From f40146b6fb7863afcbd4a3f06fb49e3257b300ba Mon Sep 17 00:00:00 2001 From: Duncan Gillespie Date: Wed, 25 Nov 2020 11:13:08 +0000 Subject: [PATCH] edit readme --- README.Rmd | 8 +++++--- README.md | 12 +++++++++--- public/index.html | 7 ++++--- public/pkgdown.yml | 2 +- vignettes/smoking-disease-risks.Rmd | 2 +- 5 files changed, 20 insertions(+), 11 deletions(-) diff --git a/README.Rmd b/README.Rmd index 5f683ac..34f68e4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -35,11 +35,13 @@ The disease lists and risk functions in this package all have published sources, The high-level function for alcohol is `tobalcepi::RRalc()`, which calculates individual risks of diseases as follows: 1. **Alcohol - partially-attributable chronic conditions**: dose-response effects of current alcohol consumption on disease risk [@Angus2018] are hard-coded into the function `tobalcepi::RRalc()`. Updates to these risk functions must therefore be made by changing the function code. -1. **Alcohol - partially-attributable acute conditions**: dose-response effects of single-occasion alcohol consumption are hard coded into the function `tobalcepi::PArisk()`, which is called by `tobalcepi::RRalc()`. See `vignette("alc_pa_risk")`. -1. **Alcohol - wholly-attributable acute conditions**: these are not based on published risk functions but are based on thresholds, in UK standard units of alcohol drunk on a single occasion, over which individuals begin to experience an elevated risk for acute diseases that are wholly attributable to alcohol. This is applied by the function `tobalcepi::WArisk_acute()`, which is called by `tobalcepi::RRalc()`. See `vignette("alc_wa_ac_risk")`. -1. **Alcohol - wholly-attributable chronic conditions**: these are also based on thresholds in UK standard units of alcohol drunk on average in a week, over which individuals begin to experience an elevated risk for chronic diseases that are wholly attributable to alcohol. This is applied by code within the function `tobalcepi::RRalc()`. See `vignette("alc_wa_ch_risk")`. +1. **Alcohol - partially-attributable acute conditions**: dose-response effects of single-occasion alcohol consumption are hard coded into the function `tobalcepi::PArisk()`, which is called by `tobalcepi::RRalc()`. See [vignette("alc_pa_risk")](https://stapm.gitlab.io/r-packages/tobalcepi/articles/alc_partially_attrib_acute.html). +1. **Alcohol - wholly-attributable acute conditions**: these are not based on published risk functions but are based on thresholds, in UK standard units of alcohol drunk on a single occasion, over which individuals begin to experience an elevated risk for acute diseases that are wholly attributable to alcohol. This is applied by the function `tobalcepi::WArisk_acute()`, which is called by `tobalcepi::RRalc()`. See [vignette("alc_wa_ac_risk")](https://stapm.gitlab.io/r-packages/tobalcepi/articles/alc_wholly_attrib_acute.html). +1. **Alcohol - wholly-attributable chronic conditions**: these are also based on thresholds in UK standard units of alcohol drunk on average in a week, over which individuals begin to experience an elevated risk for chronic diseases that are wholly attributable to alcohol. This is applied by code within the function `tobalcepi::RRalc()`. See [vignette("alc_wa_ch_risk")](https://stapm.gitlab.io/r-packages/tobalcepi/articles/alc_wholly_attrib_chronic.html). ### Tobacco +See [vignette("smoke_risks")](https://stapm.gitlab.io/r-packages/tobalcepi/articles/smoking-disease-risks.html) + 1. `RRtob()` takes a lookup table of the risks associated with current vs. never smoking and assigns these to individuals based on their smoking state, age and sex [@webster2018risk]. 1. We are in the process of developing the function `RRTobDR()` to stratify the risks of some cancers according to the amount smoked per day by current smokers. There is limited info on these dose-reponse effects, so we are gradually building up the epidemiological detail in this area as we review, critically appraise and integrate new risk data into our modelling. diff --git a/README.md b/README.md index cb2cbd0..376b6e7 100644 --- a/README.md +++ b/README.md @@ -50,23 +50,29 @@ calculates individual risks of diseases as follows: 2. **Alcohol - partially-attributable acute conditions**: dose-response effects of single-occasion alcohol consumption are hard coded into the function `tobalcepi::PArisk()`, which is called by - `tobalcepi::RRalc()`. See `vignette("alc_pa_risk")`. + `tobalcepi::RRalc()`. See + [vignette(“alc\_pa\_risk”)](https://stapm.gitlab.io/r-packages/tobalcepi/articles/alc_partially_attrib_acute.html). 3. **Alcohol - wholly-attributable acute conditions**: these are not based on published risk functions but are based on thresholds, in UK standard units of alcohol drunk on a single occasion, over which individuals begin to experience an elevated risk for acute diseases that are wholly attributable to alcohol. This is applied by the function `tobalcepi::WArisk_acute()`, which is called by - `tobalcepi::RRalc()`. See `vignette("alc_wa_ac_risk")`. + `tobalcepi::RRalc()`. See + [vignette(“alc\_wa\_ac\_risk”)](https://stapm.gitlab.io/r-packages/tobalcepi/articles/alc_wholly_attrib_acute.html). 4. **Alcohol - wholly-attributable chronic conditions**: these are also based on thresholds in UK standard units of alcohol drunk on average in a week, over which individuals begin to experience an elevated risk for chronic diseases that are wholly attributable to alcohol. This is applied by code within the function `tobalcepi::RRalc()`. - See `vignette("alc_wa_ch_risk")`. + See + [vignette(“alc\_wa\_ch\_risk”)](https://stapm.gitlab.io/r-packages/tobalcepi/articles/alc_wholly_attrib_chronic.html). ### Tobacco +See +[vignette(“smoke\_risks”)](https://stapm.gitlab.io/r-packages/tobalcepi/articles/smoking-disease-risks.html) + 1. `RRtob()` takes a lookup table of the risks associated with current vs. never smoking and assigns these to individuals based on their smoking state, age and sex (Webster et al. diff --git a/public/index.html b/public/index.html index 1936401..3dbf620 100644 --- a/public/index.html +++ b/public/index.html @@ -105,18 +105,19 @@

Alcohol - partially-attributable chronic conditions: dose-response effects of current alcohol consumption on disease risk (Angus et al. 2018) are hard-coded into the function tobalcepi::RRalc(). Updates to these risk functions must therefore be made by changing the function code.
  • -Alcohol - partially-attributable acute conditions: dose-response effects of single-occasion alcohol consumption are hard coded into the function tobalcepi::PArisk(), which is called by tobalcepi::RRalc(). See vignette("alc_pa_risk").
    +Alcohol - partially-attributable acute conditions: dose-response effects of single-occasion alcohol consumption are hard coded into the function tobalcepi::PArisk(), which is called by tobalcepi::RRalc(). See vignette(“alc_pa_risk”).
  • -Alcohol - wholly-attributable acute conditions: these are not based on published risk functions but are based on thresholds, in UK standard units of alcohol drunk on a single occasion, over which individuals begin to experience an elevated risk for acute diseases that are wholly attributable to alcohol. This is applied by the function tobalcepi::WArisk_acute(), which is called by tobalcepi::RRalc(). See vignette("alc_wa_ac_risk").
    +Alcohol - wholly-attributable acute conditions: these are not based on published risk functions but are based on thresholds, in UK standard units of alcohol drunk on a single occasion, over which individuals begin to experience an elevated risk for acute diseases that are wholly attributable to alcohol. This is applied by the function tobalcepi::WArisk_acute(), which is called by tobalcepi::RRalc(). See vignette(“alc_wa_ac_risk”).
  • -Alcohol - wholly-attributable chronic conditions: these are also based on thresholds in UK standard units of alcohol drunk on average in a week, over which individuals begin to experience an elevated risk for chronic diseases that are wholly attributable to alcohol. This is applied by code within the function tobalcepi::RRalc(). See vignette("alc_wa_ch_risk").
    • +Alcohol - wholly-attributable chronic conditions: these are also based on thresholds in UK standard units of alcohol drunk on average in a week, over which individuals begin to experience an elevated risk for chronic diseases that are wholly attributable to alcohol. This is applied by code within the function tobalcepi::RRalc(). See vignette(“alc_wa_ch_risk”).

    Tobacco

    +

    See vignette(“smoke_risks”)

    1. RRtob() takes a lookup table of the risks associated with current vs. never smoking and assigns these to individuals based on their smoking state, age and sex (Webster et al. 2018).
      diff --git a/public/pkgdown.yml b/public/pkgdown.yml index d849682..dee26a5 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: 2020-11-25T09:57Z +last_built: 2020-11-25T11:12Z urls: reference: https://stapm.gitlab.io/tobalcepi/reference article: https://stapm.gitlab.io/tobalcepi/articles diff --git a/vignettes/smoking-disease-risks.Rmd b/vignettes/smoking-disease-risks.Rmd index de57c5e..d38fef3 100644 --- a/vignettes/smoking-disease-risks.Rmd +++ b/vignettes/smoking-disease-risks.Rmd @@ -2,7 +2,7 @@ title: "Smoking disease risks" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Smoking disease risks} + %\VignetteIndexEntry{smoke_risks} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} bibliography: disease-risks.bib