Difference between revisions of "Burden of disease"
(→See also) |
(→Global Burden of Disease Study 2010) |
||
Line 140: | Line 140: | ||
{{comment|# |The rest were already in the list above, so there's no point digging out the links twice|--[[User:Heta|Heta]] ([[User talk:Heta|talk]]) 10:50, 4 February 2016 (UTC)}} | {{comment|# |The rest were already in the list above, so there's no point digging out the links twice|--[[User:Heta|Heta]] ([[User talk:Heta|talk]]) 10:50, 4 February 2016 (UTC)}} | ||
}} | }} | ||
+ | |||
+ | === Calculations === | ||
+ | |||
+ | These ovariables are used to calculate burden of disease based either on relative or absolute risks, and counted as [[DALY]]s. For ovariables that calculate numbers of cases, see [[Health impact assessment]]. | ||
+ | |||
+ | BoDt is an ovariable to calculate total burden of disease for selected endpoints based on IHME data. | ||
+ | |||
+ | <rcode name="BoDt" label="Initiate BoDt (for developers only)"> | ||
+ | # This is code Op_en7422/BoDt on page [[Burden of disease]] | ||
+ | library(OpasnetUtils) | ||
+ | |||
+ | dummy <- 0 | ||
+ | |||
+ | BoDt <- Ovariable( | ||
+ | "BoDt", | ||
+ | dependencies = data.frame(Name="dummy"), | ||
+ | formula = function(...) { | ||
+ | BoDt <- opbase.data("Op_en5917", subset = "IHME_Goherr")# [[Disease risk]] | ||
+ | BoDt <- BoDt[BoDt[[1]]=="DALY" , -1] | ||
+ | # Measure has a special character in name, so use position. | ||
+ | |||
+ | # levels(BoDt$Country) | ||
+ | # [1] "Denmark" "Estonia" "Finland" "Sweden" | ||
+ | levels(BoDt$Country) <- c("DK", "EST", "FI", "SWE") | ||
+ | |||
+ | # levels(BoDt$Age) | ||
+ | #[1] "1 to 4" "10 to 14" "15 to 19" "20 to 24" "25 to 29" "30 to 34" "35 to 39" "40 to 44" | ||
+ | #[9] "45 to 49" "5 to 9" "50 to 54" "55 to 59" "60 to 64" "65 to 69" "70 to 74" "75 to 79" | ||
+ | #[17] "80 plus" "All Ages" | ||
+ | BoDt$Ages <- BoDt$Age | ||
+ | levels(BoDt$Ages) <- c(NA,NA,rep("18-45",6),">45","18-45",rep(">45",7),NA) | ||
+ | BoDt <- BoDt[!is.na(BoDt$Ages) , ] | ||
+ | |||
+ | #levels(BoDt$Response) | ||
+ | #[1] "Hemorrhagic stroke" "Ischemic heart disease" "Ischemic stroke" | ||
+ | #[4] "Permanent caries" | ||
+ | levels(BoDt$Response) <- c("Stroke","Ischaemic heart disease","Stroke","Tooth defect") | ||
+ | |||
+ | BoDt$Result <- paste(BoDt$Lower, BoDt$Result, BoDt$Upper, sep=":") | ||
+ | BoDt<- Ovariable( | ||
+ | data = BoDt[!colnames(BoDt) %in% c("Upper", "Lower", "Year")] | ||
+ | ) | ||
+ | BoDt <- EvalOutput(BoDt) | ||
+ | BoDt$Source <- NULL | ||
+ | BoDt@marginal <- colnames(BoDt@output) != "Result" | ||
+ | BoDt <- oapply(BoDt, cols="Age", FUN=sum) | ||
+ | return(BoDt) | ||
+ | } | ||
+ | ) | ||
+ | |||
+ | # dummy is needed to fill an empty dependencies table. | ||
+ | objects.store(BoDt, dummy) | ||
+ | cat("Ovariable BoDt and a dummy stored.\n") | ||
+ | </rcode> | ||
+ | |||
+ | Burden of disease estimate for responses that can be calculated based on population attributable fraction (PAF). | ||
+ | |||
+ | <rcode name="BoDpaf" label="Initiate BoDpaf (for developers only)"> | ||
+ | # This is code Op_en7422/BoDpaf on page [[Burden of disease]] | ||
+ | library(OpasnetUtils) | ||
+ | |||
+ | BoDpaf <- Ovariable( | ||
+ | "BoDpaf", # This calculates the burden of disease for endpoints using PAF. | ||
+ | dependencies = data.frame( | ||
+ | Name = c( | ||
+ | "population", # Population relative to the scale (often 1 or 1M) of BoDt | ||
+ | "BoDt", # Total burden of disease of the studied responses per a defined time interval | ||
+ | "RR", # Relative risks for the given exposure | ||
+ | "sumExposcen" # function that calculates difference between exposure scenarios | ||
+ | ), | ||
+ | Ident = c( | ||
+ | "Op_en2261/population", # [[Health impact assessment]] | ||
+ | "Op_en5917/BoDt", # [[Disease risk]] | ||
+ | "Op_en2261/RR", # [[Health impact assessment]] | ||
+ | "Op_en2261/sumExposcen" # [[Health impact assessment]] | ||
+ | ) | ||
+ | ), | ||
+ | formula = function(...) { | ||
+ | |||
+ | out <- BoDt * population * (RR-1)/RR | ||
+ | |||
+ | return(sumExposcen(out)) | ||
+ | |||
+ | } | ||
+ | ) | ||
+ | |||
+ | objects.store(BoDpaf) | ||
+ | cat("Ovariable BoDpaf stored.\n") | ||
+ | </rcode> | ||
+ | |||
+ | BoDcase calculates burden of disease based on numbers of cases, durations of diseases, and disability weights. | ||
+ | |||
+ | <rcode name="BoDcase" label="Initiate BoDcase (for developers only)"> | ||
+ | # This is code Op_en7422/BoDcase on page [[Burden of disease]] | ||
+ | library(OpasnetUtils) | ||
+ | |||
+ | BoDcase <- Ovariable( | ||
+ | "BoDcase", # This calculates the burden of disease for endpoints using numbers of cases. | ||
+ | dependencies = data.frame( | ||
+ | Name = c( | ||
+ | "casesrr", # Number of cases from relative endpoints with RR. | ||
+ | "casesabs", # Number of cases from absolute ERFs. | ||
+ | "disabilityweight", # Disability weights for each response. | ||
+ | "duration" # Duration of a response case. | ||
+ | ), | ||
+ | Ident = c( | ||
+ | "Op_en2261/casesrr", # [[Health impact assessment]] | ||
+ | "Op_en2261/casesabs", # [[Health impact assessment]] | ||
+ | "Op_en2307/disabilityweight", # [[Disability weights]] | ||
+ | "Op_en2307/duration" # [[Disability weights]] | ||
+ | ) | ||
+ | ), | ||
+ | formula = function(...) { | ||
+ | |||
+ | out <- combine(casesrr, casesabs) | ||
+ | out <- out * disabilityweight * duration | ||
+ | return(out) | ||
+ | |||
+ | } | ||
+ | ) | ||
+ | |||
+ | objects.store(BoDcase) | ||
+ | cat("Ovariable BoDcase stored.\n") | ||
+ | </rcode> | ||
+ | |||
+ | BoD calculates burden of disease as a combination of burdens of disease based on either PAF or cases. | ||
+ | |||
+ | '''Note!''' There may double counting if there are responses that have both BoDt and incidence. | ||
+ | The ovariable gives a warning against double counting, if both methods have calculated a burden estimate for the same response. | ||
+ | |||
+ | <rcode name="BoD" label="Initiate BoD (for developers only)"> | ||
+ | # This is code Op_en7422/BoD on page [[Burden of disease]] | ||
+ | library(OpasnetUtils) | ||
+ | |||
+ | BoD <- Ovariable( | ||
+ | "BoD", # This calculates the total burden of disease. | ||
+ | dependencies = data.frame( | ||
+ | Name = c( | ||
+ | "BoDpaf", # Burden of disease as calculated from PAF | ||
+ | "BoDcase" # Burden of disease as calculated from number of cases | ||
+ | ), | ||
+ | Ident = c( | ||
+ | "Op_en7422/BoDpaf", # [[Burden of disease]] | ||
+ | "Op_en7422/BoDcase" # [[Burden of disease]] | ||
+ | ) | ||
+ | ), | ||
+ | formula = function(...) { | ||
+ | doublecount <- intersect(unique(BoDpaf$Response), unique(BoDcase$Response)) | ||
+ | if(length(doublecount>0)) warning(paste( | ||
+ | "The following response(s) are probably double counted from both disease burdens and incidences:", | ||
+ | paste(doublecount, collapse = ", ") | ||
+ | )) | ||
+ | return(combine(BoDpaf, BoDcase)) | ||
+ | } | ||
+ | ) | ||
+ | |||
+ | objects.store(BoD) | ||
+ | cat("Ovariable BoD stored.\n") | ||
+ | </rcode> | ||
==See also== | ==See also== |
Revision as of 14:11, 2 June 2017
This page is a method.
The page identifier is Op_en7422 |
---|
Moderator:Heta (see all) |
Give your opinion to the peer rating of the content of this page. |
Upload data
|
In Opasnet many pages being worked on and are in different classes of progression. Thus the information on those pages should be regarded with consideration. The progression class of this page has been assessed:
|
The content and quality of this page is being curated by THL. Error creating thumbnail: Unable to save thumbnail to destination
The quality was last checked: 2016-04-10. |
Contents
Question
How to estimate the disease burden of important risk factors?
Answer
⇤# : THIS PAGE SHOULD CONTAIN AN OVERVIEW ON HOW TO PERFORM DISEASE BURDEN STUDIES. --Jouni (talk) 16:16, 10 April 2016 (UTC)
Rationale
Global Burden of Disease Study 2010
Instructions
- Download the data from this page as csv
- Change names of columns: Causes of disease or injury -> Response; Measurement -> Unit; Value -> Result. Move Result to the rightmost column.
- Upload the csv to Opasnet Base using OpasnetBaseImport to table "GBD by risk factor" and unit "several". (This is for archiving purposes only: the latter tasks may be easier directly from the csv file.)
- Pick only rows with Unit = DALY per 100000.
- Sum over causes of disease so that you get one value for each risk factor.
- Go to Wikidata and suggest that "disease burden" is taken as a new property. When the property is available,
- go to each Item of the risk factor and add property disease burden to that item. Include qualifiers Global, Both sexes, Year 2013, all ages, all causes. (Find out what properties are available)
- Make references to the link above, the IHME institute, this article, and secondarily to this Opasnet page. Remember to put date of entry.
Show details |
---|
Causes of death, disease, and injury
Politically interesting causes of death and disease
Important due to public health relevance
--# : The rest were already in the list above, so there's no point digging out the links twice --Heta (talk) 10:50, 4 February 2016 (UTC) |
Calculations
These ovariables are used to calculate burden of disease based either on relative or absolute risks, and counted as DALYs. For ovariables that calculate numbers of cases, see Health impact assessment.
BoDt is an ovariable to calculate total burden of disease for selected endpoints based on IHME data.
Burden of disease estimate for responses that can be calculated based on population attributable fraction (PAF).
BoDcase calculates burden of disease based on numbers of cases, durations of diseases, and disability weights.
BoD calculates burden of disease as a combination of burdens of disease based on either PAF or cases.
Note! There may double counting if there are responses that have both BoDt and incidence. The ovariable gives a warning against double counting, if both methods have calculated a burden estimate for the same response.
See also
- IHME Institute visualization tool
- WHO estimates of disease burden for 2000-2012
- Wikidata property: disease burden
- Disease burden (a method for estimating disease burden in Wikidata) related page in Wikipedia
Keywords
References
- ↑ Reference to the Lim Lancet article