Active Duty Readiness

[jawalonoski]

This pull request adds very high-level modules that affect active duty readiness status within armed forces.

• Musculoskeletal Disorders
• Mental Health Disorders
• Injury/Poisoning

Musculoskeletal Disorders

This module simulates the annual rate of ambulatory visits due to the major diagnostic category Musculoskeletal Disorders (ICD-10-CM: M00-M99) in 2018 in U.S. Armed Forces [1]. Rates are stratified by age and gender. These grouped ICD-10-CM codes are simulated by the post-coordinated SNOMED CT code [2]: 225888002|:42752001|=105606008, which textual translates to 'Unfit due to injury of musculoskeletal system (disorder). For up-to-date individual-level data, you may request a Defense Medical Epidemiology Database (DMED) account here:

https://www.health.mil/Military-Health-Topics/Combat-Support/Armed-Forces-Health-Surveillance-Branch/Data-Management-and-Technical-Support/Defense-Medical-Epidemiology-Database

1. Armed Forces Health Surveillance Branch. Ambulatory Visits, Active Component, U.S. Armed Forces, 2018. MSMR 2019; 26(5): 2-25. Available at: https://health.mil/Reference-Center/Reports/2019/05/01/Medical-Surveillance-Monthly-Report-Volume-26-Number-5.
2. SNOMED International. SNOMED CT Starter Guide: SNOMED CT Expressions. Available at: https://confluence.ihtsdotools.org/display/DOCSTART/7.+SNOMED+CT+Expressions.

Mental Health Disorders

This module simulates the annual rate of ambulatory visits due to the major diagnostic category Mental Health Disorders (ICD-10-CM: F01-F99) in 2018 in U.S. Armed Forces [1]. Rates are stratified by age and gender. These grouped ICD-10-CM codes are simulated by the post-coordinated SNOMED CT code [2]: 225888002|:42752001|=74732009, which textual translates to 'Unfit due to mental disorder (disorder). For up-to-date individual-level data, you may request a Defense Medical Epidemiology Database (DMED) account here:

https://www.health.mil/Military-Health-Topics/Combat-Support/Armed-Forces-Health-Surveillance-Branch/Data-Management-and-Technical-Support/Defense-Medical-Epidemiology-Database

1. Armed Forces Health Surveillance Branch. Ambulatory Visits, Active Component, U.S. Armed Forces, 2018. MSMR 2019; 26(5): 2-25. Available at: https://health.mil/Reference-Center/Reports/2019/05/01/Medical-Surveillance-Monthly-Report-Volume-26-Number-5.
2. SNOMED International. SNOMED CT Starter Guide: SNOMED CT Expressions. Available at: https://confluence.ihtsdotools.org/display/DOCSTART/7.+SNOMED+CT+Expressions.

Injury/Poisoning

This module simulates the annual rate of ambulatory visits due to the major diagnostic category Injury/Poisoning (ICD-10-CM: S00-T98) in 2018 in U.S. Armed Forces [1]. Rates are stratified by age and gender. These grouped ICD-10-CM codes are simulated by the post-coordinated SNOMED CT code [2]: 225888002|:42752001|=417163006, which textual translates to 'Unfit due to traumatic and/or non-traumatic injury (disorder). For up-to-date individual-level data, you may request a Defense Medical Epidemiology Database (DMED) account here:

https://www.health.mil/Military-Health-Topics/Combat-Support/Armed-Forces-Health-Surveillance-Branch/Data-Management-and-Technical-Support/Defense-Medical-Epidemiology-Database

1. Armed Forces Health Surveillance Branch. Ambulatory Visits, Active Component, U.S. Armed Forces, 2018. MSMR 2019; 26(5): 2-25. Available at: https://health.mil/Reference-Center/Reports/2019/05/01/Medical-Surveillance-Monthly-Report-Volume-26-Number-5.
2. SNOMED International. SNOMED CT Starter Guide: SNOMED CT Expressions. Available at: https://confluence.ihtsdotools.org/display/DOCSTART/7.+SNOMED+CT+Expressions.

[codecov]

Codecov Report

Merging #721 into master will increase coverage by 0%.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master    #721    +/-   ##
=========================================
  Coverage        78%     79%            
- Complexity     2430    2470    +40     
=========================================
  Files            96      96            
  Lines         16020   16325   +305     
  Branches       2191    2246    +55     
=========================================
+ Hits          12518   12897   +379     
+ Misses         2811    2748    -63     
+ Partials        691     680    -11     

Impacted Files	Coverage Δ	Complexity Δ
...in/java/org/mitre/synthea/export/ExportHelper.java	65% <0%> (-4%)	17% <0%> (-1%)
...ain/java/org/mitre/synthea/export/CDWExporter.java	80% <0%> (-1%)	44% <0%> (+2%)	⬇️
...e/synthea/modules/CardiovascularDiseaseModule.java	94% <0%> (-1%)	83% <0%> (-1%)
...c/main/java/org/mitre/synthea/export/FhirStu3.java	83% <0%> (-1%)	128% <0%> (-1%)
...org/mitre/synthea/export/ClinicalNoteExporter.java	77% <0%> (ø)	14% <0%> (+1%)
src/main/java/org/mitre/synthea/export/FhirR4.java	78% <0%> (+<1%)	154% <0%> (-1%)	⬆️
.../main/java/org/mitre/synthea/export/FhirDstu2.java	76% <0%> (+<1%)	89% <0%> (+1%)
...ava/org/mitre/synthea/modules/LifecycleModule.java	91% <0%> (+<1%)	131% <0%> (ø%)
...ain/java/org/mitre/synthea/export/CSVExporter.java	89% <0%> (+<1%)	66% <0%> (+1%)
...org/mitre/synthea/world/concepts/HealthRecord.java	90% <0%> (+<1%)	69% <0%> (ø%)
... and 4 more

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[dehall]

Thoughts on a new "module repository" along the lines of synthea-international where we can put things like this? i.e., modules that have niche value but we know aren't at the right level to be merged to master/probably never will be.
I'd copy the module JSONs over there then close this PR with a comment pointing to that new repo

[jawalonoski]

Thoughts on a new "module repository" along the lines of synthea-international where we can put things like this? i.e., modules that have niche value but we know aren't at the right level to be merged to master/probably never will be.
I'd copy the module JSONs over there then close this PR with a comment pointing to that new repo

Interesting idea. I'm not opposed to this, but the module builder won't be able to select them via a branch.