Difference between revisions of "Burden of disease"

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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.

Show details
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: waterborne disease (Q2006636), en:Drinking water wikidata: drinking water (Q7892)), sanitation (en:Sanitation wikidata: sanitation (Q949149)), and handwashing (en:Hand washing wikidata: Hand washing (Q552461)) Air pollution (en:Air pollution wikidata: air pollution Q131123)) Other environmental risks (en:Environmental health environmental health Q932068) Child and maternal malnutrition (en:Malnutrition in children, also has Maternal factors, en:Malnutrition wikidata: malnutrition (Q12167)) Tobacco smoke (en:Tobacco smoke wikidata: tobacco Q1566) Alcohol and drug use (en:Substance abuse?? wikidata: substance abuse (Q3184856)) High fasting plasma glucose (en:Hyperglycemia wikidata: Hyperglycemia (Q271993)) High total cholesterol (en:Hypercholesterolemia wikidata: hypercholesterolemia (Q762713)) High systolic blood pressure (en:Hypertension wikidata: hypertension (Q41861)) High body-mass index (en:Obesity wikidata: obesity (Q12174)) Low bone mineral density (en:Osteoporosis wikidata: Osteoporosis (Q165328)) Dietary risks (en:Healthy diet wikidata: healthy diet (Q5906358)) Low physical activity (en:Physical exercise wikidata: physical exercise (Q219067)) Occupational risks ⇤# : On each occupation's own wikipedia page. Any kind of general page about occupational risks can't be found. --Heta (talk) 09:18, 30 January 2016 (UTC) Sexual abuse and violence (en:Sexual abuse wikidata: sexual abuse (Q43414), en:Sexual violence wikidata: sexual violence (Q558075)) Low glomerular filtration rate (en:Renal function wikidata: Glomerular filtration rate (Q1542839)) Unsafe sex (en:Safe sex wikidata: safe sex (Q318529)) Go to Wikipedia to each relevant page and add the wikidata value in a proper place. Use a sentence something like this: "This risk factor caused globally years of healthy life lost (DALYs).^[1]" where PXXX is the identifier for disease burden property and QYYY is the identifier for the item in question. Causes of death, disease, and injury Data that contains 163 causes. The 30 largest (based on 2013 DALY), and some politically important (i.e. causes that are actually small but are perceived very large --# : what are these? --Heta (talk) 12:08, 3 February 2016 (UTC)) are located from Wikipedia and Wikidata. (You can also look other data views from the IHME visualization tool) Disease burden property is added to the disease pages as soon as it gets accepted on this page. Ischemic heart disease, en:Coronary artery disease, wikidata: coronary artery disease (Q844935) Lower respiratory infections, en:Lower respiratory tract infection, wikidata: [1] lower respiratory tract infection (Q3631290) Diarrheal diseases, en:Diarrhea, wikidata: diarrhea (Q40878) Low back pain, en:Low back pain, wikidata: lower back pain (Q852163) Chronic obstructive pulmonary disease, en:Chronic obstructive pulmonary disease, wikidata: chronic obstructive pulmonary disease (Q199804) Preterm birth complications, en:Preterm birth, wikidata: premature birth (Q625506) Malaria, en:Malaria, wikidata: malaria (Q12156) Hemorrhagic stroke, en:Stroke, wikidata: stroke (Q12202) HIV/AIDS resulting in other diseases, en:HIV/AIDS, wikidata: AIDS (Q12199) Neonatal encephalopathy due to birth asphyxia and trauma, en:Neonatal encephalopathy, wikidata: encephalopathy (Q576349) Diabetes mellitus, en:Diabetes mellitus, wikidata: diabetes mellitus (Q12206) Major depressive disorder, en:Major depressive disorcer, wikidata: major depressive disorder (Q42844) Tuberculosis, en:Tuberculosis, wikidata: tuberculosis (Q12204) Ischemic stroke, en:Stroke, wikidata: stroke (Q12202) Iron-deficiency anemia, en:Iron-deficiency anemia, wikidata: iron deficiency anemia (Q954674) Self-harm, en:Self-harm, wikidata: self-injury (Q622527) Tracheal, bronchus, and lung cancer, en:Lung cancer, wikidata: lung cancer (Q47912) Neck pain, en:Neck pain, wikidata: neck pain (Q3567802) Other hearing loss, en:Hearing loss, wikidata: no "hearing loss" page, but multiple kinds of hearing loss. I don't know what "other" refers to. Neonatal sepsis and other neonatal infections, en:Neonatal infection, wikidata: Neonatal infection (Q22084957) Migraine, en:Migraine, wikidata: migraine (Q133823) Protein-energy malnutrition, en:Protein-energy malnutrition, wikidata: Protein–energy malnutrition (Q4082071) Motor vehicle road injuries, en:Traffic collision, wikidata: traffic accident (Q9687) Falls, en:Falling (accident), wikidata: falling (Q333495) Congenital heart anomalies, en:Congenital heart defect, wikidata: Congenital heart defect (Q939364) Other neonatal disorders, en:Infant, wikidata: baby (Q998) Pedestrian road injuries, en:Road traffic safety? en:Pedestrian?, wikidata: road traffic safety (Q1147899), pedestrian (Q221488) Other musculoskeletal disorders, en:Musculoskeletal disorder, wikidata: musculoskeletal disorder (Q4116663) Anxiety disorders, en:Anxiety disorder, wikidata: anxiety disorder (Q544006) Alzheimer disease and other dementias, en:Alzheimer's disease, en:Dementia, wikidata: Alzheimer's disease (Q11081), dementia (Q83030) Infobox for public health should also be designed. What data do we want to show in an infobox that could be added to Wikipedia pages of diseases and risk factors? Some first ideas: Numbers of deaths to this disease/risk factor globally (current) Numbers of deaths to this disease/risk factor in a particular country (e.g. Finland in fi) DALYs to this disease/risk factor globally DALYs to this disease/risk factor in a particular country Rate of improvement globally (% change in DALYs per year 1990-2013) Rank of DALYs globally based on level 3 diseases (163 diseases) Rank of DALYs globally based on level 4 risk factors (63 risk factors) ICD-10 code of the disease (this is already in the existing infobox) What else? Politically interesting causes of death and disease Interpersonal violence, en:Violence, wikidata: violence (Q124490) Schizophrenia, en:Schizophrenia, wikidata: schizophrenia (Q41112) Sexually transmitted diseases excluding HIV, en:Sexually transmitted infection, wikidata: sexually transmitted disease (Q12198) Alcohol use disorders, en:Alcohol abuse, wikidata: alcohol abuse (Q7331102) Cirrhosis due to alcohol use, en:Cirrhosis, wikidata: cirrhosis (Q147778) Other transport injuries, Traffic collisions, already in the list above? Also en:Aviation accidents and incidents? wikidata: aviation accident (Q744913) Collective violence and legal intervention, en:Violence#Collective violence, wikidata: (already in the list above) violence (Q124490), en:Justifiable homicide, wikidata: justifiable homicide (Q6317275) Other neglected tropical diseases, en:Tropical disease, wikidata: tropical disease (Q1345671) Exposure to forces of nature, disaster, en:Disaster, wikidata: disaster (Q3839081), en:Natural hazard, wikidata: Natural hazard (Q3567666) Important due to public health relevance Ischemic heart disease Lower respiratory infections Cerebrovascular disease, en:Cerebrovascular disease, wikidata: cerebrovascular disease (Q3360664) Low back and neck pain Road injuries Diarrheal diseases Chronic obstructive pulmonary disease Preterm birth complications HIV/AIDS Malaria Depressive disorders Neonatal encephalopathy due to birth asphyxia and trauma Congenital anomalies (Congenital heart anomalies?) Diabetes mellitus Sense organ diseases en:Sensory system#Diseases, wikidata: sensory system disease (Q18553219)? Sensory system (Q11101) Tuberculosis Iron-deficiency anemia Skin and subcutaneous diseases, en:Cutaneous condition, wikidata: cutaneous disease (Q949302) Self-harm Tracheal, bronchus, and lung cancer Chronic kidney disease, en:Chronic kidney disease, wikidata: chronic kidney disease (Q736715) Neonatal sepsis and other neonatal infections Migraine Protein-energy malnutrition Falls Other neonatal disorders Other musculoskeletal disorders Anxiety disorders Hemoglobinopathies and hemolytic anemias, en:Hemoglobinopathy, wikidata: Hemoglobinopathy (Q1642147), en:Hemolytic anemia, wikidata: hemolytic anemia (Q1145668) Alzheimer disease and other dementias Asthma en:Asthma, wikidata: asthma (Q35869) --# : 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).

+ Show code - Hide code

# 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")

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

+ Show code - Hide code

# 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")

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.

+ Show code - Hide code

# 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")

Keywords

References

↑ Reference to the Lim Lancet article

[1] Reference to the Lim Lancet article

[1]

@@ Line 144: / Line 144: @@
 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).

Difference between revisions of "Burden of disease"

Revision as of 16:22, 2 June 2017

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Question

Answer

Rationale

Global Burden of Disease Study 2010

Calculations

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Keywords

References

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