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COVID-19 Related Updates #931

Merged
merged 25 commits into from
Sep 16, 2021
Merged

COVID-19 Related Updates #931

merged 25 commits into from
Sep 16, 2021

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eedrummer
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This PR contains several changes to COVID-19 simulation in Synthea:

  • Case rates per day are now based on national case rate per 100K per day
  • Implementation of COVID-19 vaccination
  • Vaccination rates and administration based off of national data
  • Scripts to update case and vaccination data

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codecov bot commented Sep 1, 2021

Codecov Report

Merging #931 (86de12d) into master (6ed19ab) will increase coverage by 0%.
The diff coverage is 87%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master    #931    +/-   ##
=========================================
  Coverage        81%     81%            
- Complexity     2817    3003   +186     
=========================================
  Files           107     113     +6     
  Lines         17064   17879   +815     
  Branches       2433    2622   +189     
=========================================
+ Hits          13838   14527   +689     
- Misses         2457    2563   +106     
- Partials        769     789    +20     
Impacted Files Coverage Δ
...va/org/mitre/synthea/modules/covid/C19Vaccine.java 70% <70%> (ø)
...thea/modules/covid/C19VaccineAgeDistributions.java 86% <86%> (ø)
.../mitre/synthea/modules/covid/LateAdopterModel.java 87% <87%> (ø)
...e/synthea/modules/covid/C19ImmunizationModule.java 93% <93%> (ø)
src/main/java/org/mitre/synthea/engine/Module.java 81% <100%> (+<1%) ⬆️
...ain/java/org/mitre/synthea/helpers/Attributes.java 85% <100%> (+<1%) ⬆️
.../mitre/synthea/helpers/SyncedEnumeratedDistro.java 100% <100%> (ø)
...thea/world/agents/behaviors/PayerFinderRandom.java 85% <0%> (-15%) ⬇️
...n/java/org/mitre/synthea/world/concepts/Claim.java 87% <0%> (-7%) ⬇️
...c/main/java/org/mitre/synthea/export/FhirStu3.java 79% <0%> (-5%) ⬇️
... and 26 more

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@jawalonoski jawalonoski self-assigned this Sep 8, 2021
@jawalonoski jawalonoski mentioned this pull request Sep 15, 2021
Created a new SyncedEnumeratedDistro that allows for easy, thread safe use of
EnumeratedDistributions.
Vaccination encounters now have more provider information, which should allow for
all exporters to work.
@jawalonoski jawalonoski merged commit a3482c8 into master Sep 16, 2021
@jawalonoski jawalonoski deleted the c19-updates branch September 16, 2021 14:01
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2 participants