edit readme

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.  
 

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.

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

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