From 52c3a0611cd65db2670955a23e7c8effecf9f7b9 Mon Sep 17 00:00:00 2001 From: Duncan Gillespie Date: Wed, 6 Oct 2021 17:02:34 +0100 Subject: [PATCH] update site --- DESCRIPTION | 3 +- R/AlcBinge_stapm.R | 4 +- R/AlcLags.R | 7 +- R/ExpandCodes.R | 2 +- R/PAFcalc.R | 10 +- R/RRAlc.R | 8 +- R/RRFunc.R | 4 +- R/RRtob.R | 2 +- R/TobAlcInt.R | 2 +- R/TobLags.R | 2 +- R/WArisk_acute.R | 4 +- R/binge_params.R | 4 +- R/icd10_lookups.R | 12 +- R/subgroupRisk.R | 2 +- R/tob_alc_risk_int.R | 2 +- _pkgdown.yml | 12 +- ...cessing.R => 10_HSE_variable_processing.R} | 0 .../{12 Imputation.R => 12_Imputation.R} | 0 .../{20 working code.R => 20_working_code.R} | 0 inst/REFERENCES.bib | 109 +- inst/REFERENCES.bib.bak | 990 ++++++++ man/AlcBinge_stapm.Rd | 4 +- man/AlcLags.Rd | 7 +- man/ExpandCodes.Rd | 2 +- man/PAFcalc.Rd | 6 +- man/RRFunc.Rd | 4 +- man/RRalc.Rd | 8 +- man/RRtob.Rd | 2 +- man/TobAlcInt.Rd | 2 +- man/TobLags.Rd | 2 +- man/WArisk_acute.Rd | 4 +- man/alc_icd10_lookups.Rd | 4 +- man/binge_params_stapm.Rd | 4 +- man/subgroupRisk.Rd | 2 +- man/tob_alc_risk_int.Rd | 4 +- man/tob_icd10_lookups.Rd | 4 +- man/tobalc_icd10_lookups.Rd | 4 +- public/404.html | 2 +- public/LICENSE.html | 40 +- public/articles/index.html | 19 +- public/articles/tobalcepi.html | 4 +- .../header-attrs-2.11/header-attrs.js | 12 + .../use_of_disease_risks_in_stapm.html | 405 ++++ .../figure-html/wa_acute_risk_function-1.png | Bin 0 -> 42277 bytes .../wa_chronic_risk_function-1.png | Bin 0 -> 36724 bytes .../header-attrs-2.11/header-attrs.js | 12 + public/authors.html | 2 +- public/index.html | 2 +- public/pkgdown.yml | 9 +- public/reference/AlcBinge.html | 2 +- public/reference/AlcBinge_stapm.html | 12 +- public/reference/AlcLags.html | 16 +- public/reference/ExpandCodes.html | 8 +- public/reference/PAFcalc.html | 37 +- public/reference/PArisk.html | 22 +- public/reference/RRFunc.html | 12 +- public/reference/RRTobDR.html | 2 +- public/reference/RRalc.html | 14 +- public/reference/RRtob.html | 8 +- public/reference/TobAlcInt.html | 16 +- public/reference/TobLags.html | 8 +- public/reference/WArisk_acute.html | 26 +- public/reference/alc_disease_names.html | 5 +- public/reference/alc_icd10_lookups.html | 12 +- public/reference/binge_params.html | 2 +- public/reference/binge_params_stapm.html | 12 +- public/reference/disease_groups.html | 7 +- public/reference/index.html | 42 +- public/reference/intervalprob.html | 218 ++ public/reference/subgroupRisk.html | 8 +- public/reference/tob_alc_risk_int.html | 20 +- public/reference/tob_disease_names.html | 2 +- public/reference/tob_icd10_lookups.html | 12 +- public/reference/tobacco_lag_times.html | 2 +- public/reference/tobacco_relative_risks.html | 2 +- public/reference/tobalc_icd10_lookups.html | 12 +- public/reference/tobalcepi-package.html | 2 +- public/sitemap.xml | 56 +- vignettes/disease-risks.bib | 109 +- vignettes/disease-risks.bib.bak | 855 +++++++ vignettes/use_of_disease_risks_in_stapm.Rmd | 2004 +---------------- 81 files changed, 2973 insertions(+), 2341 deletions(-) rename data-raw/binge_params/{10 HSE variable processing.R => 10_HSE_variable_processing.R} (100%) mode change 100755 => 100644 rename data-raw/binge_params/{12 Imputation.R => 12_Imputation.R} (100%) mode change 100755 => 100644 rename data-raw/binge_params/{20 working code.R => 20_working_code.R} (100%) create mode 100644 inst/REFERENCES.bib.bak create mode 100644 public/articles/tobalcepi_files/header-attrs-2.11/header-attrs.js create mode 100644 public/articles/use_of_disease_risks_in_stapm.html create mode 100644 public/articles/use_of_disease_risks_in_stapm_files/figure-html/wa_acute_risk_function-1.png create mode 100644 public/articles/use_of_disease_risks_in_stapm_files/figure-html/wa_chronic_risk_function-1.png create mode 100644 public/articles/use_of_disease_risks_in_stapm_files/header-attrs-2.11/header-attrs.js create mode 100644 public/reference/intervalprob.html create mode 100644 vignettes/disease-risks.bib.bak diff --git a/DESCRIPTION b/DESCRIPTION index a56b12d..b64d7e5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -48,7 +48,8 @@ Imports: lifecycle, crayon, TTR, - Rfast + Rfast, + stapmr RdMacros: Rdpack, lifecycle VignetteBuilder: knitr RoxygenNote: 7.1.2 diff --git a/R/AlcBinge_stapm.R b/R/AlcBinge_stapm.R index e348976..558ccf1 100644 --- a/R/AlcBinge_stapm.R +++ b/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, diff --git a/R/AlcLags.R b/R/AlcLags.R index 230d90e..a21263f 100644 --- a/R/AlcLags.R +++ b/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 #' #' diff --git a/R/ExpandCodes.R b/R/ExpandCodes.R index 411fff4..1709b47 100644 --- a/R/ExpandCodes.R +++ b/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. #' diff --git a/R/PAFcalc.R b/R/PAFcalc.R index 31e87bf..d566d3a 100644 --- a/R/PAFcalc.R +++ b/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) { diff --git a/R/RRAlc.R b/R/RRAlc.R index ccdcc7d..d24c59f 100644 --- a/R/RRAlc.R +++ b/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 diff --git a/R/RRFunc.R b/R/RRFunc.R index 922c060..2139211 100644 --- a/R/RRFunc.R +++ b/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, diff --git a/R/RRtob.R b/R/RRtob.R index 4476755..0d53dba 100644 --- a/R/RRtob.R +++ b/R/RRtob.R @@ -1,5 +1,5 @@ -#' Tobacco relative risks \lifecycle{maturing} +#' Tobacco relative risks #' #' Relative risks for current vs. never cigarette smokers. #' diff --git a/R/TobAlcInt.R b/R/TobAlcInt.R index 710fb21..055fbe6 100644 --- a/R/TobAlcInt.R +++ b/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. diff --git a/R/TobLags.R b/R/TobLags.R index 947e515..59df391 100644 --- a/R/TobLags.R +++ b/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) diff --git a/R/WArisk_acute.R b/R/WArisk_acute.R index 313c87a..4d0d2d2 100644 --- a/R/WArisk_acute.R +++ b/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 diff --git a/R/binge_params.R b/R/binge_params.R index a739b35..875a740 100644 --- a/R/binge_params.R +++ b/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. diff --git a/R/icd10_lookups.R b/R/icd10_lookups.R index 363afd9..418ee1a 100755 --- a/R/icd10_lookups.R +++ b/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 #' diff --git a/R/subgroupRisk.R b/R/subgroupRisk.R index 13610d5..5d7cac8 100644 --- a/R/subgroupRisk.R +++ b/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. diff --git a/R/tob_alc_risk_int.R b/R/tob_alc_risk_int.R index 2d3d83f..70635a1 100644 --- a/R/tob_alc_risk_int.R +++ b/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 #' diff --git a/_pkgdown.yml b/_pkgdown.yml index 2e6e059..0c158fb 100644 --- a/_pkgdown.yml +++ b/_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 diff --git a/data-raw/binge_params/10 HSE variable processing.R b/data-raw/binge_params/10_HSE_variable_processing.R old mode 100755 new mode 100644 similarity index 100% rename from data-raw/binge_params/10 HSE variable processing.R rename to data-raw/binge_params/10_HSE_variable_processing.R diff --git a/data-raw/binge_params/12 Imputation.R b/data-raw/binge_params/12_Imputation.R old mode 100755 new mode 100644 similarity index 100% rename from data-raw/binge_params/12 Imputation.R rename to data-raw/binge_params/12_Imputation.R diff --git a/data-raw/binge_params/20 working code.R b/data-raw/binge_params/20_working_code.R similarity index 100% rename from data-raw/binge_params/20 working code.R rename to data-raw/binge_params/20_working_code.R diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib index e536554..237ad4f 100644 --- a/inst/REFERENCES.bib +++ b/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 = {://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 = {://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: +0 AllEntriesGroup:; +1 StaticGroup:Markings\;2\;1\;\;\;\;; +2 StaticGroup:[cm1dog:]\;2\;1\;\;\;\;; +2 StaticGroup:cm1dog:6\;2\;1\;\;\;\;; +} diff --git a/inst/REFERENCES.bib.bak b/inst/REFERENCES.bib.bak new file mode 100644 index 0000000..237ad4f --- /dev/null +++ b/inst/REFERENCES.bib.bak @@ -0,0 +1,990 @@ +% Encoding: UTF-8 + + + + +@misc{webster2018risk, + Author = {Webster, Laura and Angus, Colin and Brennan, Alan and Gillespie, Duncan}, + Date-Added = {2020-11-25 09:40:25 +0000}, + Date-Modified = {2020-11-25 09:40:25 +0000}, + Doi = {10.15131/shef.data.7411451.v1}, + Month = {Dec}, + Publisher = {The University of Sheffield}, + Title = {Smoking and the risks of adult diseases}, + Url = {https://figshare.shef.ac.uk/articles/Smoking_and_the_risks_of_adult_diseases/7411451/1}, + Year = {2018}, + Bdsk-Url-1 = {https://figshare.shef.ac.uk/articles/Smoking_and_the_risks_of_adult_diseases/7411451/1}, + Bdsk-Url-2 = {https://doi.org/10.15131/shef.data.7411451.v1}} + +@article{turati2014alcohol, + Author = {Turati, F and Galeone, C and Rota, M and Pelucchi, Claudio and Negri, E and Bagnardi, V and Corrao, G and Boffetta, P and La Vecchia, C}, + Date-Added = {2020-10-27 14:09:32 +0000}, + Date-Modified = {2020-10-27 14:09:32 +0000}, + Journal = {Annals of oncology}, + Number = {8}, + Pages = {1526--1535}, + Publisher = {Oxford University Press}, + Title = {Alcohol and liver cancer: a systematic review and meta-analysis of prospective studies}, + Volume = {25}, + Year = {2014}} + +@article{sherk2020international, + Author = {Sherk, Adam and Stockwell, Tim and Rehm, J{\"u}rgen and Dorocicz, John and Shield, Kevin D and Churchill, Samuel}, + Date-Added = {2020-10-27 14:08:28 +0000}, + Date-Modified = {2020-10-27 14:08:28 +0000}, + Journal = {Journal of studies on alcohol and drugs}, + Number = {3}, + Pages = {339--351}, + Publisher = {Rutgers University}, + Title = {The International Model of Alcohol Harms and Policies: A new method for estimating alcohol health harms with application to alcohol-attributable mortality in Canada}, + Volume = {81}, + Year = {2020}} + +@article{samokhvalov2015alcohol, + Author = {Samokhvalov, Andriy V and Rehm, J{\"u}rgen and Roerecke, Michael}, + Date-Added = {2020-10-27 14:07:05 +0000}, + Date-Modified = {2020-10-27 14:07:05 +0000}, + Journal = {EBioMedicine}, + Number = {12}, + Pages = {1996--2002}, + Publisher = {Elsevier}, + Title = {Alcohol consumption as a risk factor for acute and chronic pancreatitis: a systematic review and a series of meta-analyses}, + Volume = {2}, + Year = {2015}} + +@article{samokhvalov2010alcoholpneumonia, + Author = {Samokhvalov, AV and Irving, HM and Rehm, J}, + Date-Added = {2020-10-27 14:05:57 +0000}, + Date-Modified = {2020-10-27 14:06:07 +0000}, + Journal = {Epidemiology \& Infection}, + Number = {12}, + Pages = {1789--1795}, + Publisher = {Cambridge University Press}, + Title = {Alcohol consumption as a risk factor for pneumonia: a systematic review and meta-analysis}, + Volume = {138}, + Year = {2010}} + +@article{samokhvalov2010alcoholepi, + Author = {Samokhvalov, Andriy V and Irving, Hyacinth and Mohapatra, Satya and Rehm, J{\"u}rgen}, + Date-Added = {2020-10-27 14:04:05 +0000}, + Date-Modified = {2020-10-27 14:04:22 +0000}, + Journal = {Epilepsia}, + Number = {7}, + Pages = {1177--1184}, + Publisher = {Wiley Online Library}, + Title = {Alcohol consumption, unprovoked seizures, and epilepsy: A systematic review and meta-analysis}, + Volume = {51}, + Year = {2010}} + +@article{samokhvalov2010alcohol, + Author = {Samokhvalov, Andriy V and Irving, Hyacinth M and Rehm, J{\"u}rgen}, + Date-Added = {2020-10-27 14:01:44 +0000}, + Date-Modified = {2020-10-27 14:01:44 +0000}, + Journal = {European Journal of Cardiovascular Prevention \& Rehabilitation}, + Number = {6}, + Pages = {706--712}, + Publisher = {SAGE Publications Sage UK: London, England}, + Title = {Alcohol consumption as a risk factor for atrial fibrillation: a systematic review and meta-analysis}, + Volume = {17}, + Year = {2010}} + +@article{roerecke2012cardioprotective, + Author = {Roerecke, Michael and Rehm, J{\"u}rgen}, + Date-Added = {2020-10-27 14:00:30 +0000}, + Date-Modified = {2020-10-27 14:00:30 +0000}, + Journal = {Addiction}, + Number = {7}, + Pages = {1246--1260}, + Publisher = {Wiley Online Library}, + Title = {The cardioprotective association of average alcohol consumption and ischaemic heart disease: a systematic review and meta-analysis}, + Volume = {107}, + Year = {2012}} + +@article{roerecke2010irregular, + Author = {Roerecke, Michael and Rehm, J{\"u}rgen}, + Date-Added = {2020-10-27 13:58:08 +0000}, + Date-Modified = {2020-10-27 13:58:08 +0000}, + Journal = {American journal of epidemiology}, + Number = {6}, + Pages = {633--644}, + Publisher = {Oxford University Press}, + Title = {Irregular heavy drinking occasions and risk of ischemic heart disease: a systematic review and meta-analysis}, + Volume = {171}, + Year = {2010}} + +@article{rehm2010alcohol, + Author = {Rehm, J{\"u}rgen and Taylor, Benjamin and Mohapatra, Satya and Irving, Hyacinth and Baliunas, Dolly and Patra, Jayadeep and Roerecke, Michael}, + Date-Added = {2020-10-27 13:56:36 +0000}, + Date-Modified = {2020-10-27 13:56:36 +0000}, + Journal = {Drug and alcohol review}, + Number = {4}, + Pages = {437--445}, + Publisher = {Wiley Online Library}, + Title = {Alcohol as a risk factor for liver cirrhosis: a systematic review and meta-analysis}, + Volume = {29}, + Year = {2010}} + +@article{rehm2016modelling, + Author = {Rehm, J{\"u}rgen and Shield, Kevin D and Roerecke, Michael and Gmel, Gerrit}, + Date-Added = {2020-10-27 13:54:29 +0000}, + Date-Modified = {2020-10-27 13:54:29 +0000}, + Journal = {BMC public health}, + Number = {1}, + Pages = {1--9}, + Publisher = {BioMed Central}, + Title = {Modelling the impact of alcohol consumption on cardiovascular disease mortality for comparative risk assessments: an overview}, + Volume = {16}, + Year = {2016}} + +@article{rehm2017relationship, + Author = {Rehm, J{\"u}rgen and Gmel Sr, Gerhard E and Gmel, Gerrit and Hasan, Omer SM and Imtiaz, Sameer and Popova, Svetlana and Probst, Charlotte and Roerecke, Michael and Room, Robin and Samokhvalov, Andriy V and others}, + Date-Added = {2020-10-27 13:53:29 +0000}, + Date-Modified = {2020-10-27 13:53:29 +0000}, + Journal = {Addiction}, + Number = {6}, + Pages = {968--1001}, + Publisher = {Wiley Online Library}, + Title = {The relationship between different dimensions of alcohol use and the burden of disease---an update}, + Volume = {112}, + Year = {2017}} + +@book{rehm2017risk, + Author = {Rehm, J and Sherk, A and Shield, KD and Gmel, G}, + Date-Added = {2020-10-27 13:51:32 +0000}, + Date-Modified = {2020-10-27 13:52:04 +0000}, + Publisher = {Institute for Mental Health Policy Research}, + Title = {Risk relations between alcohol use and non-injury causes of death}, + Url = {Retrieved from https://www.camh.ca/en/research/news_and_publications/reports_and_books/Documents/CAMH-Risk-relations-between-alcohol-use-and-non-injury-causes-of-death-Sept2017.pdf}, + Year = {2017}, + Bdsk-Url-1 = {Retrieved%20from%20https://www.camh.ca/en/research/news_and_publications/reports_and_books/Documents/CAMH-Risk-relations-between-alcohol-use-and-non-injury-causes-of-death-Sept2017.pdf}} + +@article{patra2010alcohol, + Author = {Patra, Jayadeep and Taylor, Benjamin and Irving, Hyacinth and Roerecke, Michael and Baliunas, Dolly and Mohapatra, Satya and Rehm, J{\"u}rgen}, + Date-Added = {2020-10-27 13:50:03 +0000}, + Date-Modified = {2020-10-27 13:50:03 +0000}, + Journal = {BMC public health}, + Number = {1}, + Pages = {1--12}, + Publisher = {BioMed Central}, + Title = {Alcohol consumption and the risk of morbidity and mortality for different stroke types-a systematic review and meta-analysis}, + Volume = {10}, + Year = {2010}} + +@article{meier2016estimated, + Author = {Meier, Petra S and Holmes, John and Angus, Colin and Ally, Abdallah K and Meng, Yang and Brennan, Alan}, + Date-Added = {2020-10-27 13:49:02 +0000}, + Date-Modified = {2020-10-27 13:49:02 +0000}, + Journal = {PLoS Medicine}, + Number = {2}, + Pages = {e1001963}, + Publisher = {Public Library of Science San Francisco, CA USA}, + Title = {Estimated effects of different alcohol taxation and price policies on health inequalities: a mathematical modelling study}, + Volume = {13}, + Year = {2016}} + +@article{knott2015alcohol, + Author = {Knott, Craig and Bell, Steven and Britton, Annie}, + Date-Added = {2020-10-27 13:47:25 +0000}, + Date-Modified = {2020-10-27 13:47:25 +0000}, + Journal = {Diabetes care}, + Number = {9}, + Pages = {1804--1812}, + Publisher = {Am Diabetes Assoc}, + Title = {Alcohol consumption and the risk of type 2 diabetes: a systematic review and dose-response meta-analysis of more than 1.9 million individuals from 38 observational studies}, + Volume = {38}, + Year = {2015}} + +@article{imtiaz2017alcohol, + Author = {Imtiaz, Sameer and Shield, Kevin D and Roerecke, Michael and Samokhvalov, Andriy V and L{\"o}nnroth, Knut and Rehm, J{\"u}rgen}, + Date-Added = {2020-10-27 13:45:49 +0000}, + Date-Modified = {2020-10-27 13:45:49 +0000}, + Journal = {European Respiratory Journal}, + Number = {1}, + Publisher = {Eur Respiratory Soc}, + Title = {Alcohol consumption as a risk factor for tuberculosis: meta-analyses and burden of disease}, + Volume = {50}, + Year = {2017}} + +@article{chuang2015alcohol, + Author = {Chuang, Shu-Chun and Lee, Yuan-Chin Amy and Wu, Guo-Jie and Straif, Kurt and Hashibe, Mia}, + Date-Added = {2020-10-27 13:44:09 +0000}, + Date-Modified = {2020-10-27 13:44:09 +0000}, + Journal = {Cancer Causes \& Control}, + Number = {9}, + Pages = {1205--1231}, + Publisher = {Springer}, + Title = {Alcohol consumption and liver cancer risk: a meta-analysis}, + Volume = {26}, + Year = {2015}} + +@article{cherpitel2015relative, + Author = {Cherpitel, Cheryl J 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dose--response meta-analysis}, + Volume = {112}, + Year = {2015}} + +@article{RCP2018, + Author = {{Tobacco Advisory Group of the Royal College of Physicians}}, + Journal = {Available from: https://www.rcplondon.ac.uk/projects/outputs/hiding-plain-sight-treating-tobacco-dependency-nhs}, + Title = {{Hiding in plain sight: {T}reating tobacco dependency in the NHS}}, + Type = {resreport}, + Year = {2018}} + +@techreport{Angus2018, + Author = {Angus, Colin and Henney, M and Webster, L and Gillespie, Duncan}, + Date-Modified = {2020-11-25 12:09:57 +0000}, + Institution = {The University of Sheffield}, + Title = {Alcohol-attributable diseases and dose-response curves for the Sheffield Alcohol Policy Model version 4.0}, + Url = {https://doi.org/10.15131/shef.data.6819689.v2}, + Year = {2018}, + Bdsk-Url-1 = {https://figshare.com/articles/Alcohol-attributable_diseases_and_dose-response_curves_for_the_Sheffield_Alcohol_Policy_Model_version_4_0/6819689}, + Bdsk-Url-2 = 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Comparison of methods for estimating smoking-attributable mortality when smoking prevalence changes}, + Type = {Journal Article}, + Volume = {52}, + Year = {2011}} + +@article{Peters2013, + Author = {Peters, Sanne AE and Huxley, Rachel R and Woodward, Mark}, + Issn = {0039-2499}, + Journal = {Stroke}, + Number = {10}, + Pages = {2821-2828}, + Title = {Smoking as a risk factor for stroke in women compared with men: A systematic review and meta-analysis of 81 cohorts, including 3 980 359 individuals and 42 401 strokes}, + Type = {Journal Article}, + Volume = {44}, + Year = {2013}} + +@article{Prabhu2013, + Author = {Prabhu, A and Obi, KO and Rubenstein, JH}, + Issn = {0269-2813}, + Journal = {Alimentary pharmacology \& therapeutics}, + Number = {10}, + Pages = {1145-1155}, + Title = {Systematic review with meta‐analysis: race‐specific effects of alcohol and tobacco on the risk of oesophageal squamous cell carcinoma}, + Type = {Journal Article}, + Volume = {38}, + Year = {2013}} + +@article{Prabhu2014, + Author = {Prabhu, A. and Obi, K. 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H.}, + Date-Modified = {2020-11-26 11:27:38 +0000}, + Doi = {10.1038/ajg.2014.71}, + Issn = {0002-9270}, + Journal = {American Journal of Gastroenterology}, + Number = {6}, + Pages = {821-827}, + Title = {The Synergistic Effects of Alcohol and Tobacco Consumption on the Risk of Esophageal Squamous Cell Carcinoma: A Meta-Analysis}, + Type = {Journal Article}, + Volume = {109}, + Year = {2014}, + Bdsk-Url-1 = {%3CGo%20to%20ISI%3E://WOS:000344458900006}, + Bdsk-Url-2 = {https://doi.org/10.1038/ajg.2014.71}} + +@article{Rostron2012, + Author = {Rostron, Brian}, + Issn = {1462-2203}, + Journal = {Nicotine \& Tobacco Research}, + Number = {1}, + Pages = {238-246}, + Title = {Smoking-attributable mortality by cause in the United States: revising the CDC's data and estimates}, + Type = {Journal Article}, + Volume = {15}, + Year = {2012}} + +@article{Shen2015, + Author = {Shen, Guang Si and Li, Yong and Zhao, GuoYang and Zhou, Hai Bin and Xie, Zong Gang and Xu, Wei and Chen, Hai Nan and Dong, Qi Rong and Xu, You Jia}, + Issn = {0020-1383}, + Journal = {Injury}, + Number = {7}, + Pages = {1333-1340}, + Title = {Cigarette smoking and risk of hip fracture in women: a meta-analysis of prospective cohort studies}, + Type = {Journal Article}, + Volume = {46}, + Year = {2015}} + +@article{Solmi2016, + Author = {Solmi, Marco and Veronese, Nicola and Sergi, Giuseppe and Luchini, Claudio and Favaro, Angela and Santonastaso, Paolo and Vancampfort, Davy and Correll, Christoph U. and Ussher, Michael and Thapa-Chhetri, Nita and Fornaro, Michele and Stubbs, Brendon}, + Doi = {10.1111/add.13457}, + Issn = {1360-0443}, + Journal = {Addiction}, + Number = {11}, + Pages = {1914-1922}, + Title = {The association between smoking prevalence and eating disorders: a systematic review and meta-analysis}, + Type = {Journal Article}, + Url = {http://dx.doi.org/10.1111/add.13457}, + Volume = {111}, + Year = {2016}, + Bdsk-Url-1 = {http://dx.doi.org/10.1111/add.13457}} + +@article{Tramacere2011, + Author = {Tramacere, Irene and La Vecchia, Carlo and Negri, Eva}, + Issn = {1044-3983}, + Journal = {Epidemiology}, + Pages = {344-349}, + Title = {Brief Report: Tobacco Smoking and Esophageal and Gastric Cardia Adenocarcinoma: A Meta-analysis}, + Type = {Journal Article}, + Year = {2011}} + +@article{Osch2016, + Author = {van Osch, Frits HM and Jochems, Sylvia HJ and van Schooten, Frederik-Jan and Bryan, Richard T and Zeegers, Maurice P}, + Issn = {1464-3685}, + Journal = {International journal of epidemiology}, + Number = {3}, + Pages = {857-870}, + Title = {Quantified relations between exposure to tobacco smoking and bladder cancer risk: a meta-analysis of 89 observational studies}, + Type = {Journal Article}, + Volume = {45}, + Year = {2016}} + +@article{Zhong2015, + Author = {Zhong, Guochao and Wang, Yi and Zhang, Yong and Guo, Jeff Jianfei and Zhao, Yong}, + Issn = {1932-6203}, + Journal = {PLoS One}, + Number = {3}, + Pages = {e0118333}, + Title = {Smoking is associated with an increased risk of dementia: a meta-analysis of prospective cohort studies with investigation of potential effect modifiers}, + Type = {Journal Article}, + Volume = {10}, + Year = {2015}} + +@article{Zuo2017, + Author = {Zuo, Jing-Jing and Tao, Ze-Zhang and Chen, Chen and Hu, Zhang-Wei and Xu, Ye-Xing and Zheng, An-Yuan and Guo, Yi}, + Issn = {0937-4477}, + Journal = {European Archives of Oto-Rhino-Laryngology}, + Number = {3}, + Pages = {1617-1631}, + Title = {Characteristics of cigarette smoking without alcohol consumption and laryngeal cancer: overall and time-risk relation. 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US Department of Health and Human Services, Centers for Disease Control and Prevention}, + Type = {Journal Article}, + Year = {2014}} + +@techreport{Digital2018, + Author = {{NHS Digital}}, + Title = {Statistics on Smoking: England, 2018}, + Type = {Report}, + Year = {2018}} + +@techreport{Pokhrel2013, + Author = {Pokhrel, S. and Owen, L. and Lester-George, A. and Coyle, K. and Coyle D. and West R. and Trapero-Bertran M. and C., Meads}, + Institution = {National Institute for Health and Care Excellence}, + Title = {Tobacco Control Return on Investment Tool}, + Type = {Report}, + Year = {2013}} + +@article{Doll2004, + Author = {Doll, Richard and Peto, Richard and Boreham, Jillian and Sutherland, Isabelle}, + Issn = {0959-8138}, + Journal = {Bmj}, + Number = {7455}, + Pages = {1519}, + Title = {Mortality in relation to smoking: 50 years' observations on male British doctors}, + Type = {Journal Article}, + Volume = {328}, + Year = {2004}} + +@article{Liang2009, + Author = {Liang, PS and Chen, TY and Giovannucci, E}, + Journal = {International Journal of Cancer}, + Number = {10}, + Pages = {2406-15}, + Title = {Cigarette smoking and colorectal cancer incidence and mortality: systematic review and meta-analysis}, + Type = {Journal Article}, + Url = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/ijc.24191}, + Volume = {124}, + Year = {2009}, + Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/ijc.24191}} + +@article{Macacu2015, + Author = {Macacu, A. and Autier, P. and Boniol, M. and Boyle, P.}, + Doi = {10.1007/s10549-015-3628-4}, + Issn = {0167-6806}, + Journal = {Breast Cancer Research and Treatment}, + Number = {2}, + Pages = {213-224}, + Title = {Active and passive smoking and risk of breast cancer: a meta-analysis}, + Type = {Journal Article}, + Url = {://WOS:000365188600001}, + Volume = {154}, + Year = {2015}, + Bdsk-Url-1 = {%3CGo%20to%20ISI%3E://WOS:000365188600001}, + Bdsk-Url-2 = {https://doi.org/10.1007/s10549-015-3628-4}} + +@article{Tredaniel, + Author = {Tredaniel, J. and Boffetta, P. and Buiatti, E. and Saracci, R. and Hirsch, A.}, + Journal = {International Journal of Cancer}, + Number = {4}, + Pages = {565-73}, + Title = {Tobacco smoking and gastric cancer: review and meta-analysis}, + Type = {Journal Article}, + Url = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/%28SICI%291097-0215%2819970807%2972%3A4%3C565%3A%3AAID-IJC3%3E3.0.CO%3B2-O}, + Volume = {72}, + Year = {1997}, + Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/%28SICI%291097-0215%2819970807%2972%3A4%3C565%3A%3AAID-IJC3%3E3.0.CO%3B2-O}} + +@article{Xu2012, + Author = {Xu, F. H. and Xiong, D. and Xu, Y. F. and Cao, S. M. and Xue, W. Q. and Qin, H. D. and Liu, W. S. and Cao, J. Y. and Zhang, Y. and Feng, Q. S. and Chen, L. Z. and Li, M. Z. and Liu, Z. W. and Liu, Q. and Hong, M. H. and Shugart, Y. Y. and Zeng, Y. X. and Zeng, M. S. and Jia, W. H.}, + Doi = {10.1093/jnci/djs320}, + Issn = {0027-8874}, + Journal = {Jnci-Journal of the National Cancer Institute}, + Number = {18}, + Pages = {1396-1410}, + Title = {An Epidemiological and Molecular Study of the Relationship Between Smoking, Risk of Nasopharyngeal Carcinoma, and EpsteinBarr Virus Activation}, + Type = {Journal Article}, + Url = {://WOS:000309132500010 https://watermark.silverchair.com/djs320.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlgwggJUBgkqhkiG9w0BBwagggJFMIICQQIBADCCAjoGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMDiGi4rQEqFfGycXwAgEQgIICCzN13nTwYsxEiim2ei9s3_wKrOP8F5s2jtaqkDBsOdGTeJWXn69XoIvuWqTJSDZfC5w6csW0C2VgPzHYZ9qTauDUZTB07v6yU5feujlz0Z2zORc4rOpmgZl6lbVbPQaTMsN-BOltw2nyUsnTiU7DT7znNKFX31MTjP60cXT7VcR-Ll4uQAwHGkUySP-qJBJ6fCYzfByLbUaaqUiYN3LsYP4sh9R9xcdPvYMWo8VD8fDR3bnWXoHQ0ZzoA7pPJRZ_eMyuyLKOGIk874r5le4O4WOEktfqeic6KFJC_WZBK_G2lJfgmpc1Ew3AFw9fFUxDXEEj2TPu5p9Q-e0kAPqrN7drxvRwE3CC3p7yGf8j-3QcSHvMZvZmKHUBVTLOSFD2LC7xoYUa4X6x7iKkAPiddDhfd2TVjxgPQIAYSJiBY_QuurfsO_hqC496gjklqdtLIpoIbSFIwhTbGhy2PQl-W-bbcUsjrcP9FZ6aEk0AjTK3N571rJWvPQBMMeH--kXORSEdwVCwNtTAvqpbez8SKZQA89d8zX80Dnzm3mbZMEGKifBag1n-weP0RnoB0nBWFPyIVdDzlp4MstRGP_qbwYXkKupQvzd95Lv1mR54UYTVOlWOGdQdmnG3WYmmOgFRbhsMToGyC0hdbWmfzpERXhB7o495zT26Fv0aRquZV6nrWAID-5-kKsnAf1Q}, + Volume = {104}, + Year = {2012}, + Bdsk-Url-1 = {%3CGo%20to%20ISI%3E://WOS:000309132500010%20https://watermark.silverchair.com/djs320.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlgwggJUBgkqhkiG9w0BBwagggJFMIICQQIBADCCAjoGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMDiGi4rQEqFfGycXwAgEQgIICCzN13nTwYsxEiim2ei9s3_wKrOP8F5s2jtaqkDBsOdGTeJWXn69XoIvuWqTJSDZfC5w6csW0C2VgPzHYZ9qTauDUZTB07v6yU5feujlz0Z2zORc4rOpmgZl6lbVbPQaTMsN-BOltw2nyUsnTiU7DT7znNKFX31MTjP60cXT7VcR-Ll4uQAwHGkUySP-qJBJ6fCYzfByLbUaaqUiYN3LsYP4sh9R9xcdPvYMWo8VD8fDR3bnWXoHQ0ZzoA7pPJRZ_eMyuyLKOGIk874r5le4O4WOEktfqeic6KFJC_WZBK_G2lJfgmpc1Ew3AFw9fFUxDXEEj2TPu5p9Q-e0kAPqrN7drxvRwE3CC3p7yGf8j-3QcSHvMZvZmKHUBVTLOSFD2LC7xoYUa4X6x7iKkAPiddDhfd2TVjxgPQIAYSJiBY_QuurfsO_hqC496gjklqdtLIpoIbSFIwhTbGhy2PQl-W-bbcUsjrcP9FZ6aEk0AjTK3N571rJWvPQBMMeH--kXORSEdwVCwNtTAvqpbez8SKZQA89d8zX80Dnzm3mbZMEGKifBag1n-weP0RnoB0nBWFPyIVdDzlp4MstRGP_qbwYXkKupQvzd95Lv1mR54UYTVOlWOGdQdmnG3WYmmOgFRbhsMToGyC0hdbWmfzpERXhB7o495zT26Fv0aRquZV6nrWAID-5-kKsnAf1Q}, + Bdsk-Url-2 = {https://doi.org/10.1093/jnci/djs320}} + +@article{Zou2014, + Author = {Zou, L. and Zhong, R. and Shen, N. and Chen, W. and Zhu, B. and Ke, J. and Lu, X. and Zhang, T. and Lou, J. and Wang, Z. and Liu, L. and Qi, L. and Miao, X.}, + Journal = {European Journal of Cancer}, + Number = {1}, + Pages = {193-203}, + Title = {Non-linear dose-response relationship between cigarette smoking and pancreatic cancer risk: evidence from a meta-analysis of 42 observational studies}, + Type = {Journal Article}, + Volume = {50}, + Year = {2014}} + +@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 = {://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: +0 AllEntriesGroup:; +1 StaticGroup:Markings\;2\;1\;\;\;\;; +2 StaticGroup:[cm1dog:]\;2\;1\;\;\;\;; +2 StaticGroup:cm1dog:6\;2\;1\;\;\;\;; +} diff --git a/man/AlcBinge_stapm.Rd b/man/AlcBinge_stapm.Rd index 5513300..d36037e 100644 --- a/man/AlcBinge_stapm.Rd +++ b/man/AlcBinge_stapm.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/AlcBinge_stapm.R \name{AlcBinge_stapm} \alias{AlcBinge_stapm} -\title{Calculate variables to inform alcohol binge model - STAPM version \lifecycle{maturing}} +\title{Calculate variables to inform alcohol binge model - STAPM version} \usage{ AlcBinge_stapm(data, params = tobalcepi::binge_params_stapm) } @@ -20,7 +20,7 @@ Returns data plus the estimated variables. \description{ 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. } \details{ diff --git a/man/AlcLags.Rd b/man/AlcLags.Rd index 133df85..b352f38 100644 --- a/man/AlcLags.Rd +++ b/man/AlcLags.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/AlcLags.R \name{AlcLags} \alias{AlcLags} -\title{Alcohol lag times \lifecycle{stable}} +\title{Alcohol lag times} \usage{ AlcLags(disease_name = c("Pharynx", "Oral_cavity"), n_years = 20) } @@ -23,7 +23,7 @@ gradually has an effect on the relative risk of disease incidence over time (up since alcohol consumption changed. } \details{ -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. } \examples{ @@ -31,3 +31,6 @@ All lag times are taken from the review by Holmes et al. 2012, AlcLags("Pharynx") } } +\references{ +\insertRef{holmes2012temporal}{tobalcepi} +} diff --git a/man/ExpandCodes.Rd b/man/ExpandCodes.Rd index 383ba70..919f53f 100644 --- a/man/ExpandCodes.Rd +++ b/man/ExpandCodes.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/ExpandCodes.R \name{ExpandCodes} \alias{ExpandCodes} -\title{Convert groups of ICD-10 codes to single codes \lifecycle{stable}} +\title{Convert groups of ICD-10 codes to single codes} \usage{ ExpandCodes(lkup) } diff --git a/man/PAFcalc.Rd b/man/PAFcalc.Rd index ce000e9..3057fe9 100644 --- a/man/PAFcalc.Rd +++ b/man/PAFcalc.Rd @@ -5,7 +5,7 @@ \title{Calculate Population Attributable Fractions} \usage{ PAFcalc( - data, + data = NULL, rrdata = NULL, substance, tob_include_risk_in_former_smokers = TRUE, @@ -23,7 +23,7 @@ PAFcalc( ) } \arguments{ -\item{data}{Data table of individual characteristics} +\item{data}{Data table of individual characteristics. Defaults to NULL.} \item{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. @@ -75,7 +75,7 @@ should refer to mortality or morbidity. Values could be "mort" or "morb". Defaul Returns a data.table containing the estimated PAFs. } \description{ -Uses \code{RRFunc()} and \code{subgroupRisk()} to +Uses [tobalcepi::RRFunc()] and [tobalcepi::subgroupRisk()] to calculate population attributable fractions based on the survey data provided. } diff --git a/man/RRFunc.Rd b/man/RRFunc.Rd index 3dc3091..a450b65 100644 --- a/man/RRFunc.Rd +++ b/man/RRFunc.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RRFunc.R \name{RRFunc} \alias{RRFunc} -\title{Individual relative risks of disease \lifecycle{maturing}} +\title{Individual relative risks of disease} \usage{ RRFunc( data, @@ -107,7 +107,7 @@ 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, diff --git a/man/RRalc.Rd b/man/RRalc.Rd index b6f0d41..7a834e9 100644 --- a/man/RRalc.Rd +++ b/man/RRalc.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RRAlc.R \name{RRalc} \alias{RRalc} -\title{Relative risks for alcohol related diseases \lifecycle{stable}} +\title{Relative risks for alcohol related diseases} \usage{ RRalc( data, @@ -69,13 +69,13 @@ separate risk functions for morbidity and mortality. For conditions that show a 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 diff --git a/man/RRtob.Rd b/man/RRtob.Rd index ca097b1..057eab2 100644 --- a/man/RRtob.Rd +++ b/man/RRtob.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RRtob.R \name{RRtob} \alias{RRtob} -\title{Tobacco relative risks \lifecycle{maturing}} +\title{Tobacco relative risks} \usage{ RRtob( data, diff --git a/man/TobAlcInt.Rd b/man/TobAlcInt.Rd index f20ec08..ac33173 100644 --- a/man/TobAlcInt.Rd +++ b/man/TobAlcInt.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/TobAlcInt.R \name{TobAlcInt} \alias{TobAlcInt} -\title{Risk interaction between tobacco and alcohol \lifecycle{maturing}} +\title{Risk interaction between tobacco and alcohol} \usage{ TobAlcInt( data, diff --git a/man/TobLags.Rd b/man/TobLags.Rd index 3afce58..09c80a8 100644 --- a/man/TobLags.Rd +++ b/man/TobLags.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/TobLags.R \name{TobLags} \alias{TobLags} -\title{Tobacco lag times \lifecycle{stable}} +\title{Tobacco lag times} \usage{ TobLags( disease_name = c("Pharynx", "Oral_cavity"), diff --git a/man/WArisk_acute.Rd b/man/WArisk_acute.Rd index 064320e..55674fc 100644 --- a/man/WArisk_acute.Rd +++ b/man/WArisk_acute.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/WArisk_acute.R \name{WArisk_acute} \alias{WArisk_acute} -\title{Risk of acute conditions wholly-attributable to alcohol \lifecycle{stable}} +\title{Risk of acute conditions wholly-attributable to alcohol} \usage{ WArisk_acute( interval_prob_vec, @@ -43,7 +43,7 @@ The calculation is based on the link between average weekly alcohol consumption 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 diff --git a/man/alc_icd10_lookups.Rd b/man/alc_icd10_lookups.Rd index 4b928cd..06893d9 100644 --- a/man/alc_icd10_lookups.Rd +++ b/man/alc_icd10_lookups.Rd @@ -3,7 +3,7 @@ \docType{data} \name{alc_icd10_lookups} \alias{alc_icd10_lookups} -\title{Diseases related to alcohol and their ICD-10 defintions} +\title{Diseases related to alcohol and their ICD-10 definitions} \format{ A data table } @@ -16,6 +16,6 @@ alc_icd10_lookups \description{ 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. } \keyword{datasets} diff --git a/man/binge_params_stapm.Rd b/man/binge_params_stapm.Rd index fe8b7e8..d6dec25 100644 --- a/man/binge_params_stapm.Rd +++ b/man/binge_params_stapm.Rd @@ -3,7 +3,7 @@ \docType{data} \name{binge_params_stapm} \alias{binge_params_stapm} -\title{Parameters to estimate amount drunk on single occassions - STAPM version} +\title{Parameters to estimate amount drunk on single occasions - STAPM version} \format{ A list of four data tables (1 = Negative binomial regression model for the number of weekly drinking occasions, 2 = Fitted Heckman selection model for probability that an individual drinks on at least 3 separate occasions during the diary period, @@ -18,7 +18,7 @@ binge_params_stapm } \description{ 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. diff --git a/man/subgroupRisk.Rd b/man/subgroupRisk.Rd index 218208a..3806e51 100644 --- a/man/subgroupRisk.Rd +++ b/man/subgroupRisk.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/subgroupRisk.R \name{subgroupRisk} \alias{subgroupRisk} -\title{Summarise relative risk \lifecycle{stable}} +\title{Summarise relative risk} \usage{ subgroupRisk( data, diff --git a/man/tob_alc_risk_int.Rd b/man/tob_alc_risk_int.Rd index 0b43e31..ebf7cdb 100644 --- a/man/tob_alc_risk_int.Rd +++ b/man/tob_alc_risk_int.Rd @@ -3,7 +3,7 @@ \docType{data} \name{tob_alc_risk_int} \alias{tob_alc_risk_int} -\title{Synergstic effects of tobacco and alcohol risks} +\title{Synergistic effects of tobacco and alcohol risks} \format{ A data table. We currently include estimates of synergistic effects for oral, pharyngeal, laryngeal and oesophageal cancers @@ -16,7 +16,7 @@ The data sources we use are \insertCite{Prabhu2014;textual}{tobalcepi} tob_alc_risk_int } \description{ -Synergstic effects of tobacco and alcohol risks +Synergistic effects of tobacco and alcohol risks } \references{ \insertRef{webster2018risk}{tobalcepi} diff --git a/man/tob_icd10_lookups.Rd b/man/tob_icd10_lookups.Rd index 4d3c3d8..1f02655 100644 --- a/man/tob_icd10_lookups.Rd +++ b/man/tob_icd10_lookups.Rd @@ -3,7 +3,7 @@ \docType{data} \name{tob_icd10_lookups} \alias{tob_icd10_lookups} -\title{Diseases related to tobacco and their ICD-10 defintions} +\title{Diseases related to tobacco and their ICD-10 definitions} \format{ A data table } @@ -16,6 +16,6 @@ tob_icd10_lookups \description{ 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. } \keyword{datasets} diff --git a/man/tobalc_icd10_lookups.Rd b/man/tobalc_icd10_lookups.Rd index f75258b..f9af130 100644 --- a/man/tobalc_icd10_lookups.Rd +++ b/man/tobalc_icd10_lookups.Rd @@ -3,7 +3,7 @@ \docType{data} \name{tobalc_icd10_lookups} \alias{tobalc_icd10_lookups} -\title{Diseases related to both tobacco and alcohol and their ICD-10 defintions} +\title{Diseases related to both tobacco and alcohol and their ICD-10 definitions} \format{ A data table } @@ -16,6 +16,6 @@ tobalc_icd10_lookups \description{ 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. } \keyword{datasets} diff --git a/public/404.html b/public/404.html index c184559..c632117 100644 --- a/public/404.html +++ b/public/404.html @@ -114,7 +114,7 @@
  • - +
    • diff --git a/public/LICENSE.html b/public/LICENSE.html index b8ccc48..a1b7727 100644 --- a/public/LICENSE.html +++ b/public/LICENSE.html @@ -114,7 +114,7 @@
  • - +
    • @@ -331,27 +331,27 @@

    How to Apply These Terms to Your New Programs

    If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

    To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

    -
    <one line to give the program's name and a brief idea of what it does.>
-Copyright (C) 2020 The University of Sheffield
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
    +
    <one line to give the program's name and a brief idea of what it does.>
+Copyright (C) 2020 The University of Sheffield
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

    Also add information on how to contact you by electronic and paper mail.

    If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:

    -
    tobalcepi Copyright (C) 2020 The University of Sheffield
-This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type 'show c' for details.
    +
    tobalcepi Copyright (C) 2020 The University of Sheffield
+This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type 'show c' for details.

    The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.

    You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.

    The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.

    diff --git a/public/articles/index.html b/public/articles/index.html index ed78955..8199642 100644 --- a/public/articles/index.html +++ b/public/articles/index.html @@ -114,7 +114,7 @@
  • - +
    • @@ -135,24 +135,13 @@

    Articles

    -

    Tobacco relative risks

    +

    Technical information

    -
    Smoking disease risks
    +
    Get started
    -
    -
    -
    -

    Alcohol relative risks

    -

    - -
    -
    Risk of acute conditions partially-attributable to alcohol
    -
    -
    Risk of acute conditions wholly-attributable to alcohol
    -
    -
    Risk of chronic conditions wholly-attributable to alcohol
    +
    Use of disease risks in STAPM
    diff --git a/public/articles/tobalcepi.html b/public/articles/tobalcepi.html index 0398868..1e42ccc 100644 --- a/public/articles/tobalcepi.html +++ b/public/articles/tobalcepi.html @@ -69,7 +69,7 @@
  • - +
    • @@ -83,7 +83,7 @@ -
    +

    Get started

    diff --git a/public/articles/tobalcepi_files/header-attrs-2.11/header-attrs.js b/public/articles/tobalcepi_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 0000000..dd57d92 --- /dev/null +++ b/public/articles/tobalcepi_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/public/articles/use_of_disease_risks_in_stapm.html b/public/articles/use_of_disease_risks_in_stapm.html new file mode 100644 index 0000000..fe6f2b2 --- /dev/null +++ b/public/articles/use_of_disease_risks_in_stapm.html @@ -0,0 +1,405 @@ + + + + + + + +Use of disease risks in STAPM • tobalcepi + + + + + + + + + + + + + + + + + +
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    Use of disease risks in STAPM

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    +Background

    +

    Tobacco and alcohol are leading causes of preventable disease and of socio-demographic inequalities in health and there is a great deal of literature that reports estimates of the relationship between tobacco or alcohol consumption and the risk of having or dying from a wide range of conditions. There is less information available to estimate how tobacco and alcohol consumption might combine to influence disease risk, and so for STAPM we needed to collate and understand the available information.

    +

    This vignette describes how we use the relative risks of disease in STAPM, written as a guide to help understand the functions in the tobalcepi package.

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    +Approach taken to develop the tobalcepi package

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    +Literature reviewing

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    The list of diseases, their ICD-10 code definitions and the associated risk functions were collated from periodic reviews of the literature, drawing primarily on other existing reviews. See these technical reports for further information:

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    +Developing R functions to assign relative risks of disease to individuals

    +

    To organise the information on the relative risks of diseases due to tobacco and alcohol consumption, and to provide functions to easily work with these data in modelling, we built the tobalcepi R code package (click on the link to the package webpage for introductory information). The R code functions are version controlled so that each project works with a specified version of the package (see the version tracking sheet), and error-fixes and new developments can be tracked (see the issues log and software development tasks tracking sheet.

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    The function tobalcepi::RRFunc() does the job of assigning the relative risks of each disease to a sample of individuals according to their current alcohol and/or tobacco consumption status. tobalcepi::RRFunc() has options that can tailor it to assign risks based on tobacco consumption only, alcohol consumption only, or both tobacco and alcohol consumption.

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    +Example calculations using functions from the tobalcepi package

    +

    To illustrate the use of the tobalcepi functions for different tasks, we have begun to create example workflows. You can use these examples to help understand how the code works, run them to generate model inputs, or use them as a starting point for the development of a new project (at the moment, these workflows are accessible only to the project team).

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    The workflows are listed below:

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      +
    • +Population attributable fractions. Working code repository for the estimation and exploration of the fractions of disease attributable to tobacco and/or alcohol. See also the experimental Shiny app that aims to make the population attributable fraction estimates more accessible.
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    +Tobacco–Alcohol interactions in disease risk

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    See the smoking and disease risks report (Webster et al. 2018) for a short section on tobacco-alcohol risk interactions.

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    There is evidence for the risk of disease in someone who consumes both tobacco and alcohol (\(RR_{ta}\)) being higher than would be expected from combining the independent risks from tobacco (\(RR_t\)) and alcohol (\(RR_a\)). This additional risk due to tobacco-alcohol interaction (over and above the combination of the independent contributions to risk from tobacco and alcohol) can be expressed as a “synergy factor” (1) (Prabhu, Obi, and Rubenstein 2014; Hashibe et al. 2009).

    +

    \[\begin{equation} +SF = \frac{RR_{ta}}{(RR_t - 1) + (RR_a - 1)} +\end{equation}\]

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    Data on the synergistic effects of tobacco and alcohol risks are stored in tobalcepi::tob_alc_risk_int and applied in modelling by the function tobalcepi::TobAlcInt().

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    +
    +

    +References

    +
    +
    +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. +
    +
    +Brown, Katrina F., Harriet Rumgay, Casey Dunlop, Margaret Ryan, Frances Quartly, Alison Cox, Andrew Deas, et al. 2018. “The Fraction of Cancer Attributable to Modifiable Risk Factors in England, Wales, Scotland, Northern Ireland, and the United Kingdom in 2015.” Journal Article. British Journal of Cancer 118 (8): 1130–41. https://doi.org/10.1038/s41416-018-0029-6. +
    +
    +Callum, Christine, and Patti White. 2004. Tobacco in London: The Preventable Burden. Book. SmokeFree London. +
    +
    +Carter, Brian D., Christian C. Abnet, Diane Feskanich, Neal D. Freedman, Patricia Hartge, Cora E. Lewis, Judith K. Ockene, et al. 2015. “Smoking and Mortality - Beyond Established Causes.” Journal Article. New England Journal of Medicine 372 (7): 631–40. https://doi.org/10.1056/NEJMsa1407211. +
    +
    +Cherpitel, Cheryl J, Yu Ye, Jason Bond, Guilherme Borges, and Maristela Monteiro. 2015. “Relative Risk of Injury from Acute Alcohol Consumption: Modeling the Dose–Response Relationship in Emergency Department Data from 18 Countries.” Addiction 110 (2): 279–88. https://doi.org/https://doi.org/10.1111/add.12755. +
    +
    +Hashibe, M., P. Brennan, S. C. Chuang, S. Boccia, X. Castellsague, C. Chen, M. P. Curado, et al. 2009. “Interaction Between Tobacco and Alcohol Use and the Risk of Head and Neck Cancer: Pooled Analysis in the International Head and Neck Cancer Epidemiology Consortium.” Journal Article. Cancer Epidemiology Biomarkers & Prevention 18 (2): 541–50. https://doi.org/10.1158/1055-9965.epi-08-0347. +
    +
    +Hill-McManus, D., C. R. Angus, Y. Meng, J. Holmes, A. Brennan, and P. Meier. 2014. “Injury Alcohol-Attributable Fractions: Methodological Issues and Developments.” Discussion Paper. HEDS Discussion Paper Series. Sheffield: ARRAY(0x7f690bf0c680); Health Economics; Decision Science, School of Health; Related Research (ScHARR), University of Sheffield. http://eprints.whiterose.ac.uk/97968/. +
    +
    +Hill-McManus, Daniel, Colin Angus, Yang Meng, John Holmes, Alan Brennan, and Petra Sylvia Meier. 2014. “Estimation of Usual Occasion-Based Individual Drinking Patterns Using Diary Survey Data.” Drug and Alcohol Dependence 134: 136–43. https://doi.org/https://doi.org/10.1016/j.drugalcdep.2013.09.022. +
    +
    +Holmes, John, Petra S Meier, Andrew Booth, Yelan Guo, and Alan Brennan. 2012. “The Temporal Relationship Between Per Capita Alcohol Consumption and Harm: A Systematic Review of Time Lag Specifications in Aggregate Time Series Analyses.” Drug and Alcohol Dependence 123 (1-3): 7–14. +
    +
    +Knowler, William C, Elizabeth Barrett-Connor, Sarah E Fowler, Richard F Hamman, John M Lachin, Elizabeth A Walker, and David M Nathan. 2002. “Reduction in the Incidence of Type 2 Diabetes with Lifestyle Intervention or Metformin.” Journal Article. The New England Journal of Medicine 346 (6): 393–403. +
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    +Kontis, Vasilis, Colin D Mathers, Jürgen Rehm, Gretchen A Stevens, Kevin D Shield, Ruth Bonita, Leanne M Riley, Vladimir Poznyak, Robert Beaglehole, and Majid Ezzati. 2014. “Contribution of Six Risk Factors to Achieving the 25× 25 Non-Communicable Disease Mortality Reduction Target: A Modelling Study.” Journal Article. The Lancet 384 (9941): 427–37. +
    +
    +NHS Digital. 2018. “Statistics on Smoking: England, 2018.” Report. +
    +
    +Oza, Shefali, Michael J Thun, S Jane Henley, Alan D Lopez, and Majid Ezzati. 2011. “How Many Deaths Are Attributable to Smoking in the United States? Comparison of Methods for Estimating Smoking-Attributable Mortality When Smoking Prevalence Changes.” Journal Article. Preventive Medicine 52 (6): 428–33. +
    +
    +Pokhrel, S., L. Owen, A. Lester-George, K. Coyle, Coyle D., West R., Trapero-Bertran M., and Meads C. 2013. “Tobacco Control Return on Investment Tool.” Report. National Institute for Health; Care Excellence. +
    +
    +Posey, Douglas, and Ashraf Mozayani. 2007. “The Estimation of Blood Alcohol Concentration.” Journal Article. Forensic Science, Medicine, and Pathology 3 (1): 33–39. https://doi.org/https://doi.org/10.1385/FSMP:3:1:33. +
    +
    +Prabhu, A., K. O. Obi, and J. H. Rubenstein. 2014. “The Synergistic Effects of Alcohol and Tobacco Consumption on the Risk of Esophageal Squamous Cell Carcinoma: A Meta-Analysis.” Journal Article. American Journal of Gastroenterology 109 (6): 821–27. https://doi.org/10.1038/ajg.2014.71. +
    +
    +Purshouse R, Latimer N, Brennan A. 2009. “Modelling to Assess the Effectiveness and Cost-Effectiveness of Public Health Related Strategies and Intervention to Reduce Alcohol Attributable Harm in England Using the Sheffield Alcohol Policy Model Version 2.0.” Report to the NICE Public Health Programme Development Group. https://www.nice.org.uk/guidance/ph24/evidence/economic-modelling-report-371533357. +
    +
    +Taylor, Benjamin J, Kevin D Shield, and Jürgen T Rehm. 2011. “Combining Best Evidence: A Novel Method to Calculate the Alcohol-Attributable Fraction and Its Variance for Injury Mortality.” BMC Public Health 11 (1): 265. https://doi.org/https://doi.org/10.1186/1471-2458-11-265. +
    +
    +Tobacco Advisory Group of the Royal College of Physicians. 2018. “Hiding in plain sight: Treating tobacco dependency in the NHS.” Research report. Available from: Https://Www.rcplondon.ac.uk/Projects/Outputs/Hiding-Plain-Sight-Treating-Tobacco-Dependency-Nhs. +
    +
    +US Surgeon General. 2014. “The Health Consequences of Smoking–50 Years of Progress: A Report of the Surgeon General. US Department of Health and Human Services, Centers for Disease Control and Prevention.” Journal Article. National Center for Chronic Disease Prevention and Health Promotion, Office on Smoking and Health. +
    +
    +Watson, Patricia E, Ian D Watson, and Richard D Batt. 1981. “Prediction of Blood Alcohol Concentrations in Human Subjects. Updating the Widmark Equation.” Journal of Studies on Alcohol 42 (7): 547–56. https://doi.org/10.15288/jsa.1981.42.547. +
    +
    +Webster, L, C Angus, A Brennan, and D. Gillespie. 2018. “Smoking and the Risks of Adult Diseases.” Journal Article. Https://Www.sheffield.ac.uk/Polopoly_fs/1.812908!/File/Smokingandtherisksofdisease.pdf: School of Health and Related Research, University of Sheffield. +
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z=19wnDnC?`+YC&@n`jG}6#8G9RmVc_sxe#H8ABAq`|{QwUsLipTP7lxWS=-7{(0D>F56=^xFO%PnAv%_ zLR6kXu(U8D26Ku&tc%i{#fcQ5DN}5EzG?Rd#jud4jJkhbKL2|3z00fX_l^BnNDtvk zPdo3}*RV--zI^_AfLD-hMrI^lcJc;Y0-wCa%Gj03rYKmaMX9}(i#NE2Myb#z8gX_iD>>m9u-get< literal 0 HcmV?d00001 diff --git a/public/articles/use_of_disease_risks_in_stapm_files/header-attrs-2.11/header-attrs.js b/public/articles/use_of_disease_risks_in_stapm_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 0000000..dd57d92 --- /dev/null +++ b/public/articles/use_of_disease_risks_in_stapm_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/public/authors.html b/public/authors.html index 823a4e9..464a0ff 100644 --- a/public/authors.html +++ b/public/authors.html @@ -114,7 +114,7 @@

  • - +
    • diff --git a/public/index.html b/public/index.html index eef5c15..c792cef 100644 --- a/public/index.html +++ b/public/index.html @@ -69,7 +69,7 @@
  • - +
    • diff --git a/public/pkgdown.yml b/public/pkgdown.yml index 66b2a1c..46a4cee 100644 --- a/public/pkgdown.yml +++ b/public/pkgdown.yml @@ -1,13 +1,10 @@ -pandoc: 2.9.2.1 +pandoc: 2.14.0.3 pkgdown: 1.6.1 pkgdown_sha: ~ articles: - alc_partially_attrib_acute: alc_partially_attrib_acute.html - 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 tobalcepi: tobalcepi.html -last_built: 2021-06-11T06:35Z + use_of_disease_risks_in_stapm: use_of_disease_risks_in_stapm.html +last_built: 2021-10-06T16:00Z urls: reference: https://stapm.gitlab.io/r-packages/tobalcepi//reference article: https://stapm.gitlab.io/r-packages/tobalcepi//articles diff --git a/public/reference/AlcBinge.html b/public/reference/AlcBinge.html index ceb50c2..4174afc 100644 --- a/public/reference/AlcBinge.html +++ b/public/reference/AlcBinge.html @@ -117,7 +117,7 @@
  • - +
    • diff --git a/public/reference/AlcBinge_stapm.html b/public/reference/AlcBinge_stapm.html index 84b92d2..e8a4cb7 100644 --- a/public/reference/AlcBinge_stapm.html +++ b/public/reference/AlcBinge_stapm.html @@ -6,7 +6,7 @@ -Calculate variables to inform alcohol binge model - STAPM version — AlcBinge_stapm • tobalcepi +Calculate variables to inform alcohol binge model - STAPM version — AlcBinge_stapm • tobalcepi @@ -46,10 +46,10 @@ - + @@ -118,7 +118,7 @@
  • - +
    • @@ -135,7 +135,7 @@
    -

    Calculate variables to inform alcohol binge model - STAPM version [Maturing]

    +

    Calculate variables to inform alcohol binge model - STAPM version

    @@ -143,7 +143,7 @@

    Calculate variables to inform alcohol binge model - STAPM version [Stable]

    +

    Alcohol lag times

    @@ -168,8 +168,14 @@

    Value

    on an individual's relative risk of disease has so far emerged.

    Details

    -

    All lag times are taken from the review by Holmes et al. 2012, +

    All lag times are taken from the review by Holmes et al. (2012) + , and are the numbers used in the current version of SAPM.

    +

    References

    + +

    Holmes J, Meier PS, Booth A, Guo Y, Brennan A (2012). +“The temporal relationship between per capita alcohol consumption and harm: a systematic review of time lag specifications in aggregate time series analyses.” +Drug and alcohol dependence, 123(1-3), 7--14.

    Examples

    if (FALSE) {
diff --git a/public/reference/ExpandCodes.html b/public/reference/ExpandCodes.html
index eafd555..4af958a 100644
--- a/public/reference/ExpandCodes.html
+++ b/public/reference/ExpandCodes.html
@@ -6,7 +6,7 @@
 
 
 
-Convert groups of ICD-10 codes to single codes  — ExpandCodes • tobalcepi
+Convert groups of ICD-10 codes to single codes — ExpandCodes • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
 
@@ -115,7 +115,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -132,7 +132,7 @@
 
    
   
    
     
    
-    
    Convert groups of ICD-10 codes to single codes [Stable]
    
+    
    Convert groups of ICD-10 codes to single codes
    
     
     
     
    
diff --git a/public/reference/PAFcalc.html b/public/reference/PAFcalc.html
index ad8022c..59ae247 100644
--- a/public/reference/PAFcalc.html
+++ b/public/reference/PAFcalc.html
@@ -6,7 +6,7 @@
 
 
 
-Calculate Population Attributable Fractions  — PAFcalc • tobalcepi
+Calculate Population Attributable Fractions — PAFcalc • tobalcepi
 
 
 
@@ -46,8 +46,8 @@
 
 
 
-
-
+
 
@@ -117,7 +117,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -134,19 +134,20 @@
 
    
   
    
     
    
-    
    Calculate Population Attributable Fractions [Maturing]
    
+    
    Calculate Population Attributable Fractions
    
     
     
     
    
 
     
    
-    
    Uses RRFunc() and subgroupRisk() to 
+    
    Uses [tobalcepi::RRFunc()] and [tobalcepi::subgroupRisk()] to 
 calculate population attributable fractions 
 based on the survey data provided.
    
     
    
 
     
    PAFcalc(
-  data,
+  data = NULL,
+  rrdata = NULL,
   substance,
   tob_include_risk_in_former_smokers = TRUE,
   alc_protective = TRUE,
@@ -157,7 +158,9 @@ 
    Calculate Population Attributable Fractions = "all",
   pool = FALSE,
   subgroups = c("sex", "age_cat"),
-  tobalc_include_int = FALSE
+  tobalc_include_int = FALSE,
+  within_model = FALSE,
+  mort_or_morb = c("mort", "morb")[1]
 )
    
 
     
    Arguments
    
@@ -165,7 +168,13 @@ 
    Arg
     
     
       data
-      
    Data table of individual characteristics
    
+      
    Data table of individual characteristics. Defaults to NULL.
    
+    
+    
+      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.
    
     
     
       substance
@@ -224,6 +233,16 @@ 
    Arg
 should a (synergistic/multiplicative) interaction between exposure to tobacco and alcohol be included.
 Defaults to FALSE. If TRUE, then only interactive effects for oesophageal, pharynx, oral cavity and larynx cancers
 are considered.
    
+    
+    
+      within_model
+      
    Logical - is the function being used to calculate PAFs 
+from the results of a STAPM model simulation. Defaults to FALSE.
    
+    
+    
+      mort_or_morb
+      
    Character string - whether the risk functions for conditions with separate mortality and morbidity risk functions 
+should refer to mortality or morbidity. Values could be "mort" or "morb". Default is "mort".
    
     
     
 
diff --git a/public/reference/PArisk.html b/public/reference/PArisk.html
index f4aaf52..2f38067 100644
--- a/public/reference/PArisk.html
+++ b/public/reference/PArisk.html
@@ -6,7 +6,7 @@
 
 
 
-Relative risks for alcohol-related injuries  — PArisk • tobalcepi
+Relative risks for alcohol-related injuries — PArisk • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
@@ -116,7 +116,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -133,7 +133,7 @@
 
    
   
    
     
    
-    
    Relative risks for alcohol-related injuries [Stable]
    
+    
    Relative risks for alcohol-related injuries
    
     
     
     
    
@@ -144,8 +144,7 @@ 
    Relative risks for alcohol-related injuries PArisk(
-  SODMean = NULL,
-  SODSDV = NULL,
+  interval_prob_vec = NULL,
   SODFreq = NULL,
   Weight = NULL,
   Widmark_r = NULL,
@@ -160,14 +159,9 @@ 
    Arg
     
-      
-      
-    
-    
-      
-      
+      
+      
diff --git a/public/reference/RRFunc.html b/public/reference/RRFunc.html
index e04cfbd..f116ded 100644
--- a/public/reference/RRFunc.html
+++ b/public/reference/RRFunc.html
@@ -6,7 +6,7 @@
 
 
-Individual relative risks of disease  — RRFunc • tobalcepi
+Individual relative risks of disease — RRFunc • tobalcepi
@@ -46,7 +46,7 @@
 
 
 
-
+
-    
+    
@@ -135,7 +135,7 @@
 
    
   
    
     
    
-    
    Individual relative risks of disease [Maturing]
    
+    
    Individual relative risks of disease
    
     
     
     
    
@@ -262,7 +262,7 @@ 
    Arg
     
    
-      
    
     
     
    SODMean
    Numeric vector - the average amount that each individual is expected to
-drink on a single drinking occasion.
    SODSDV
    Numeric vector - the standard deviation of the amount that each individual is expected to
-drink on a single drinking occasion.
    		interval_prob_vec
    Column of vectors - the probabilities that each individual 
+drinks each amount of grams of ethanol (1:600) on a single drinking occasion.
    		
     
    
     
    
       SODFreq
 
 
 
 
 
      
   
 
    
     
    
       within_model
    Logical - is the function being used within a new-style STAPM simulation. 
+      
    Logical - is the function being used within a STAPM simulation. 
 Defaults to TRUE.
    		
     
    
     
    
@@ -284,7 +284,7 @@ 
    <
     
 
 
    For alcohol, the relative risk for each individual for each disease is calculated based on 
-their average weekly alcohol consumption (using 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, 
diff --git a/public/reference/RRTobDR.html b/public/reference/RRTobDR.html
index bf8e9e2..35fe93c 100644
--- a/public/reference/RRTobDR.html
+++ b/public/reference/RRTobDR.html
@@ -115,7 +115,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
diff --git a/public/reference/RRalc.html b/public/reference/RRalc.html
index c1f08fc..7411335 100644
--- a/public/reference/RRalc.html
+++ b/public/reference/RRalc.html
@@ -6,7 +6,7 @@
 
 
 
-Relative risks for alcohol related diseases  — RRalc • tobalcepi
+Relative risks for alcohol related diseases — RRalc • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
 
@@ -115,7 +115,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -132,7 +132,7 @@
 
    
   
    
     
    
-    
    Relative risks for alcohol related diseases [Stable]
    
+    
    Relative risks for alcohol related diseases
    
     
     
     
    
@@ -231,12 +231,12 @@ 
    Details
 separate risk functions for morbidity and mortality. For conditions that show a J-shaped risk function that
 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 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 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 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
diff --git a/public/reference/RRtob.html b/public/reference/RRtob.html
index e5e1c2f..d0ac4e9 100644
--- a/public/reference/RRtob.html
+++ b/public/reference/RRtob.html
@@ -6,7 +6,7 @@
 
 
 
-Tobacco relative risks  — RRtob • tobalcepi
+Tobacco relative risks — RRtob • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
 
@@ -115,7 +115,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -132,7 +132,7 @@
 
    
   
    
     
    
-    
    Tobacco relative risks [Maturing]
    
+    
    Tobacco relative risks
    
     
     
     
    
diff --git a/public/reference/TobAlcInt.html b/public/reference/TobAlcInt.html
index e404ea6..0746c92 100644
--- a/public/reference/TobAlcInt.html
+++ b/public/reference/TobAlcInt.html
@@ -6,7 +6,7 @@
 
 
 
-Risk interaction between tobacco and alcohol  — TobAlcInt • tobalcepi
+Risk interaction between tobacco and alcohol — TobAlcInt • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
@@ -116,7 +116,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -133,7 +133,7 @@
 
    
   
    
     
    
-    
    Risk interaction between tobacco and alcohol [Maturing]
    
+    
    Risk interaction between tobacco and alcohol
    
     
     
     
    
@@ -207,14 +207,14 @@ 
    R
 , https://figshare.shef.ac.uk/articles/Smoking_and_the_risks_of_adult_diseases/7411451/1.
    
 
    Hashibe M, Brennan P, Chuang SC, Boccia S, Castellsague X, Chen C, Curado MP, Dal Maso L, Daudt AW, Fabianova E, Fernandez L, Wunsch-Filho V, Franceschi S, Hayes RB, Herrero R, Kelsey K, Koifman S, La Vecchia C, Lazarus P, Levi F, Lence JJ, Mates D, Matos E, Menezes A, McClean MD, Muscat J, Eluf-Neto J, Olshan AF, Purdue M, Rudnai P, Schwartz SM, Smith E, Sturgis EM, Szeszenia-Dabrowska N, Talamini R, Wei QY, Winn DM, Shangina O, Pilarska A, Zhang ZF, Ferro G, Berthiller J, Boffetta P (2009).
 “Interaction between Tobacco and Alcohol Use and the Risk of Head and Neck Cancer: Pooled Analysis in the International Head and Neck Cancer Epidemiology Consortium.”
-Cancer Epidemiology Biomarkers \& Prevention, 18(2), 541--550.
+Cancer Epidemiology Biomarkers \& Prevention, 18(2), 541-550.
 ISSN 1055-9965, doi: 10.1158/1055-9965.epi-08-0347
-, https://doi.org/10.1158/1055-9965.epi-08-0347.
    
+.
    
 
    Prabhu A, Obi KO, Rubenstein JH (2014).
 “The Synergistic Effects of Alcohol and Tobacco Consumption on the Risk of Esophageal Squamous Cell Carcinoma: A Meta-Analysis.”
-American Journal of Gastroenterology, 109(6), 821--827.
+American Journal of Gastroenterology, 109(6), 821-827.
 ISSN 0002-9270, doi: 10.1038/ajg.2014.71
-, https://doi.org/10.1038/ajg.2014.71.
    
+.
    
 
     
    Examples
    
     
    
diff --git a/public/reference/TobLags.html b/public/reference/TobLags.html
index 568e2b1..a5c62ed 100644
--- a/public/reference/TobLags.html
+++ b/public/reference/TobLags.html
@@ -6,7 +6,7 @@
 
 
 
-Tobacco lag times  — TobLags • tobalcepi
+Tobacco lag times — TobLags • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
@@ -117,7 +117,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -134,7 +134,7 @@
 
    
   
    
     
    
-    
    Tobacco lag times [Stable]
    
+    
    Tobacco lag times
    
     
     
     
    
diff --git a/public/reference/WArisk_acute.html b/public/reference/WArisk_acute.html
index a7e2bcb..6d7f825 100644
--- a/public/reference/WArisk_acute.html
+++ b/public/reference/WArisk_acute.html
@@ -6,7 +6,7 @@
 
 
 
-Risk of acute conditions wholly-attributable to alcohol  — WArisk_acute • tobalcepi
+Risk of acute conditions wholly-attributable to alcohol — WArisk_acute • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
@@ -117,7 +117,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -134,7 +134,7 @@
 
    
   
    
     
    
-    
    Risk of acute conditions wholly-attributable to alcohol [Stable]
    
+    
    Risk of acute conditions wholly-attributable to alcohol
    
     
     
     
    
@@ -146,8 +146,7 @@ 
    Risk of acute conditions wholly-attributable to alcohol WArisk_acute(
-  SODMean,
-  SODSDV,
+  interval_prob_vec,
   SODFreq,
   sex,
   grams_ethanol_per_unit = 8,
@@ -158,14 +157,9 @@ 
    Arg
     
-      
-      
-    
-    
-      
-      
+      
+      
@@ -199,7 +193,7 @@ 
    Details
 The calculation is based on the link between average weekly alcohol consumption and 
 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
@@ -215,6 +209,8 @@ 
    Examp
     
    
 if (FALSE) {
 
+# example needs updating
+
 # Function called within RRAlc()
 
 data[ , ar := 
diff --git a/public/reference/alc_disease_names.html b/public/reference/alc_disease_names.html
index d8b4506..d7fe35e 100644
--- a/public/reference/alc_disease_names.html
+++ b/public/reference/alc_disease_names.html
@@ -115,7 +115,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -154,8 +154,7 @@ 
    R
     
    Angus C, Henney M, Webster L, Gillespie D (2018).
 “Alcohol-attributable diseases and dose-response curves for the Sheffield Alcohol Policy Model version 4.0.”
 The University of Sheffield.
-doi: 10.15131/shef.data.6819689.v2
-, https://doi.org/10.15131/shef.data.6819689.v2.
    
+https://doi.org/10.15131/shef.data.6819689.v2.
    
 
   
    
   
    
+        
-        
+        
-        
+        
@@ -199,7 +199,7 @@ 
    
           
    RRtob() 
    
         
-        
    
+        
-        
+        
-        
+        
-        
+        
-        
+        
       
@@ -313,19 +313,19 @@ 
    AlcBinge_stapm() 
    
         
-        
    
+        
-        
+        
-        
+        
-        
+        
       
@@ -356,7 +356,7 @@ 
    AlcLags() 
    
         
-        
    
+        
@@ -375,19 +375,19 @@ 
    TobAlcInt() 
    
         
-        
    
+        
-        
+        
-        
+        
@@ -406,13 +406,19 @@ 
    <
         
    
-        
+        
+      
+        
+        
+        
    
     
     
    SODMean
    Numeric - the average amount that each individual is expected to
-drink on a single drinking occasion.
    SODSDV
    Numeric - the standard deviation of the amount that each individual is expected to
-drink on a single drinking occasion.
    		interval_prob_vec
    Column of vectors - the probabilities that each individual 
+drinks each amount of grams of ethanol (1:600) on a single drinking occasion.
    		
     
    
     
    
       SODFreq
    Individual relative risks of disease [Maturing]
    Individual relative risks of disease
    		
       
    
         
         
           
    subgroupRisk() 
    
         
    Summarise relative risk [Stable]
    Summarise relative risk
    		
       
    
         
         
           
    PAFcalc() 
    
         
    Calculate Population Attributable Fractions [Maturing]
    Calculate Population Attributable Fractions
    		
       
    
         
       
    Tobacco relative risks [Maturing]
    Tobacco relative risks
    		
       
    
         
         
@@ -217,7 +217,7 @@ 
    
           
    tob_icd10_lookups 
    
         
    Diseases related to tobacco and their ICD-10 defintions
    Diseases related to tobacco and their ICD-10 definitions
    		
       
    
         
         
@@ -242,7 +242,7 @@ 
    TobLags() 
    
         
    Tobacco lag times [Stable]
    Tobacco lag times
    		
       
    
         
         
@@ -276,7 +276,7 @@ 
    
           
    RRalc() 
    
         
    Relative risks for alcohol related diseases [Stable]
    Relative risks for alcohol related diseases
    		
       
    
         
         
@@ -288,7 +288,7 @@ 
    
           
    alc_icd10_lookups 
    
         
    Diseases related to alcohol and their ICD-10 defintions
    Diseases related to alcohol and their ICD-10 definitions
    		
       
    
     
    Calculate variables to inform alcohol binge model - STAPM version [Maturing]
    Calculate variables to inform alcohol binge model - STAPM version
    		
       
    
         
         
           
    PArisk() 
    
         
    Relative risks for alcohol-related injuries [Stable]
    Relative risks for alcohol-related injuries
    		
       
    
         
         
           
    WArisk_acute() 
    
         
    Risk of acute conditions wholly-attributable to alcohol [Stable]
    Risk of acute conditions wholly-attributable to alcohol
    		
       
    
         
         
@@ -337,7 +337,7 @@ 
    binge_params_stapm 
    
         
    Parameters to estimate amount drunk on single occassions - STAPM version
    Parameters to estimate amount drunk on single occasions - STAPM version
    		
       
    
     
    Alcohol lag times [Stable]
    Alcohol lag times
    		
       
    
         
       
    Risk interaction between tobacco and alcohol [Maturing]
    Risk interaction between tobacco and alcohol
    		
       
    
         
         
           
    tob_alc_risk_int 
    
         
    Synergstic effects of tobacco and alcohol risks
    Synergistic effects of tobacco and alcohol risks
    		
       
    
         
         
           
    tobalc_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
    		
       
    
         
       
    
           
    ExpandCodes() 
    
         
    Convert groups of ICD-10 codes to single codes [Stable]
    Convert groups of ICD-10 codes to single codes
    		
       
    
         
         
           
    disease_groups 
    
             		
         
    Groupings of diseases into disease types
    
+          
    intervalprob() 
    
+        
    Distribution of single-occasion drinking amount
    		
       
    
         
     
    
diff --git a/public/reference/intervalprob.html b/public/reference/intervalprob.html
new file mode 100644
index 0000000..6abb81f
--- /dev/null
+++ b/public/reference/intervalprob.html
@@ -0,0 +1,218 @@
+
+
+
+  
+  
+
+
+
+Distribution of single-occasion drinking amount — intervalprob • tobalcepi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    
    
+      
    
+      
+
+      
+
+      
    
+
+
    
+  
    
+    
    
+    
    Distribution of single-occasion drinking amount
    
+    
+    
+    
    
+
+    
    
+    
    Computes the probability that each integer number of grams of ethanol per day 
+is consumed on a single drinking occasion.
    
+    
    
+
+    
    intervalprob(
+  grams_ethanol = 1:600,
+  SODMean = NULL,
+  SODSDV = NULL,
+  SODFreq = NULL,
+  grams_ethanol_per_unit = 8
+)
    
+
+    
    Arguments
    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
    grams_ethanol
    Integer vector - the potential grams of ethanol drunk on a single occasion.
    SODMean
    Numeric vector - the average amount that each individual is expected to
+drink on a single drinking occasion.
    SODSDV
    Numeric vector - the standard deviation of the amount that each individual is expected to
+drink on a single drinking occasion.
    SODFreq
    Numeric vector - the expected number of drinking occasions that
+each individual has each week.
    grams_ethanol_per_unit
    Numeric value giving the conversion factor for the number of grams of pure
+ethanol in one UK standard unit of alcohol.
    
+
+    
    Value
    
+
+    
    Returns a numeric vector containing the probability that each amount of alcohol is consumed
    
+
+    
    Examples
    
+    
    
+
+
    
+  
    
+  
+
    
+
+
+      
+   
    
+
+  
+
+
+  
+
+
+
diff --git a/public/reference/subgroupRisk.html b/public/reference/subgroupRisk.html
index 6f221e7..e5b0ec7 100644
--- a/public/reference/subgroupRisk.html
+++ b/public/reference/subgroupRisk.html
@@ -6,7 +6,7 @@
 
 
 
-Summarise relative risk  — subgroupRisk • tobalcepi
+Summarise relative risk — subgroupRisk • tobalcepi
 
 
 
@@ -46,7 +46,7 @@
 
 
 
-
+
 
 
@@ -116,7 +116,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -133,7 +133,7 @@
 
    
   
    
     
    
-    
    Summarise relative risk [Stable]
    
+    
    Summarise relative risk
    
     
     
     
    
diff --git a/public/reference/tob_alc_risk_int.html b/public/reference/tob_alc_risk_int.html
index fbf9c05..824858f 100644
--- a/public/reference/tob_alc_risk_int.html
+++ b/public/reference/tob_alc_risk_int.html
@@ -6,7 +6,7 @@
 
 
 
-Synergstic effects of tobacco and alcohol risks — tob_alc_risk_int • tobalcepi
+Synergistic effects of tobacco and alcohol risks — tob_alc_risk_int • tobalcepi
 
 
 
@@ -46,8 +46,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -115,7 +115,7 @@
 
 
  • 
   
-    
+    
      
   
 
    • 
@@ -132,13 +132,13 @@
 
    
   
    
     
    
-    
    Synergstic effects of tobacco and alcohol risks
    
+    
    Synergistic effects of tobacco and alcohol risks
    
     
     
     
    
 
     
    
-    
    Synergstic effects of tobacco and alcohol risks
    
+    
    Synergistic effects of tobacco and alcohol risks
    
     
    
 
     
    tob_alc_risk_int
    
@@ -163,14 +163,14 @@ 
    R
 , https://figshare.shef.ac.uk/articles/Smoking_and_the_risks_of_adult_diseases/7411451/1.
    
 
    Hashibe M, Brennan P, Chuang SC, Boccia S, Castellsague X, Chen C, Curado MP, Dal Maso L, Daudt AW, Fabianova E, Fernandez L, Wunsch-Filho V, Franceschi S, Hayes RB, Herrero R, Kelsey K, Koifman S, La Vecchia C, Lazarus P, Levi F, Lence JJ, Mates D, Matos E, Menezes A, McClean MD, Muscat J, Eluf-Neto J, Olshan AF, Purdue M, Rudnai P, Schwartz SM, Smith E, Sturgis EM, Szeszenia-Dabrowska N, Talamini R, Wei QY, Winn DM, Shangina O, Pilarska A, Zhang ZF, Ferro G, Berthiller J, Boffetta P (2009).
 “Interaction between Tobacco and Alcohol Use and the Risk of Head and Neck Cancer: Pooled Analysis in the International Head and Neck Cancer Epidemiology Consortium.”
-Cancer Epidemiology Biomarkers \& Prevention, 18(2), 541--550.
+Cancer Epidemiology Biomarkers \& Prevention, 18(2), 541-550.
 ISSN 1055-9965, doi: 10.1158/1055-9965.epi-08-0347
-, https://doi.org/10.1158/1055-9965.epi-08-0347.
    
+.
    
 
    Prabhu A, Obi KO, Rubenstein JH (2014).
 “The Synergistic Effects of Alcohol and Tobacco Consumption on the Risk of Esophageal Squamous Cell Carcinoma: A Meta-Analysis.”
-American Journal of Gastroenterology, 109(6), 821--827.
+American Journal of Gastroenterology, 109(6), 821-827.
 ISSN 0002-9270, doi: 10.1038/ajg.2014.71
-, https://doi.org/10.1038/ajg.2014.71.
    
+.