From 065475a195a2b2e783f43df1548dcdf858cf7131 Mon Sep 17 00:00:00 2001 From: Duncan Gillespie Date: Tue, 6 Jun 2023 15:53:50 +0100 Subject: [PATCH] edit TobLags function documentation --- R/TobLags.R | 21 ++++++++++------- ...able_diseases_and_dose-response_curves.pdf | Bin 493511 -> 493510 bytes ...moking_and_the_risks_of_adult_diseases.pdf | Bin 302703 -> 302703 bytes docs/pkgdown.yml | 2 +- docs/reference/TobLags.html | 22 ++++++++++++++---- man/TobLags.Rd | 14 +++++++---- 6 files changed, 41 insertions(+), 18 deletions(-) diff --git a/R/TobLags.R b/R/TobLags.R index b458998..525ca5a 100644 --- a/R/TobLags.R +++ b/R/TobLags.R @@ -5,8 +5,9 @@ #' 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 -#' The values were sent to us by Kontis. Lags are smoothed functions over time describing the proportion of +#' All lag times are taken from a re-analysis of the Cancer prevention II study by \insertCite{Oza2011;textual}{tobalcepi} +#' and \insertCite{Kontis2014;textual}{tobalcepi}. +#' The values were sent to us on request 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., @@ -23,8 +24,8 @@ #' on diabetes risk occur within a few years, more similar to the CVDs than cancers. #' Therefore, we used the CVD curve for diabetes." In-line with Kontis, we apply the rate of decline #' in risk of CVD after quitting smoking to type 2 diabetes. -#' For other diseases, we assume that the relative risk reverts to 1 immediately after quitting -#' i.e. an immediate rather than a gradual decline in risk. +#' For all remaining conditions we apply the most conservative estimate available +#' and assume that the decline in risk follows the cancer estimate provided by Kontis et al., as this has the slowest decline in risk. #' #' @param disease_name Character - the name of the disease under consideration. #' @param n_years Integer - the number of years from 1 to n over which the effect of a change in @@ -39,7 +40,11 @@ #' @importFrom data.table := setDT setnames data.table #' #' @export -#' +#' @references +#' \insertRef{Kontis2014}{tobalcepi} +#' +#' \insertRef{Oza2011}{tobalcepi} +#' #' #' @examples #' @@ -63,12 +68,10 @@ TobLags <- function( copd_lags <- c("Chronic_obstructive_pulmonary_disease") - # For other conditions assume that the excess risk is zero 1 year after cessation - + ################################# # Specify the functional forms of the lags - # The numbers are taken from SAPM - Holmes et al. 2012 - + ################## # Set the default diff --git a/docs/articles/Alcohol-attributable_diseases_and_dose-response_curves.pdf b/docs/articles/Alcohol-attributable_diseases_and_dose-response_curves.pdf index f530b8d158abc61c20b26b9130a42bf94a90ff17..4f18e6ca42ee57901308508dc09f36c3df7e3f8e 100644 GIT binary patch delta 9361 zcmaiXRaYDgkSy*l!QBZ?aJM12yAw3Q-Dhz3z~CO-Z3q%(kl^m_?k-7Szuo%-?n9lf zhd!sfU%IM>lBs_uQ-fOJMOfi^z%WfjHlVSVE5%Rzkfnz0y`R!Q_fzud;yXXS6Y2JVuOe_uQT*u$CkP_Y$UTf)ZH6 z>Ha>6mTqPR&JvG%xSZDEVl`mh%)F9)M#bl=9LE*Zi@-eub{fFYI^<^k2E z!{XXKUpnD6CO6k@?a<)i!d-oclfKT*X_&gq>PF za>$5$7-mG!Xld!NN9Zb^Y77_Fungnrd_;W&GQLb^F?@+l7~ZzR_c$<55Q_P&aV!RJ z_Axy?Jv(&~NKcOhm1uAPx|*gH3Or;LA!PU>p=qV6i6s4jwK?I)%TEeWF z)Z()V*H@-4;uI0rWUWMFUk2?r2_vNJdwV-+SD@5>JmE%IlsB@FMP?60Ggn4e!Hbrd 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zQUG@_!NFGIX&ghBf9f!02iF~q?_tl2m-fJQ!Yc29gYeo1$H_rWr)iu_+depK^5h%9 zB+k%YIHXj`D$_XZyX9XWrf?SH^0)KnX)IHa0^wLp3!qLPIr1GB!g+H#amgFhMvlHbOEpMMg$GAUrTOHbXT- jH8n9pLp4S+HbX@>H#9OZK{zlrLNYT&Mn<=LnFRC%(di;7 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e98f35d..744afd7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,7 +7,7 @@ articles: PAF_methodology_report: PAF_methodology_report.html Smoking_and_the_risks_of_adult_diseases: Smoking_and_the_risks_of_adult_diseases.pdf tobalcepi: tobalcepi.html -last_built: 2023-06-06T10:27Z +last_built: 2023-06-06T14:51Z urls: reference: https://stapm.github.io/tobalcepi/reference article: https://stapm.github.io/tobalcepi/articles diff --git a/docs/reference/TobLags.html b/docs/reference/TobLags.html index 77d71d6..da538a7 100644 --- a/docs/reference/TobLags.html +++ b/docs/reference/TobLags.html @@ -127,8 +127,11 @@

Value

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 +

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 on request 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., producing three functions to describe the decline in risk after quitting for each of cancers, CVD and COPD. @@ -143,8 +146,19 @@

Details

on diabetes risk occur within a few years, more similar to the CVDs than cancers. Therefore, we used the CVD curve for diabetes." In-line with Kontis, we apply the rate of decline in risk of CVD after quitting smoking to type 2 diabetes. - For other diseases, we assume that the relative risk reverts to 1 immediately after quitting - i.e. an immediate rather than a gradual decline in risk.

+ For all remaining conditions we apply the most conservative estimate available + and assume that the decline in risk follows the cancer estimate provided by Kontis et al., as this has the slowest decline in risk.

+
+
+

References

+

Kontis V, Mathers CD, Rehm J, Stevens GA, Shield KD, Bonita R, Riley LM, Poznyak V, Beaglehole R, Ezzati M (2014). +“Contribution of six risk factors to achieving the 25× 25 non-communicable disease mortality reduction target: a modelling study.” +The Lancet, 384(9941), 427-437. +ISSN 0140-6736.

+

Oza S, Thun MJ, Henley SJ, Lopez AD, Ezzati M (2011). +“How many deaths are attributable to smoking in the United States? Comparison of methods for estimating smoking-attributable mortality when smoking prevalence changes.” +Preventive medicine, 52(6), 428-433. +ISSN 0091-7435.

diff --git a/man/TobLags.Rd b/man/TobLags.Rd index 3329aaa..716398d 100644 --- a/man/TobLags.Rd +++ b/man/TobLags.Rd @@ -30,8 +30,9 @@ gradually has an effect on the relative risk of disease incidence over time (up 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 +All lag times are taken from a re-analysis of the Cancer prevention II study by \insertCite{Oza2011;textual}{tobalcepi} + and \insertCite{Kontis2014;textual}{tobalcepi}. +The values were sent to us on request 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., @@ -48,11 +49,16 @@ CVD or COPD. Kontis et al. state that on diabetes risk occur within a few years, more similar to the CVDs than cancers. Therefore, we used the CVD curve for diabetes." In-line with Kontis, we apply the rate of decline in risk of CVD after quitting smoking to type 2 diabetes. - For other diseases, we assume that the relative risk reverts to 1 immediately after quitting - i.e. an immediate rather than a gradual decline in risk. + For all remaining conditions we apply the most conservative estimate available + and assume that the decline in risk follows the cancer estimate provided by Kontis et al., as this has the slowest decline in risk. } \examples{ TobLags("Pharynx") } +\references{ +\insertRef{Kontis2014}{tobalcepi} + +\insertRef{Oza2011}{tobalcepi} +}