycle{stable}
+#' Summarise relative risk
 #'
 #' 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.

R/tob_alc_risk_int.R

@@ -1,5 +1,5 @@
 
-#' Synergstic effects of tobacco and alcohol risks
+#' Synergistic effects of tobacco and alcohol risks
 #'
 #' @docType data
 #'

_pkgdown.yml

@@ -39,15 +39,10 @@ navbar:
       href: https://stapm.gitlab.io/software.html
 
 articles:
-- title: "Tobacco relative risks"
-  contents:
-  - smoking-disease-risks
-
-- title: "Alcohol relative risks"
+- title: "Technical information"
   contents:
-  - alc_partially_attrib_acute
-  - alc_wholly_attrib_acute
-  - alc_wholly_attrib_chronic
+  - tobalcepi
+  - use_of_disease_risks_in_stapm
 
 reference:
 - title: "Use of risk functions"
@@ -99,6 +94,7 @@ reference:
   contents:
   - ExpandCodes
   - disease_groups
+  - intervalprob
 
 
 

inst/REFERENCES.bib

@@ -1,13 +1,5 @@
-%% This BibTeX bibliography file was created using BibDesk.
-%% https://bibdesk.sourceforge.io/
+% Encoding: UTF-8
 
-%% Created for Duncan Gillespie at 2020-11-26 11:27:40 +0000 
-
-
-%% Saved with string encoding Unicode (UTF-8) 
-
-
-@comment{jabref-meta: databaseType:bibtex;}
 
 
 
@@ -936,42 +928,63 @@ @article{Zou2014
 	Volume = {50},
 	Year = {2014}}
 
-@article{Pang2015,
-	__Markedentry = {[cm1dog:]},
-	Author = {Pang, Q. and Qu, K. and Zhang, J. and Xu, X. and Liu, S. and Song, S. and Wang, R. and Zhang, L. and Wang, Z. and Liu, C.},
-	Journal = {Journal of Gastroenterology \& Hepatology},
-	Number = {10},
-	Pages = {1450-60},
-	Title = {Cigarette smoking increases the risk of mortality from liver cancer: A clinical-based cohort and meta-analysis},
-	Type = {Journal Article},
-	Volume = {30},
-	Year = {2015}}
-
-@article{Brennan2015,
-	__Markedentry = {[cm1dog:6]},
-	Author = {Brennan, Alan and Meier, Petra and Purshouse, Robin and Rafia, Rachid and Meng, Yang and Hill-Macmanus, Daniel and Angus, Colin and Holmes, John},
-	Doi = {10.1002/hec.3105},
-	Issn = {1099-1050},
-	Journal = {Health Economics},
-	Number = {10},
-	Pages = {1368-1388},
-	Title = {The Sheffield Alcohol Policy Model -- A Mathematical Description},
-	Type = {Journal Article},
-	Url = {http://dx.doi.org/10.1002/hec.3105},
-	Volume = {24},
-	Year = {2015},
-	Bdsk-Url-1 = {http://dx.doi.org/10.1002/hec.3105}}
-
-@article{Gunningschepers1989,
-	__Markedentry = {[cm1dog:6]},
-	Author = {Gunningschepers, L.},
-	Issn = {0168-8510},
-	Journal = {Health Policy},
-	Number = {1-2},
-	Pages = {1-255},
-	Title = {The health benefits of preventions - a simulation approach},
-	Type = {Journal Article},
-	Url = {<Go to ISI>://WOS:A1989AD34000001},
-	Volume = {12},
-	Year = {1989},
-	Bdsk-Url-1 = {%3CGo%20to%20ISI%3E://WOS:A1989AD34000001}}
+@Article{Pang2015,
+  author  = {Pang, Q. and Qu, K. and Zhang, J. and Xu, X. and Liu, S. and Song, S. and Wang, R. and Zhang, L. and Wang, Z. and Liu, C.},
+  journal = {Journal of Gastroenterology \& Hepatology},
+  title   = {Cigarette smoking increases the risk of mortality from liver cancer: A clinical-based cohort and meta-analysis},
+  year    = {2015},
+  number  = {10},
+  pages   = {1450-60},
+  volume  = {30},
+  groups  = {[cm1dog:]},
+  type    = {Journal Article},
+}
+
+@Article{Brennan2015,
+  author     = {Brennan, Alan and Meier, Petra and Purshouse, Robin and Rafia, Rachid and Meng, Yang and Hill-Macmanus, Daniel and Angus, Colin and Holmes, John},
+  journal    = {Health Economics},
+  title      = {The Sheffield Alcohol Policy Model -- A Mathematical Description},
+  year       = {2015},
+  issn       = {1099-1050},
+  number     = {10},
+  pages      = {1368-1388},
+  volume     = {24},
+  bdsk-url-1 = {http://dx.doi.org/10.1002/hec.3105},
+  doi        = {10.1002/hec.3105},
+  groups     = {cm1dog:6},
+  type       = {Journal Article},
+  url        = {http://dx.doi.org/10.1002/hec.3105},
+}
+
+@Article{Gunningschepers1989,
+  author     = {Gunningschepers, L.},
+  journal    = {Health Policy},
+  title      = {The health benefits of preventions - a simulation approach},
+  year       = {1989},
+  issn       = {0168-8510},
+  number     = {1-2},
+  pages      = {1-255},
+  volume     = {12},
+  bdsk-url-1 = {%3CGo%20to%20ISI%3E://WOS:A1989AD34000001},
+  groups     = {cm1dog:6},
+  type       = {Journal Article},
+  url        = {<Go to ISI>://WOS:A1989AD34000001},
+}
+@article{holmes2012temporal,
+  title={The temporal relationship between per capita alcohol consumption and harm: a systematic review of time lag specifications in aggregate time series analyses},
+  author={Holmes, John and Meier, Petra S and Booth, Andrew and Guo, Yelan and Brennan, Alan},
+  journal={Drug and alcohol dependence},
+  volume={123},
+  number={1-3},
+  pages={7--14},
+  year={2012},
+  publisher={Elsevier}
+}
+@Comment{jabref-meta: databaseType:bibtex;}
+
+@Comment{jabref-meta: grouping:
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+}