diff --git a/R/AlcBinge.R b/R/AlcBinge.R index 4647909..39fa6d2 100644 --- a/R/AlcBinge.R +++ b/R/AlcBinge.R @@ -1,7 +1,5 @@ -#' Calculate variables to inform alcohol binge model -#' -#' \lifecycle{superseded} +#' Calculate variables to inform alcohol binge model \lifecycle{superseded} #' #' Designed to work with cross-sectional survey data with a wide range of individual-level covariates. #' Uses survey data and previously estimated coefficients to describe diff --git a/R/AlcBinge_stapm.R b/R/AlcBinge_stapm.R index db5fa1d..64bb3d9 100644 --- a/R/AlcBinge_stapm.R +++ b/R/AlcBinge_stapm.R @@ -1,7 +1,5 @@ -#' Calculate variables to inform alcohol binge model - STAPM version -#' -#' \lifecycle{maturing} +#' Calculate variables to inform alcohol binge model - STAPM version \lifecycle{maturing} #' #' Designed to work with simulated individual trajectories of alcohol consumption - stratified by #' age category, sex and IMD quintile. Assigns coefficients stratified by age category, sex and IMD quintile to diff --git a/R/AlcLags.R b/R/AlcLags.R index aabb795..35d3e3b 100644 --- a/R/AlcLags.R +++ b/R/AlcLags.R @@ -1,7 +1,5 @@ -#' Alcohol lag times -#' -#' \lifecycle{stable} +#' Alcohol lag times \lifecycle{stable} #' #' Prepare the disease specific functions that describe how a change in alcohol consumption #' gradually has an effect on the relative risk of disease incidence over time (up to 20 years) diff --git a/R/ExpandCodes.R b/R/ExpandCodes.R index b3ba653..3c99b3b 100644 --- a/R/ExpandCodes.R +++ b/R/ExpandCodes.R @@ -1,8 +1,6 @@ -#' Convert groups of ICD-10 codes to single codes -#' -#' \lifecycle{stable} +#' Convert groups of ICD-10 codes to single codes \lifecycle{stable} #' #' Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol. #' diff --git a/R/PArisk.R b/R/PArisk.R index 2c7a329..c2214de 100644 --- a/R/PArisk.R +++ b/R/PArisk.R @@ -1,8 +1,6 @@ -#' Relative risks for alcohol-related injuries -#' -#' \lifecycle{stable} +#' Relative risks for alcohol-related injuries \lifecycle{stable} #' #' Uses the 'new' binge model methods to calculate a relative risk #' for each individual for experiencing each cause during one year. diff --git a/R/RRAlc.R b/R/RRAlc.R index acab300..b286d30 100644 --- a/R/RRAlc.R +++ b/R/RRAlc.R @@ -1,8 +1,6 @@ -#' Relative risks for alcohol related diseases -#' -#' \lifecycle{stable} +#' Relative risks for alcohol related diseases \lifecycle{stable} #' #' Computes the relative risks for each alcohol related disease based on the published risk curves. #' diff --git a/R/RRFunc.R b/R/RRFunc.R index 99c81e8..30c1d5b 100644 --- a/R/RRFunc.R +++ b/R/RRFunc.R @@ -1,7 +1,5 @@ -#' Individual relative risks of disease -#' -#' \lifecycle{maturing} +#' Individual relative risks of disease \lifecycle{maturing} #' #' @description #' This function takes a sample of individuals and computes each individual's relative risk diff --git a/R/RRTobDR.R b/R/RRTobDR.R index b0fc23e..97f2ebb 100644 --- a/R/RRTobDR.R +++ b/R/RRTobDR.R @@ -1,6 +1,4 @@ -#' Dose-response relative risks for tobacco-related cancers -#' -#' \lifecycle{experimental} +#' Dose-response relative risks for tobacco-related cancers \lifecycle{experimental} #' #' Computes the relative risks for each tobacco-related cancer based on the published risk curves. #' diff --git a/R/RRtob.R b/R/RRtob.R index 798c340..6bedbf1 100644 --- a/R/RRtob.R +++ b/R/RRtob.R @@ -1,7 +1,5 @@ -#' Tobacco relative risks -#' -#' \lifecycle{maturing} +#' Tobacco relative risks \lifecycle{maturing} #' #' Relative risks for current vs. never cigarette smokers. #' diff --git a/R/TobAlcInt.R b/R/TobAlcInt.R index 0ba33d0..fbc3225 100644 --- a/R/TobAlcInt.R +++ b/R/TobAlcInt.R @@ -1,8 +1,6 @@ -#' Risk interaction between tobacco and alcohol -#' -#' \lifecycle{maturing} +#' Risk interaction between tobacco and alcohol \lifecycle{maturing} #' #' Assigns the disease-specific interaction term (synergy index) appropriate to each #' individual's tobacco and alcohol consumption. diff --git a/R/TobLags.R b/R/TobLags.R index 9d61e63..4456aa5 100644 --- a/R/TobLags.R +++ b/R/TobLags.R @@ -1,7 +1,5 @@ -#' Tobacco lag times -#' -#' \lifecycle{stable} +#' Tobacco lag times \lifecycle{stable} #' #' Prepare the disease specific functions that describe how a change in tobacco consumption #' gradually has an effect on the relative risk of disease incidence over time (up to 40 years) diff --git a/R/WArisk_acute.R b/R/WArisk_acute.R index d4ca467..c2e6e4c 100644 --- a/R/WArisk_acute.R +++ b/R/WArisk_acute.R @@ -1,7 +1,5 @@ -#' Risk of acute conditions wholly-attributable to alcohol -#' -#' \lifecycle{stable} +#' Risk of acute conditions wholly-attributable to alcohol \lifecycle{stable} #' #' Uses the 'new' binge model methods to calculate the risk #' that each individual experiences each acute consequence of drinking during one year diff --git a/R/subgroupRisk.R b/R/subgroupRisk.R index 9305a97..8bd45c3 100644 --- a/R/subgroupRisk.R +++ b/R/subgroupRisk.R @@ -1,7 +1,5 @@ -#' Summarise relative risk -#' -#' \lifecycle{stable} +#' Summarise relative risk \lifecycle{stable} #' #' Calculate the sum of the relative risk for all individuals in a subgroup, #' or calculate the subgroup specific attributable fraction based on the current relative risks. diff --git a/_pkgdown.yml b/_pkgdown.yml index 6af9052..5339fae 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -28,11 +28,12 @@ reference: - title: Tobacco relative risks - subtitle: Disease definitions and relative risks contents: + - RRtob + - RRTobDR - tob_disease_names - tob_icd10_lookups - tobacco_relative_risks - - RRtob - - RRTobDR + - subtitle: Tobacco lag times contents: - TobLags @@ -41,9 +42,10 @@ reference: - title: Alcohol relative risks - subtitle: Disease definitions and relative risks contents: + - RRalc - alc_disease_names - alc_icd10_lookups - - RRalc + - subtitle: Disease risk linked to intoxication contents: - AlcBinge diff --git a/man/AlcBinge.Rd b/man/AlcBinge.Rd index 548923b..642da62 100644 --- a/man/AlcBinge.Rd +++ b/man/AlcBinge.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/AlcBinge.R \name{AlcBinge} \alias{AlcBinge} -\title{Calculate variables to inform alcohol binge model} +\title{Calculate variables to inform alcohol binge model \lifecycle{superseded}} \usage{ AlcBinge(data, params = tobalcepi::binge_params) } @@ -16,13 +16,11 @@ from Hill-McManus et al 2014, Tables 3, 5 and 6.} Returns data plus the estimated variables. } \description{ -\lifecycle{superseded} -} -\details{ Designed to work with cross-sectional survey data with a wide range of individual-level covariates. Uses survey data and previously estimated coefficients to describe the patterns of single occasion drinking. - +} +\details{ This is based on a study by Hill-McManus 2014, who analysed drinking occasions using data from detailed diaries in the National Diet and Nutrition Survey 2000/2001. Using the results, it possible to model each individual's expected number of drinking occasions across the year, diff --git a/man/AlcBinge_stapm.Rd b/man/AlcBinge_stapm.Rd index 6744b87..5513300 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} +\title{Calculate variables to inform alcohol binge model - STAPM version \lifecycle{maturing}} \usage{ AlcBinge_stapm(data, params = tobalcepi::binge_params_stapm) } @@ -18,14 +18,12 @@ averaged by age category, sex and IMD quintile.} Returns data plus the estimated variables. } \description{ -\lifecycle{maturing} -} -\details{ 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 -at each time step in the simulation. - +at each time step in the simulation. +} +\details{ The coefficients used come originally from a study by Hill-McManus 2014, who analysed drinking occasions using data from detailed diaries in the National Diet and Nutrition Survey 2000/2001. Using the results, it possible to model each individual's expected number of drinking occasions across the year, diff --git a/man/AlcLags.Rd b/man/AlcLags.Rd index f9f7f3e..133df85 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} +\title{Alcohol lag times \lifecycle{stable}} \usage{ AlcLags(disease_name = c("Pharynx", "Oral_cavity"), n_years = 20) } @@ -18,13 +18,11 @@ that gives the proportion by which the effect of a change in consumption on an individual's relative risk of disease has so far emerged. } \description{ -\lifecycle{stable} -} -\details{ 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. - +} +\details{ All lag times are taken from the review by Holmes et al. 2012, and are the numbers used in the current version of SAPM. } diff --git a/man/ExpandCodes.Rd b/man/ExpandCodes.Rd index 0c7eef4..383ba70 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} +\title{Convert groups of ICD-10 codes to single codes \lifecycle{stable}} \usage{ ExpandCodes(lkup) } @@ -13,11 +13,9 @@ ExpandCodes(lkup) Returns a data frame containing a row for each single ICD-10 code to be searched for. } \description{ -\lifecycle{stable} +Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol. } \details{ -Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol. - For example, if one disease category is C00-C06 (oral cancer), this includes the single codes C00,C01,C02,C03,C04,C05,C06. The number of rows will be expanded to give each single code its own row. diff --git a/man/PArisk.Rd b/man/PArisk.Rd index 1d41942..534d05d 100644 --- a/man/PArisk.Rd +++ b/man/PArisk.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/PArisk.R \name{PArisk} \alias{PArisk} -\title{Relative risks for alcohol-related injuries} +\title{Relative risks for alcohol-related injuries \lifecycle{stable}} \usage{ PArisk( SODMean = NULL, @@ -53,12 +53,10 @@ the number of grams of ethanol in one standard drink.} Returns a numeric vector of each individual's relative risk of the acute consequences of drinking. } \description{ -\lifecycle{stable} -} -\details{ Uses the 'new' binge model methods to calculate a relative risk for each individual for experiencing each cause during one year. - +} +\details{ This calculation treats an ocassion as a single point in time and therefore does not detail about the rate of alcohol absorbtion (i.e. there is no alcohol absorbtion rate constant) or the time interval between drinks within an occassion. This could introduce inaccuracies if diff --git a/man/RRFunc.Rd b/man/RRFunc.Rd index b5b717b..74493fa 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} +\title{Individual relative risks of disease \lifecycle{maturing}} \usage{ RRFunc( data, @@ -97,8 +97,6 @@ There is an option to tailor this to the alcohol only, tobacco only, or joint tobacco and alcohol contexts. } \details{ -\lifecycle{maturing} - See below } \section{Alcohol risk}{ diff --git a/man/RRTobDR.Rd b/man/RRTobDR.Rd index ef8724d..fd555ae 100644 --- a/man/RRTobDR.Rd +++ b/man/RRTobDR.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RRTobDR.R \name{RRTobDR} \alias{RRTobDR} -\title{Dose-response relative risks for tobacco-related cancers} +\title{Dose-response relative risks for tobacco-related cancers \lifecycle{experimental}} \usage{ RRTobDR(data, disease = "Pharynx", av_cigs_day = "cigs_per_day") } @@ -18,11 +18,9 @@ average number of daily cigarettes.} Returns a numeric vector of each individual's relative risks for the tobacco related disease specified by "disease". } \description{ -\lifecycle{experimental} +Computes the relative risks for each tobacco-related cancer based on the published risk curves. } \details{ -Computes the relative risks for each tobacco-related cancer based on the published risk curves. - Relative risks for come from published risk functions whose parameters have been hard-coded within this function rather than being read from an external spreadsheet. These relative risks are based on an individual's current smoking intensity. There are diff --git a/man/RRalc.Rd b/man/RRalc.Rd index 369b775..34ebde2 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} +\title{Relative risks for alcohol related diseases \lifecycle{stable}} \usage{ RRalc( data, @@ -56,11 +56,9 @@ ethanol in one UK standard unit of alcohol.} Returns a numeric vector of each individual's relative risks for the alcohol related disease specified by "disease". } \description{ -\lifecycle{stable} +Computes the relative risks for each alcohol related disease based on the published risk curves. } \details{ -Computes the relative risks for each alcohol related disease based on the published risk curves. - Relative risks for partially attributable chronic come from published risk functions whose parameters have been hard-coded within this function rather than being read from an external spreadsheet. For some conditions there are separate risk functions for morbidity and mortality. For conditions that show a J-shaped risk function that diff --git a/man/RRtob.Rd b/man/RRtob.Rd index 48321b4..ca097b1 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} +\title{Tobacco relative risks \lifecycle{maturing}} \usage{ RRtob( data, @@ -33,11 +33,9 @@ Returns a numeric vector of each individual's relative risks for the tobacco-rel specified by "disease". } \description{ -\lifecycle{maturing} +Relative risks for current vs. never cigarette smokers. } \details{ -Relative risks for current vs. never cigarette smokers. - We focus on the risks of current smoking and limit ourselves to diseases that affect the consumer themselves e.g. excluding secondary effects of smoking on children. We assume the equivalence of relative risks and odds ratios. diff --git a/man/TobAlcInt.Rd b/man/TobAlcInt.Rd index 8fdf67a..f20ec08 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} +\title{Risk interaction between tobacco and alcohol \lifecycle{maturing}} \usage{ TobAlcInt( data, @@ -31,12 +31,10 @@ Returns a numeric vector containing of each individual's relative risks for the specified by "disease". } \description{ -\lifecycle{maturing} -} -\details{ Assigns the disease-specific interaction term (synergy index) appropriate to each individual's tobacco and alcohol consumption. - +} +\details{ We currently include estimates of synergistic effects for oral, pharyngeal, laryngeal and oesophageal cancers (we describe these data and their sources in our tobacco risk functions report diff --git a/man/TobLags.Rd b/man/TobLags.Rd index 037c0a1..3afce58 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} +\title{Tobacco lag times \lifecycle{stable}} \usage{ TobLags( disease_name = c("Pharynx", "Oral_cavity"), @@ -25,13 +25,11 @@ that gives the proportion by which the effect of a change in consumption on an individual's relative risk of disease has so far emerged. } \description{ -\lifecycle{stable} -} -\details{ 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) since e.g. someone quit smoking - +} +\details{ All lag times are taken from a re-analysis of the Cancer prevention II study by Oza et al 2011 and Kontis et al 2014 The values were sent to us by Kontis. Lags are smoothed functions over time describing the proportion of the excess risk due to smoking that still remains. diff --git a/man/WArisk_acute.Rd b/man/WArisk_acute.Rd index 90f0160..6cfc4da 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} +\title{Risk of acute conditions wholly-attributable to alcohol \lifecycle{stable}} \usage{ WArisk_acute( SODMean, @@ -37,13 +37,11 @@ Defaults to 3 units/day for females and 4 units/day for males.} Returns a numeric vector of each individual's relative risk of the acute consequences of drinking. } \description{ -\lifecycle{stable} -} -\details{ Uses the 'new' binge model methods to calculate the risk that each individual experiences each acute consequence of drinking during one year -(e.g. alcohol poisoning or the effects of acute intoxication). - +(e.g. alcohol poisoning or the effects of acute intoxication). +} +\details{ The function implements a new method for estimating risk that was developed to suit the STAPM modelling. The calculation is based on the link between average weekly alcohol consumption and the distribution of characteristics of single ocassion drinking described by the diff --git a/man/subgroupRisk.Rd b/man/subgroupRisk.Rd index 5c66a54..6cf0d5d 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} +\title{Summarise relative risk \lifecycle{stable}} \usage{ subgroupRisk( data, @@ -38,12 +38,10 @@ Weight variable must be called "wt_int".} Returns a data table containing the subgroup specific summaries for each disease. } \description{ -\lifecycle{stable} -} -\details{ 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. - +} +\details{ Attributable fractions are calculated using the method as in Bellis & Jones 2014, which is also equivalent to the method described in the Brennan et al. 2015 SAPM mathematical description paper. } diff --git a/public/pkgdown.yml b/public/pkgdown.yml index 423bd79..0bd2dca 100644 --- a/public/pkgdown.yml +++ b/public/pkgdown.yml @@ -6,7 +6,7 @@ articles: alc_wholly_attrib_acute: alc_wholly_attrib_acute.html alc_wholly_attrib_chronic: alc_wholly_attrib_chronic.html smoking-disease-risks: smoking-disease-risks.html -last_built: 2020-11-28T17:05Z +last_built: 2020-11-28T17:18Z urls: reference: https://stapm.gitlab.io/tobalcepi/reference article: https://stapm.gitlab.io/tobalcepi/articles diff --git a/public/reference/AlcBinge.html b/public/reference/AlcBinge.html index 80074f3..e17afc6 100644 --- a/public/reference/AlcBinge.html +++ b/public/reference/AlcBinge.html @@ -6,7 +6,7 @@ -Calculate variables to inform alcohol binge model — AlcBinge • tobalcepi +Calculate variables to inform alcohol binge model — AlcBinge • tobalcepi @@ -39,8 +39,10 @@ - - + + @@ -124,13 +126,15 @@
-

Calculate variables to inform alcohol binge model

+

Calculate variables to inform alcohol binge model Superseded lifecycle

-

Superseded lifecycle

+

Designed to work with cross-sectional survey data with a wide range of individual-level covariates. +Uses survey data and previously estimated coefficients to describe +the patterns of single occasion drinking.

AlcBinge(data, params = tobalcepi::binge_params)
@@ -154,10 +158,7 @@

Value

Returns data plus the estimated variables.

Details

-

Designed to work with cross-sectional survey data with a wide range of individual-level covariates. -Uses survey data and previously estimated coefficients to describe -the patterns of single occasion drinking.

-

This is based on a study by Hill-McManus 2014, +

This is based on a study by Hill-McManus 2014, who analysed drinking occasions using data from detailed diaries in the National Diet and Nutrition Survey 2000/2001. Using the results, it possible to model each individual's expected number of drinking occasions across the year, the average amount they drunk on an occasion, the variability in the amount drunk among occasions, diff --git a/public/reference/AlcBinge_stapm.html b/public/reference/AlcBinge_stapm.html index 22c80e4..e0bc7f2 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 @@ -39,8 +39,11 @@ - - + + @@ -124,13 +127,16 @@

-

Calculate variables to inform alcohol binge model - STAPM version

+

Calculate variables to inform alcohol binge model - STAPM version Maturing lifecycle

-

Maturing lifecycle

+

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 +at each time step in the simulation.

AlcBinge_stapm(data, params = tobalcepi::binge_params_stapm)
@@ -156,11 +162,7 @@

Value

Returns data plus the estimated variables.

Details

-

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 -at each time step in the simulation.

-

The coefficients used come originally from a study by Hill-McManus 2014, +

The coefficients used come originally from a study by Hill-McManus 2014, who analysed drinking occasions using data from detailed diaries in the National Diet and Nutrition Survey 2000/2001. Using the results, it possible to model each individual's expected number of drinking occasions across the year, the average amount they drunk on an occasion, the variability in the amount drunk among occasions, diff --git a/public/reference/AlcLags.html b/public/reference/AlcLags.html index d8a4e5f..64098c0 100644 --- a/public/reference/AlcLags.html +++ b/public/reference/AlcLags.html @@ -6,7 +6,7 @@ -Alcohol lag times — AlcLags • tobalcepi +Alcohol lag times — AlcLags • tobalcepi @@ -39,8 +39,10 @@ - - + + @@ -124,13 +126,15 @@

-

Alcohol lag times

+

Alcohol lag times Stable lifecycle

-

Stable lifecycle

+

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.

AlcLags(disease_name = c("Pharynx", "Oral_cavity"), n_years = 20)
@@ -156,10 +160,7 @@

Value

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

Details

-

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 Holmes et al. 2012, and are the numbers used in the current version of SAPM.

Examples

diff --git a/public/reference/ExpandCodes.html b/public/reference/ExpandCodes.html index 427daa3..54d1254 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 @@ -39,8 +39,8 @@ - - + + @@ -124,13 +124,13 @@
-

Convert groups of ICD-10 codes to single codes

+

Convert groups of ICD-10 codes to single codes Stable lifecycle

-

Stable lifecycle

+

Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol.

ExpandCodes(lkup)
@@ -149,8 +149,7 @@

Value

Returns a data frame containing a row for each single ICD-10 code to be searched for.

Details

-

Creates the lookup files for search for single ICD-10 codes related to tobacco and/or alcohol.

-

For example, if one disease category is C00-C06 (oral cancer), this includes the single codes +

For example, if one disease category is C00-C06 (oral cancer), this includes the single codes C00,C01,C02,C03,C04,C05,C06. The number of rows will be expanded to give each single code its own row.

diff --git a/public/reference/PArisk.html b/public/reference/PArisk.html index 16ce47a..096d91e 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 @@ -39,8 +39,9 @@ - - + + @@ -124,13 +125,14 @@
-

Relative risks for alcohol-related injuries

+

Relative risks for alcohol-related injuries Stable lifecycle

-

Stable lifecycle

+

Uses the 'new' binge model methods to calculate a relative risk +for each individual for experiencing each cause during one year.

PArisk(
@@ -209,9 +211,7 @@ 
Value

     
Returns a numeric vector of each individual's relative risk of the acute consequences of drinking.

     
Details

 
-    
Uses the 'new' binge model methods to calculate a relative risk
-for each individual for experiencing each cause during one year.

-
This calculation treats an ocassion as a single point in time and therefore does not detail
+    
This calculation treats an ocassion as a single point in time and therefore does not detail
 about the rate of alcohol absorbtion (i.e. there is no alcohol absorbtion rate constant)
 or the time interval between drinks within an occassion. This could introduce inaccuracies if
  e.g. a drinking occassion lasted several hours. The methods to calculate the total time spent intoxicated
diff --git a/public/reference/RRFunc.html b/public/reference/RRFunc.html
index 5703c50..86951d1 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
 
 
 
@@ -39,7 +39,7 @@
 
 
 
-
+
 
   

     

-    
Individual relative risks of disease

+    
Individual relative risks of disease Maturing lifecycle

     
     
     

@@ -263,8 +263,7 @@ 
Value

 
     
Details

 
-    
Maturing lifecycle

-
See below

+    
See below

     
Alcohol risk

 
     
diff --git a/public/reference/RRTobDR.html b/public/reference/RRTobDR.html
index 9de9faf..74f4a1c 100644
--- a/public/reference/RRTobDR.html
+++ b/public/reference/RRTobDR.html
@@ -6,7 +6,7 @@
 
 
 
-Dose-response relative risks for tobacco-related cancers — RRTobDR • tobalcepi
+Dose-response relative risks for tobacco-related cancers  — RRTobDR • tobalcepi
 
 
 
@@ -39,8 +39,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +124,13 @@
 

   

     

-    
Dose-response relative risks for tobacco-related cancers

+    
Dose-response relative risks for tobacco-related cancers Experimental lifecycle

     
     
     

 
     

-    
Experimental lifecycle

+    
Computes the relative risks for each tobacco-related cancer based on the published risk curves.

     

 
     
RRTobDR(data, disease = "Pharynx", av_cigs_day = "cigs_per_day")

@@ -158,8 +158,7 @@ 
Value

     
Returns a numeric vector of each individual's relative risks for the tobacco related disease specified by "disease".

     
Details

 
-    
Computes the relative risks for each tobacco-related cancer based on the published risk curves.

-
Relative risks for come from published risk functions whose parameters have been
+    
Relative risks for come from published risk functions whose parameters have been
 hard-coded within this function rather than being read from an external spreadsheet. 
 These relative risks are based on an individual's current smoking intensity. There are 
 others measures of smoking exposure including smoking duration and pack-years, which 
diff --git a/public/reference/RRalc.html b/public/reference/RRalc.html
index a9804ca..7aa13c9 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
 
 
 
@@ -39,8 +39,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +124,13 @@
 

   

     

-    
Relative risks for alcohol related diseases

+    
Relative risks for alcohol related diseases Stable lifecycle

     
     
     

 
     

-    
Stable lifecycle

+    
Computes the relative risks for each alcohol related disease based on the published risk curves.

     

 
     
RRalc(
@@ -212,8 +212,7 @@ 
Value

     
Returns a numeric vector of each individual's relative risks for the alcohol related disease specified by "disease".

     
Details

 
-    
Computes the relative risks for each alcohol related disease based on the published risk curves.

-
Relative risks for partially attributable chronic come from published risk functions whose parameters have been
+    
Relative risks for partially attributable chronic come from published risk functions whose parameters have been
 hard-coded within this function rather than being read from an external spreadsheet. For some conditions there are
 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
diff --git a/public/reference/RRtob.html b/public/reference/RRtob.html
index 40ec91c..f53068e 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
 
 
 
@@ -39,8 +39,8 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +124,13 @@
 

   

     

-    
Tobacco relative risks

+    
Tobacco relative risks Maturing lifecycle

     
     
     

 
     

-    
Maturing lifecycle

+    
Relative risks for current vs. never cigarette smokers.

     

 
     
RRtob(
@@ -179,8 +179,7 @@ 
Value

 specified by "disease".

     
Details

 
-    
Relative risks for current vs. never cigarette smokers.

-
We focus on the risks of current smoking and limit ourselves to diseases that affect the consumer themselves e.g.
+    
We focus on the risks of current smoking and limit ourselves to diseases that affect the consumer themselves e.g.
  excluding secondary effects of smoking on children.
  We assume the equivalence of relative risks and odds ratios.
  Our starting point was the Royal College of Physician's (RCP) report "Hiding in plain sight:
diff --git a/public/reference/TobAlcInt.html b/public/reference/TobAlcInt.html
index 138df76..ef497be 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
 
 
 
@@ -39,8 +39,9 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +125,14 @@
 

   

     

-    
Risk interaction between tobacco and alcohol

+    
Risk interaction between tobacco and alcohol Maturing lifecycle

     
     
     

 
     

-    
Maturing lifecycle

+    
Assigns the disease-specific interaction term (synergy index) appropriate to each
+individual's tobacco and alcohol consumption.

     

 
     
TobAlcInt(
@@ -177,9 +179,7 @@ 
Value

 specified by "disease".

     
Details

 
-    
Assigns the disease-specific interaction term (synergy index) appropriate to each
-individual's tobacco and alcohol consumption.

-
We currently include estimates of synergistic effects for 
+    
We currently include estimates of synergistic effects for 
 oral, pharyngeal, laryngeal and oesophageal cancers 
 (we describe these data and their sources in our tobacco risk functions report 
 Webster et al. (2018)
diff --git a/public/reference/TobLags.html b/public/reference/TobLags.html
index d8f9def..f28b704 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
 
 
 
@@ -39,8 +39,10 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +126,15 @@
 

   

     

-    
Tobacco lag times

+    
Tobacco lag times Stable lifecycle

     
     
     

 
     

-    
Stable lifecycle

+    
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)
+since e.g. someone quit smoking

     

 
     
TobLags(
@@ -165,10 +169,7 @@ 
Value

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

     
Details

 
-    
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)
-since e.g. someone quit smoking

-
All lag times are taken from a re-analysis of the Cancer prevention II study by Oza et al 2011 and Kontis et al 2014
+    
All lag times are taken from a re-analysis of the Cancer prevention II study by Oza et al 2011 and Kontis et al 2014
 The values were sent to us by Kontis. Lags are smoothed functions over time describing the proportion of
 the excess risk due to smoking that still remains.

 
Kontis et al. re-analysed the change in risk after smoking in the ACS-CPS II study from Oza et al.,
diff --git a/public/reference/WArisk_acute.html b/public/reference/WArisk_acute.html
index 84a127d..409cb7e 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
 
 
 
@@ -39,8 +39,10 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +126,15 @@
 

   

     

-    
Risk of acute conditions wholly-attributable to alcohol

+    
Risk of acute conditions wholly-attributable to alcohol Stable lifecycle

     
     
     

 
     

-    
Stable lifecycle

+    
Uses the 'new' binge model methods to calculate the risk
+that each individual experiences each acute consequence of drinking during one year 
+(e.g. alcohol poisoning or the effects of acute intoxication).

     

 
     
WArisk_acute(
@@ -183,10 +187,7 @@ 
Value

     
Returns a numeric vector of each individual's relative risk of the acute consequences of drinking.

     
Details

 
-    
Uses the 'new' binge model methods to calculate the risk
-that each individual experiences each acute consequence of drinking during one year 
-(e.g. alcohol poisoning or the effects of acute intoxication).

-
The function implements a new method for estimating risk that was developed to suit the STAPM modelling. 
+    
The function implements a new method for estimating risk that was developed to suit the STAPM modelling. 
 The calculation is based on the link between average weekly alcohol consumption and 
 the distribution of characteristics of single ocassion drinking described by the 
 parameter estimates of Hill-McManus et al 2014.

diff --git a/public/reference/index.html b/public/reference/index.html
index 8b110fc..4d7e43a 100644
--- a/public/reference/index.html
+++ b/public/reference/index.html
@@ -151,13 +151,13 @@ 
RRFunc() 

         
-        
Individual relative risks of disease

+        
Individual relative risks of disease Maturing lifecycle

       
         
         
           
subgroupRisk() 

         
-        
Summarise relative risk

+        
Summarise relative risk Stable lifecycle

       
     
       
@@ -183,33 +183,33 @@ 

         
         
-          
tob_disease_names 

+          
RRtob() 

         
-        
Names of tobacco-related diseases

+        
Tobacco relative risks Maturing lifecycle

       
         
         
-          
tob_icd10_lookups 

+          
RRTobDR() 

         
-        
Diseases related to tobacco and their ICD-10 defintions

+        
Dose-response relative risks for tobacco-related cancers Experimental lifecycle

       
         
         
-          
tobacco_relative_risks 

+          
tob_disease_names 

         
-        
Tobacco relative risks

+        
Names of tobacco-related diseases

       
         
         
-          
RRtob() 

+          
tob_icd10_lookups 

         
-        
Tobacco relative risks

+        
Diseases related to tobacco and their ICD-10 defintions

       
         
         
-          
RRTobDR() 

+          
tobacco_relative_risks 

         
-        
Dose-response relative risks for tobacco-related cancers

+        
Tobacco relative risks

       
     
       
@@ -228,7 +228,7 @@ 
TobLags() 

         
-        
Tobacco lag times

+        
Tobacco lag times Stable lifecycle

       
         
         
@@ -260,21 +260,21 @@ 

         
         
-          
alc_disease_names 

+          
RRalc() 

         
-        
Names of alcohol-related diseases

+        
Relative risks for alcohol related diseases Stable lifecycle

       
         
         
-          
alc_icd10_lookups 

+          
alc_disease_names 

         
-        
Diseases related to alcohol and their ICD-10 defintions

+        
Names of alcohol-related diseases

       
         
         
-          
RRalc() 

+          
alc_icd10_lookups 

         
-        
Relative risks for alcohol related diseases

+        
Diseases related to alcohol and their ICD-10 defintions

       
     
       
@@ -293,25 +293,25 @@ 
AlcBinge() 

         
-        
Calculate variables to inform alcohol binge model

+        
Calculate variables to inform alcohol binge model Superseded lifecycle

       
         
         
           
AlcBinge_stapm() 

         
-        
Calculate variables to inform alcohol binge model - STAPM version

+        
Calculate variables to inform alcohol binge model - STAPM version Maturing lifecycle

       
         
         
           
PArisk() 

         
-        
Relative risks for alcohol-related injuries

+        
Relative risks for alcohol-related injuries Stable lifecycle

       
         
         
           
WArisk_acute() 

         
-        
Risk of acute conditions wholly-attributable to alcohol

+        
Risk of acute conditions wholly-attributable to alcohol Stable lifecycle

       
         
         
@@ -342,7 +342,7 @@ 
AlcLags() 

         
-        
Alcohol lag times

+        
Alcohol lag times Stable lifecycle

       
     
       
@@ -361,7 +361,7 @@ 
TobAlcInt() 

         
-        
Risk interaction between tobacco and alcohol

+        
Risk interaction between tobacco and alcohol Maturing lifecycle

       
         
         
@@ -392,7 +392,7 @@ 
<
         
           
ExpandCodes() 

         
-        
Convert groups of ICD-10 codes to single codes

+        
Convert groups of ICD-10 codes to single codes Stable lifecycle

       
         
         
diff --git a/public/reference/subgroupRisk.html b/public/reference/subgroupRisk.html
index ed767ea..56ac21c 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
 
 
 
@@ -39,8 +39,9 @@
 
 
 
-
-
+
+
 
 
 
@@ -124,13 +125,14 @@
 

   

     

-    
Summarise relative risk

+    
Summarise relative risk Stable lifecycle

     
     
     

 
     

-    
Stable lifecycle

+    
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.

     

 
     
subgroupRisk(
@@ -188,9 +190,7 @@ 
Value

     
Returns a data table containing the subgroup specific summaries for each disease.

     
Details

 
-    
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.

-
Attributable fractions are calculated using the method as in Bellis & Jones 2014, which is also equivalent to the
+    
Attributable fractions are calculated using the method as in Bellis & Jones 2014, which is also equivalent to the
 method described in the Brennan et al. 2015 SAPM mathematical description paper.

 
     
Examples