Difference between revisions of "Burden of disease"

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{{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)}}
 
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=== Calculations ===
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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]].
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Burden of disease estimate for responses that can be calculated based on population attributable fraction (PAF).
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<rcode name="BoDpaf" label="Initiate BoDpaf (for developers only)" embed=1>
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# This is code Op_en7422/BoDpaf on page [[Burden of disease]]
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library(OpasnetUtils)
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BoDpaf <- Ovariable(
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  "BoDpaf", # This calculates the burden of disease for endpoints using PAF.
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  dependencies = data.frame(
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    Name = c(
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#      "population", # No population; BoDt must be the total BoD in the target population
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      "BoDt", # Total burden of disease of the studied responses per a defined time interval
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      "RR", # Relative risks for the given exposure
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      "sumExposcen" # function that calculates difference between exposure scenarios
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    ),
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    Ident = c(
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#      "Op_en2261/population", # [[Health impact assessment]]
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      "Op_en5917/BoDt",      # [[Disease risk]]
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      "Op_en2261/RR",        # [[Health impact assessment]]
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      "Op_en2261/sumExposcen" # [[Health impact assessment]]
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    )
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  ),
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  formula = function(...) {
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    AF <- (RR > 1) * (1 - 1/RR) + (RR <= 1) * (RR - 1) # See [[HIA]] for explanation
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    out <- BoDt * AF
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    return(sumExposcen(out))
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  }
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)
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objects.store(BoDpaf)
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cat("Ovariable BoDpaf stored.\n")
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</rcode>
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BoDcase calculates burden of disease based on numbers of cases, durations of diseases, and disability weights.
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<rcode name="BoDcase" label="Initiate BoDcase (for developers only)" embed=1>
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# This is code Op_en7422/BoDcase on page [[Burden of disease]]
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library(OpasnetUtils)
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BoDcase <- Ovariable(
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  "BoDcase", # This calculates the burden of disease for endpoints using numbers of cases.
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  dependencies = data.frame(
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    Name = c(
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      "casesrr", # Number of cases from relative endpoints with RR.
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      "casesabs", # Number of cases from absolute ERFs.
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      "disabilityweight", # Disability weights for each response.
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      "duration" # Duration of a response case.
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    ),
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    Ident = c(
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      "Op_en2261/casesrr", # [[Health impact assessment]]
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      "Op_en2261/casesabs", # [[Health impact assessment]]
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      "Op_en2307/disabilityweight", # [[Disability weights]]
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      "Op_en2307/duration" # [[Disability weights]]
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    )
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  ),
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  formula = function(...) {
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    out <- combine(casesrr, casesabs)
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    out <- out * disabilityweight * duration
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    return(out)
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  }
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)
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objects.store(BoDcase)
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cat("Ovariable BoDcase stored.\n")
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</rcode>
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BoD calculates burden of disease as a combination of burdens of disease based on either PAF or cases. If a response estimate comes from both BoDpaf and BoDcase, one is picked by random for each unique combination, and the source of the estimate is given in a non-marginal index BurdenSource.
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<rcode name="BoD" label="Initiate BoD (for developers only)" embed=1>
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# This is code Op_en7422/BoD on page [[Burden of disease]]
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library(OpasnetUtils)
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BoD <- Ovariable(
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  "BoD", # This calculates the total burden of disease.
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  dependencies = data.frame(
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    Name = c(
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      "BoDpaf", # Burden of disease as calculated from PAF
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      "BoDcase" # Burden of disease as calculated from number of cases
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    ),
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    Ident = c(
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      "Op_en7422/BoDpaf", # [[Burden of disease]]
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      "Op_en7422/BoDcase" # [[Burden of disease]]
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    )
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  ),
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  formula = function(...) {
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    # Indices that may have NA must be removed.
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    out <- OpasnetUtils::combine(
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      unkeep(BoDpaf, sources = TRUE),
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      unkeep(BoDcase, sources = TRUE),
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      name = "Burden"
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    )
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    out@output <- fillna(out@output, colnames(out@output)[out@marginal])
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    out@output <- merge(
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      out@output,
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      aggregate(
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        out@output["BurdenSource"],
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        by = out@output[colnames(out@output)[out@marginal]],
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        FUN = function(x) if("BoDpaf" %in% x) "BoDpaf" else "BoDcase" # Prefer BoDpaf when possible.
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      )
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    )
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    return(out)
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  }
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)
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objects.store(BoD)
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cat("Ovariable BoD stored.\n")
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</rcode>
  
 
==See also==
 
==See also==

Latest revision as of 13:37, 8 September 2017

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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

Data from the study

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.



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.

Burden of disease estimate for responses that can be calculated based on population attributable fraction (PAF).

+ Show code

BoDcase calculates burden of disease based on numbers of cases, durations of diseases, and disability weights.

+ Show code

BoD calculates burden of disease as a combination of burdens of disease based on either PAF or cases. If a response estimate comes from both BoDpaf and BoDcase, one is picked by random for each unique combination, and the source of the estimate is given in a non-marginal index BurdenSource.

+ Show code

See also

Keywords

References

  1. ↑ Reference to the Lim Lancet article
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