Difference between revisions of "Burden of disease"
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− | {{ | + | {{method|moderator=Heta}} |
− | {{progression class|progression=Draft}} | + | {{progression class|progression=Draft|curator=THL|date=2016-04-10}} |
== Question == | == Question == | ||
− | + | How to estimate the disease burden of important risk factors? | |
== Answer == | == Answer == | ||
+ | {{attack|# |THIS PAGE SHOULD CONTAIN AN OVERVIEW ON HOW TO PERFORM DISEASE BURDEN STUDIES.|--[[User:Jouni|Jouni]] ([[User talk:Jouni|talk]]) 16:16, 10 April 2016 (UTC)}} | ||
== Rationale == | == Rationale == | ||
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* 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) | * 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, [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156511/ this article], and secondarily to this Opasnet page. Remember to put date of entry. | * Make references to the link above, the IHME institute, [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156511/ this article], and secondarily to this Opasnet page. Remember to put date of entry. | ||
+ | |||
+ | {{hidden| | ||
* These are the risk factors of the GBD2010 study. Before you start the work, add the name of Wikidata item to the rows, so that we know what should be done. Also find a link to the right Wikipedia page. | * These are the risk factors of the GBD2010 study. Before you start the work, add the name of Wikidata item to the rows, so that we know what should be done. Also find a link to the right Wikipedia page. | ||
** Unsafe water [[:en:Waterborne diseases]] wikidata: [https://www.wikidata.org/wiki/Q1006636 waterborne disease (Q2006636)], [[:en:Drinking water]] wikidata: [https://www.wikidata.org/wiki/Q7892 drinking water (Q7892)]), sanitation ([[:en:Sanitation]] wikidata: [https://www.wikidata.org/wiki/Q949149 sanitation (Q949149)]), and handwashing ([[:en:Hand washing]] wikidata: [https://www.wikidata.org/wiki/Q552461 Hand washing (Q552461)]) | ** Unsafe water [[:en:Waterborne diseases]] wikidata: [https://www.wikidata.org/wiki/Q1006636 waterborne disease (Q2006636)], [[:en:Drinking water]] wikidata: [https://www.wikidata.org/wiki/Q7892 drinking water (Q7892)]), sanitation ([[:en:Sanitation]] wikidata: [https://www.wikidata.org/wiki/Q949149 sanitation (Q949149)]), and handwashing ([[:en:Hand washing]] wikidata: [https://www.wikidata.org/wiki/Q552461 Hand washing (Q552461)]) | ||
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Important due to public health relevance | Important due to public health relevance | ||
− | Ischemic heart disease | + | *Ischemic heart disease |
− | Lower respiratory infections | + | *Lower respiratory infections |
− | Cerebrovascular disease | + | *Cerebrovascular disease, [[:en:Cerebrovascular disease]], wikidata: [https://www.wikidata.org/wiki/Q3360664 cerebrovascular disease (Q3360664)] |
− | Low back and neck pain | + | *Low back and neck pain |
− | Road injuries | + | *Road injuries |
− | Diarrheal diseases | + | *Diarrheal diseases |
− | Chronic obstructive pulmonary disease | + | *Chronic obstructive pulmonary disease |
− | Preterm birth complications | + | *Preterm birth complications |
− | HIV/AIDS | + | *HIV/AIDS |
− | Malaria | + | *Malaria |
− | Depressive disorders | + | *Depressive disorders |
− | Neonatal encephalopathy due to birth asphyxia and trauma | + | *Neonatal encephalopathy due to birth asphyxia and trauma |
− | Congenital anomalies | + | *Congenital anomalies (Congenital heart anomalies?) |
− | Diabetes mellitus | + | *Diabetes mellitus |
− | Sense organ diseases | + | *Sense organ diseases [[:en:Sensory system#Diseases]], wikidata: [https://www.wikidata.org/wiki/Q18553219 sensory system disease (Q18553219)]? [https://www.wikidata.org/wiki/Q11101 Sensory system (Q11101)] |
− | Tuberculosis | + | *Tuberculosis |
− | Iron-deficiency anemia | + | *Iron-deficiency anemia |
− | Skin and subcutaneous diseases | + | *Skin and subcutaneous diseases, [[:en:Cutaneous condition]], wikidata: [https://www.wikidata.org/wiki/Q949302 cutaneous disease (Q949302)] |
− | Self-harm | + | *Self-harm |
− | Tracheal, bronchus, and lung cancer | + | *Tracheal, bronchus, and lung cancer |
− | Chronic kidney disease | + | *Chronic kidney disease, [[:en:Chronic kidney disease]], wikidata: [https://www.wikidata.org/wiki/Q736715 chronic kidney disease (Q736715)] |
− | Neonatal sepsis and other neonatal infections | + | *Neonatal sepsis and other neonatal infections |
− | Migraine | + | *Migraine |
− | Protein-energy malnutrition | + | *Protein-energy malnutrition |
− | Falls | + | *Falls |
− | Other neonatal disorders | + | *Other neonatal disorders |
− | Other musculoskeletal disorders | + | *Other musculoskeletal disorders |
− | Anxiety disorders | + | *Anxiety disorders |
− | Hemoglobinopathies and hemolytic anemias | + | *Hemoglobinopathies and hemolytic anemias, [[:en:Hemoglobinopathy]], wikidata: [https://www.wikidata.org/wiki/Q1642147 Hemoglobinopathy (Q1642147)], [[:en:Hemolytic anemia]], wikidata: [https://www.wikidata.org/wiki/Q1145668 hemolytic anemia (Q1145668)] |
− | Alzheimer disease and other dementias | + | *Alzheimer disease and other dementias |
− | Asthma | + | *Asthma [[:en:Asthma]], wikidata: [https://www.wikidata.org/wiki/Q35869 asthma (Q35869)] |
+ | {{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]]. | ||
+ | |||
+ | 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)" embed=1> | ||
+ | # 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", # No population; BoDt must be the total BoD in the target population | ||
+ | "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(...) { | ||
+ | AF <- (RR > 1) * (1 - 1/RR) + (RR <= 1) * (RR - 1) # See [[HIA]] for explanation | ||
+ | out <- BoDt * AF | ||
+ | |||
+ | 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)" embed=1> | ||
+ | # 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. 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. | ||
+ | |||
+ | <rcode name="BoD" label="Initiate BoD (for developers only)" embed=1> | ||
+ | # 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(...) { | ||
+ | # Indices that may have NA must be removed. | ||
+ | out <- OpasnetUtils::combine( | ||
+ | unkeep(BoDpaf, sources = TRUE), | ||
+ | unkeep(BoDcase, sources = TRUE), | ||
+ | name = "Burden" | ||
+ | ) | ||
+ | out@output <- fillna(out@output, colnames(out@output)[out@marginal]) | ||
+ | out@output <- merge( | ||
+ | out@output, | ||
+ | aggregate( | ||
+ | out@output["BurdenSource"], | ||
+ | by = out@output[colnames(out@output)[out@marginal]], | ||
+ | FUN = function(x) if("BoDpaf" %in% x) "BoDpaf" else "BoDcase" # Prefer BoDpaf when possible. | ||
+ | ) | ||
+ | ) | ||
+ | return(out) | ||
+ | } | ||
+ | ) | ||
+ | |||
+ | objects.store(BoD) | ||
+ | cat("Ovariable BoD stored.\n") | ||
+ | </rcode> | ||
==See also== | ==See also== | ||
+ | |||
+ | * [http://vizhub.healthdata.org/gbd-compare/ IHME Institute visualization tool] | ||
+ | * [http://www.who.int/healthinfo/global_burden_disease/estimates/en/index2.html WHO estimates of disease burden for 2000-2012] | ||
+ | * [https://www.wikidata.org/wiki/Property:P2854 Wikidata property: disease burden] | ||
+ | * [https://www.wikidata.org/wiki/Q5282120 Disease burden] (a method for estimating disease burden in Wikidata) [https://en.wikipedia.org/wiki/Disease_burden related page in Wikipedia] | ||
==Keywords== | ==Keywords== | ||
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<references/> | <references/> | ||
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Latest revision as of 13:37, 8 September 2017
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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.
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. 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.
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