IHME: Difference between revisions

From Pardee Wiki
Jump to navigation Jump to search
 
(16 intermediate revisions by 3 users not shown)
Line 1: Line 1:
The Institute for Health Metrics and Evaluation (IHME) provides data on the Global Burdens of Disease that can be accessed here&nbsp;<font style="background-color: rgb(255, 255, 255);">[http://ghdx.healthdata.org/gbd-results-tool http://ghdx.healthdata.org/gbd-results-tool]. IHME provides data on multiple metrics that we pull into IFs, including deaths, DALYs, incidence, prevelance, violence and forecasts for each. The latest IFs data update for this series was in August 2019, covering 189 economies over the years 1990-2017. This data pull is done using Python.</font>
The Institute for Health Metrics and Evaluation (IHME) provides data on the Global Burdens of Disease that can be accessed here&nbsp;<font style="background-color: rgb(255, 255, 255);">[http://ghdx.healthdata.org/gbd-results-tool http://ghdx.healthdata.org/gbd-results-tool]. IHME provides data on multiple metrics that we pull into IFs, including deaths, DALYs, incidence, prevelance, violence and forecasts for each. The latest IFs data update for this series was in February 2024, covering 188 economies over the years 1990-2019.</font>
= Instructions on Pulling IHME data =


= IFs Series =
=== Preprocessors on Prevalence and Incidence ===


There are currently 146 series that are pulled from the IHME into IFs.&nbsp;
==== Update in February 2024 ====
 
The data can be accessed from the GBD tool at&nbsp;<font style="background-color: rgb(255, 255, 255);">http://ghdx.healthdata.org/gbd-results-tool. You can download the data based on the table below for each series. [https://github.com/shangkexin/The_Institute_for_Health_Metrics_and_Evaluation_IHME Python scripts] used from last data pull can be accessed and adjusted for future data pulls.</font>
= Instructions on Pulling IHME Series =
 
#The data can be accessed from the GBD tool at&nbsp;<font style="background-color: rgb(255, 255, 255);">[http://ghdx.healthdata.org/gbd-results-tool http://ghdx.healthdata.org/gbd-results-tool]. Select "Only countries and territories", "All years", "Cause", "All Ages", "Number", the correct measure (i.e. "Deaths"), "Male" "Female" and "Both", and select all causes. This process might differ depending on the series being pulled in, so just be aware of that.</font>
#<font style="background-color: rgb(255, 255, 255);">Once data is downloaded, a Python script is used to concord and clean the data so it can be pulled into IFs. To do this, you need to have the folder "PythonOutput&Scripts" and "Pythonfiles" in the file path C/Users/Public. WIthin the Pythonfiles folder, you will put the data downloaded from the IHME website in the IHMEDownloads folder, in the respective folder. For example, for Deaths by disease series, you will put the downloaded data in the HistDeathFileData folder.</font>
#<font style="background-color: rgb(255, 255, 255);">Once the data is in the folder, you can run the corresponding Python script. The Python script will pull in the data from the corresponding Excel files, clean it, correspond it to the right IFs series, and concord the countries to the correct country concordance. All you need to do is run the Python script for the series you are trying to pull. For example, for the deaths by diesease series, you will run the DataforIFs-IHME-HistoricalDeathFile.py script.</font>
#<font style="background-color: rgb(255, 255, 255);">Once the script is done running, the completed Excel file will be located in the PythonOutput&Scripts folder.</font>
#Pull in the data into IFs using the IFs data import tool.
 
= Things to Be Aware of While Pulling =
 
For the historical deaths by disease series, the data are in millions in IFs. So you will need to do this conversion before you import.
 
== August 2019 Update ==
For the 2019 update, we have added historical deaths by disease by sex data for the years 1990-2017. These are new series, as we only had totals and not aggregated by sex.
 
== HealthDetailedDeathsCtry ==
 
=== February 2024 Update ===
Original Source: [https://vizhub.healthdata.org/gbd-results/ VizHub - GBD Results (healthdata.org)]
 
GBD Estimate: Cause of death or injury
 
Measure: Deaths
 
Metric: Rate
 
Cause: Select all level 2 causes (''note: “Sense organ disease” is not available for Deaths Rate'')
{| class="wikitable"
{| class="wikitable"
|CauseID
|Variable
|GBD Estimate
|Measure
|Metric
|Cause
|Cause
|cause_name
|Location
|category
|Age
|Sex
|Year
|Decimal Places
|-
|ViolencePoliticalConflictTerror
|Cause of death  or injury
|Deaths
|Rate
|Conflict and  terrorism
|Select all countries and territories
|All Ages
|Both
|Select all
|4
|-
|-
|1
|ViolencePoliticalPoliceExecution
|Other CD
|Cause of death or  injury
|Other infectious diseases
|Deaths
|Communicable,  maternal, neonatal, and nutritional diseases
|Rate
|Executions and police conflict
|Select all countries and territories
|All Ages
|Both
|Select all
|4
|-
|-
|1
|ViolenceSelfHarm
|Other CD
|Cause of death or  injury
|Maternal and neonatal  disorders
|Deaths
|Communicable, maternal, neonatal, and nutritional diseases
|Rate
|Self-harm
|Select all countries and territories
|All Ages
|Both
|Select all
|4
|-
|-
|1
|SocietalViolenceDeathsTotal
|Other CD
|Cause of death or  injury
|Nutritional deficiencies
|Deaths
|Communicable, maternal, neonatal, and nutritional diseases
|Rate
|Interpersonal violence + Conflict and terrorism + Executions and police conflict
|Select all countries and territories
|All Ages
|Both
|Select all
|4
|-
|-
|2
|ViolenceInterpersonChild
|Malignant Neoplasms
|Cause of death or  injury
|Neoplasms
|Deaths
|Communicable, maternal, neonatal, and nutritional diseases
|Rate
|Interpersonal violence
|Select all  countries and territories
|0-14
|Both
|Select all
|4
|-
|-
|3
|ViolenceInterpersonWomenAdult
|Cardiac
|Cause of death or  injury
|Cardiovascular diseases
|Deaths
|Communicable, maternal, neonatal, and nutritional diseases
|Rate
|Interpersonal violence
|Select all countries and territories
|20 +
|Female
|Select all
|4
|-
|-
|DrOpiodPrevIHME
|Cause of death or  injury
|Prevalence
|Percent
|Opioid Use Disorders
|Select  all countries and territories
|All Ages
|Both
|Select all
|4
|4
|Digestive
|Digestive diseases
|Communicable,  maternal, neonatal, and nutritional diseases
|-
|-
|DrugPrevalenceAmphetaminesIHME
|Cause of death or  injury
|Prevalence
|Percent
|Amphetamine Use Disorders
|Select all  countries and territories
|All Ages
|Both
|Select all
|5
|5
|Respiratory
|Chronic respiratory  diseases
|Communicable,  maternal, neonatal, and nutritional diseases
|-
|-
|6
|DrugPrevalenceCocaineIHME
|Other NCD
|Cause of death or  injury
|Neurological disorders
|Prevalence
|Non-communicable
|Percent
|Cocaine Use Disorders
|Select all countries and territories
|All Ages
|Both
|Select all
|5
|-
|-
|6
|IHMEDthsHIV
|Other NCD
|Cause of death or  injury
|Substance use disorders
|Deaths
|Non-communicable
|Number
|HIV/AIDs
|Select all countries and territories
|All Ages
|Both
|Select all
|5
|-
|-
|6
|IHMEDthsMalar
|Other NCD
|Cause of death or  injury
|Skin and subcutaneous  diseases
|Deaths
|Non-communicable
|Number
|Malaria
|Select all  countries and territories
|All Ages
|Both
|Select all
|5
|-
|-
|6
|IHMEInciHIVNumber
|Other NCD
|Cause of death or  injury
|Sense organ diseases
|Incidence
|Non-communicable
|Number
|HIV/AIDs
|Select all  countries and territories
|All Ages
|Both
|Select all
|
|-
|-
|6
|IHMEInciMalariaNumber
|Other NCD
|Cause of death or  injury
|Musculoskeletal disorders
|Incidence
|Non-communicable
|Number
|Malaria
|Select all countries and territories
|All Ages
|Both
|Select all
|
|-
|-
|6
|IHMEPrevHIV
|Other NCD
|Cause of death or injury
|Other non-communicable diseases
|Prevalence
|Non-communicable
|Percent
|-
|HIV/AIDs
|7
|Select all countries and territories
|Road Injuries
|All Ages
|Transport injuries
|Both
|Non-communicable
|Select all
|-
|3
|8
|Other Unintentional  Injuries
|Unintentional injuries
|Non-communicable
|-
|9
|Intentional Injuries
|Self-harm and  interpersonal violence
|Non-communicable
|-
|10
|Diabetes
|Diabetes and kidney  diseases
|Non-communicable
|-
|11
|HIV
|HIV/AIDS and sexually  transmitted infections
|Non-communicable
|-
|-
|12
|IHMEPrevHIVNumber
|Diarrhea
|Cause of death or  injury
|Enteric infections
|Prevalence
|Non-communicable
|Number
|HIV/AIDs
|Select all  countries and territories
|All Ages
|Both
|Select all
|
|-
|-
|13
|IHMEPrevMalariaNumber
|Cause of death or  injury
|Prevalence
|Number
|Malaria
|Malaria
|Neglected tropical diseases and malaria
|Select all countries and territories
|Injuries
|All Ages
|-
|Both
|14
|Select all
|Respiratory Infection
|
|Respiratory  infections and tuberculosis
|Injuries
|-
|15
|Mental Health
|Mental disorders
|Injuries
|}
|}
Location: Select all countries and territories
Note:  


Age: Select the values in Age_Name
* ViolenceInterpersonChild & ViolenceInterpersonWomenAdult have changed a lot, we identify the Age by comparing the trend of old data in IFsHistSeries and the new data from GBD.
* Be aware of the definition of each preprocessor and its unit so that you can find the exact match in the IHME GBD variables.
* Some regions in IFs are not provided by IHME yet, we are encouraged to use proxies. For example, use Singapore, Albania, and Mali for Hong Kong, Kosovo, and Sahrawi respectively. Be mindful that for tables with units in rate or percent, proximal values can be directly applied; however, when values are in numbers or headcounts, you will need to borrow the population figures to apply values proportionally. 
 
=== Tables Used in Hist+Forecast Display ===
 
==== Update in July 2024 ====
The data can be accessed from the GBD tool at&nbsp;<font style="background-color: rgb(255, 255, 255);">http://ghdx.healthdata.org/gbd-results-tool. You can download the data based on the table below for each series. Note that a detailed death cause mapping table can be found [[IFs.db#HealthDetailedDeathsCtry|here]].</font>
 
There are 45 tables in total related to detailed death tables in IFs. For each of 15 death causes in IFs, we have a total death table and two tables by sex group. These 45 tables can be searched by using the following naming conventions IHMEDths___, IHMEDths___Females, and IHMEDths___Males, where ___ denotes the cause of death in IFs. These 15 causes are, Cardio, Diabet, Diarrh, Digest, HIV, Intlj, Malar, MalNeopl, MentHlth, OthCD, OthNCD, OthUnintlj, Respinfec, Respiratory, Roadacc.
 
= Demographic Related IHME Preprocessors =
 
=== Life Expectancy ===
Life expectancy data can be pulled from https://ghdx.healthdata.org/record/ihme-data/gbd-2019-life-tables-1950-2019. Just download Life Tables: Age < 1 year and use the IHME_GBD_2019_LIFE_TABLES_1950_2019_ID_28_NOSHOCK_Y2020M07D31.CSV (28 means "Age Group < 1 year").
{| class="wikitable"
{| class="wikitable"
|IHME_Age_ID
|Variable
|Age_Name
|Age
|Age_IFs
|Sex
|Year
|Metric Name
|Decimal Places
|-
|-
|5
|LifeExpectIHMEBothSexesHistOnly
|1 to 4
|< 1 year
|p2
|Both
|1950-2019
|Years
|3
|-
|-
|6
|LifeExpectIHMEMaleHistOnly
|5 to 9
|< 1 year
|p3
|Male
|1950-2019
|Years
|3
|-
|-
|7
|LifeExpectIHMEFemaleHistOnly
|10 to 14
|< 1 year
|p4
|Female
|1950-2019
|Years
|3
|}
 
=== Infant Mortality ===
Life expectancy data can be pulled from two different sources depending on the series. You can download the data by age group.
{| class="wikitable"
|Variable
|Age
|Sex
|Year
|Decimal Places
|Source
|-
|-
|8
|InfMortRateIHME
|15 to 19
|Summation of neonatal, 1-5 month, and 6-11 month
|p5
|Both
|1950-2019
|4
|https://ghdx.healthdata.org/record/ihme-data/global-burden-disease-study-2019-gbd-2019-under-5-mortality-detailed-age-groups-1950-2019
|-
|-
|9
|Under5MortRateIHME
|20 to 24
|Under 5
|p6
|Both
|-
|1950-2019
|10
|4
|25 to 29
|https://ghdx.healthdata.org/record/ihme-data/gbd-2019-mortality-estimates-1950-2019
|p7
|-
|11
|30 to 34
|p8
|-
|12
|35 to 39
|p9
|-
|13
|40 to 44
|p10
|-
|14
|45 to 49
|p11
|-
|15
|50 to 54
|p12
|-
|16
|55 to 59
|p13
|-
|17
|60 to 64
|p14
|-
|18
|65 to 69
|p15
|-
|19
|70 to 74
|p16
|-
|20
|75 to 79
|p17
|-
|28
|<1 year
|p1
|-
|30
|80 to 84
|p18
|-
|31
|85 to 89
|p19
|-
|32
|90 to 94
|p20
|-
|235
|95 +
|p21
|}
|}
Sex: Male(1), Female(2)
Note: InfMortRateIHME must be manually added together, the data can only be downloaded by separate age groups.
 
Year: 2019 (Use the most recent available year.)


The Source Unit is Deaths per 100,000. ([https://view.officeapps.live.com/op/view.aspx?src=https%3A%2F%2Fwww.healthdata.org%2Fsites%2Fdefault%2Ffiles%2Ffiles%2FProjects%2FGBD%2FIHME_GBD_2019_A3_MEASURE_METRIC_DEFINITIONS_Y2020M10D15.XLSX&wdOrigin=BROWSELINK IHME_GBD_2019_A3_MEASURE_METRIC_DEFINITIONS_Y2020M10D15.XLSX (live.com)] from [https://www.healthdata.org/research-analysis/about-gbd/gbd-data-and-tools-guide Global Burden of Disease (GBD) data and tools guide | Institute for Health Metrics and Evaluation (healthdata.org)])
= Tables in IFs.db =


Need to use Formula /100 to transform the Unit to Deaths per 1,000.
=== HealthDetailedDeathsCtry ===
Detailed instruction on pulling number of deaths for IFs death categories can be found [[IFs.db#HealthDetailedDeathsCtry|here]].

Latest revision as of 18:17, 30 July 2024

The Institute for Health Metrics and Evaluation (IHME) provides data on the Global Burdens of Disease that can be accessed here http://ghdx.healthdata.org/gbd-results-tool. IHME provides data on multiple metrics that we pull into IFs, including deaths, DALYs, incidence, prevelance, violence and forecasts for each. The latest IFs data update for this series was in February 2024, covering 188 economies over the years 1990-2019.

Instructions on Pulling IHME data

Preprocessors on Prevalence and Incidence

Update in February 2024

The data can be accessed from the GBD tool at http://ghdx.healthdata.org/gbd-results-tool. You can download the data based on the table below for each series. Python scripts used from last data pull can be accessed and adjusted for future data pulls.

Variable GBD Estimate Measure Metric Cause Location Age Sex Year Decimal Places
ViolencePoliticalConflictTerror Cause of death or injury Deaths Rate Conflict and terrorism Select all countries and territories All Ages Both Select all 4
ViolencePoliticalPoliceExecution Cause of death or injury Deaths Rate Executions and police conflict Select all countries and territories All Ages Both Select all 4
ViolenceSelfHarm Cause of death or injury Deaths Rate Self-harm Select all countries and territories All Ages Both Select all 4
SocietalViolenceDeathsTotal Cause of death or injury Deaths Rate Interpersonal violence + Conflict and terrorism + Executions and police conflict Select all countries and territories All Ages Both Select all 4
ViolenceInterpersonChild Cause of death or injury Deaths Rate Interpersonal violence Select all countries and territories 0-14 Both Select all 4
ViolenceInterpersonWomenAdult Cause of death or injury Deaths Rate Interpersonal violence Select all countries and territories 20 + Female Select all 4
DrOpiodPrevIHME Cause of death or injury Prevalence Percent Opioid Use Disorders Select all countries and territories All Ages Both Select all 4
DrugPrevalenceAmphetaminesIHME Cause of death or injury Prevalence Percent Amphetamine Use Disorders Select all countries and territories All Ages Both Select all 5
DrugPrevalenceCocaineIHME Cause of death or injury Prevalence Percent Cocaine Use Disorders Select all countries and territories All Ages Both Select all 5
IHMEDthsHIV Cause of death or injury Deaths Number HIV/AIDs Select all countries and territories All Ages Both Select all 5
IHMEDthsMalar Cause of death or injury Deaths Number Malaria Select all countries and territories All Ages Both Select all 5
IHMEInciHIVNumber Cause of death or injury Incidence Number HIV/AIDs Select all countries and territories All Ages Both Select all
IHMEInciMalariaNumber Cause of death or injury Incidence Number Malaria Select all countries and territories All Ages Both Select all
IHMEPrevHIV Cause of death or injury Prevalence Percent HIV/AIDs Select all countries and territories All Ages Both Select all 3
IHMEPrevHIVNumber Cause of death or injury Prevalence Number HIV/AIDs Select all countries and territories All Ages Both Select all
IHMEPrevMalariaNumber Cause of death or injury Prevalence Number Malaria Select all countries and territories All Ages Both Select all

Note:

  • ViolenceInterpersonChild & ViolenceInterpersonWomenAdult have changed a lot, we identify the Age by comparing the trend of old data in IFsHistSeries and the new data from GBD.
  • Be aware of the definition of each preprocessor and its unit so that you can find the exact match in the IHME GBD variables.
  • Some regions in IFs are not provided by IHME yet, we are encouraged to use proxies. For example, use Singapore, Albania, and Mali for Hong Kong, Kosovo, and Sahrawi respectively. Be mindful that for tables with units in rate or percent, proximal values can be directly applied; however, when values are in numbers or headcounts, you will need to borrow the population figures to apply values proportionally.

Tables Used in Hist+Forecast Display

Update in July 2024

The data can be accessed from the GBD tool at http://ghdx.healthdata.org/gbd-results-tool. You can download the data based on the table below for each series. Note that a detailed death cause mapping table can be found here.

There are 45 tables in total related to detailed death tables in IFs. For each of 15 death causes in IFs, we have a total death table and two tables by sex group. These 45 tables can be searched by using the following naming conventions IHMEDths___, IHMEDths___Females, and IHMEDths___Males, where ___ denotes the cause of death in IFs. These 15 causes are, Cardio, Diabet, Diarrh, Digest, HIV, Intlj, Malar, MalNeopl, MentHlth, OthCD, OthNCD, OthUnintlj, Respinfec, Respiratory, Roadacc.

Demographic Related IHME Preprocessors

Life Expectancy

Life expectancy data can be pulled from https://ghdx.healthdata.org/record/ihme-data/gbd-2019-life-tables-1950-2019. Just download Life Tables: Age < 1 year and use the IHME_GBD_2019_LIFE_TABLES_1950_2019_ID_28_NOSHOCK_Y2020M07D31.CSV (28 means "Age Group < 1 year").

Variable Age Sex Year Metric Name Decimal Places
LifeExpectIHMEBothSexesHistOnly < 1 year Both 1950-2019 Years 3
LifeExpectIHMEMaleHistOnly < 1 year Male 1950-2019 Years 3
LifeExpectIHMEFemaleHistOnly < 1 year Female 1950-2019 Years 3

Infant Mortality

Life expectancy data can be pulled from two different sources depending on the series. You can download the data by age group.

Variable Age Sex Year Decimal Places Source
InfMortRateIHME Summation of neonatal, 1-5 month, and 6-11 month Both 1950-2019 4 https://ghdx.healthdata.org/record/ihme-data/global-burden-disease-study-2019-gbd-2019-under-5-mortality-detailed-age-groups-1950-2019
Under5MortRateIHME Under 5 Both 1950-2019 4 https://ghdx.healthdata.org/record/ihme-data/gbd-2019-mortality-estimates-1950-2019

Note: InfMortRateIHME must be manually added together, the data can only be downloaded by separate age groups.

Tables in IFs.db

HealthDetailedDeathsCtry

Detailed instruction on pulling number of deaths for IFs death categories can be found here.