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Physiology Models (Borked) #1254

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wants to merge 180 commits into from
Closed

Physiology Models (Borked) #1254

wants to merge 180 commits into from

Commits on Feb 7, 2023

  1. WIP Medicare eligibility columns.

    @jawalonoski
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  2. Remove garbage code.

    @jawalonoski
    jawalonoski committed Feb 7, 2023
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Commits on Feb 8, 2023

  1. Expand SSD and ESRD testing for BFD RIF.

    @jawalonoski
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  2. Checkstyle fixes.

    @jawalonoski
    jawalonoski committed Feb 8, 2023
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  3. Remove unused import.

    @jawalonoski
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Commits on Feb 9, 2023

  1. Add divorced and widowed.

    @jawalonoski
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  2. Add current BIC.

    @jawalonoski
    jawalonoski committed Feb 9, 2023
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Commits on Feb 10, 2023

  1. Increase progression of CKD and ESRD. Exclude some people from BFD RIF.

    @jawalonoski
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Commits on Feb 13, 2023

  1. wearable devices - vital signs equipment

    @awatson1978
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Commits on Feb 14, 2023

  1. Code adjustments.

    @jawalonoski
    jawalonoski committed Feb 14, 2023
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Commits on Feb 15, 2023

  1. Fix a bug where DRG codes could be skipped in the SNF exporter

    @hadleynet
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  2. Tune medicare status and entitlement codes.

    @jawalonoski
    jawalonoski committed Feb 15, 2023
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  3. Adjust buyin codes.

    @jawalonoski
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Commits on Feb 16, 2023

  1. Fix #1253.

    @jawalonoski
    jawalonoski committed Feb 16, 2023
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Commits on Feb 20, 2023

  1. Update dual eligible coding algorithm to improve alignment with obser… 

    …ved data
    @hadleynet
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  2. Update medicare buyin coding algorithm to improve alignment with obse… 

    …rved data, add support for benes that decline part B coverage.
    @hadleynet
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Commits on Feb 21, 2023

  1. Module updates for ESRD and kidney treatments.

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Commits on Feb 22, 2023

  1. Don't output beneficiariary file lines for years before the claim cut… 

    …tof date. Exclude child beneficiaries.
    @hadleynet
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Commits on Feb 23, 2023

  1. Lifecycle module now sets disability attribute.

    @jawalonoski
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  2. Updates to ensure number of BFD exports matches number requested on c… 

    …ommand line. Some additional refactoring to ensure claims are only emitted for years when the beneficiary file contains entries.
    @hadleynet
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  3. Merge remote-tracking branch 'refs/remotes/origin/entitlement_codes' … 

    …into entitlement_codes
    @hadleynet
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  4. Update RxNorm codes to be prescribable codes.

    @jawalonoski
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  5. Merge branch 'entitlement_codes' of https://github.com/synthetichealt… 

    …h/synthea into entitlement_codes
    @jawalonoski
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  6. Adjust BIC algorithm since all < 65 are either diasabled or have ESRD

    @hadleynet
    hadleynet committed Feb 23, 2023
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  7. Update src/main/java/org/mitre/synthea/export/Exporter.java 

    Co-authored-by: sonatype-lift[bot] <37194012+sonatype-lift[bot]@users.noreply.github.com>
    @jawalonoski @sonatype-lift
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  8. Tweak BIC codes.

    @jawalonoski
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  9. Merge branch 'entitlement_codes' of https://github.com/synthetichealt… 

    …h/synthea into entitlement_codes
    @jawalonoski
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Commits on Feb 24, 2023

  1. Adjust ESRD detection for BIC codes.'

    @jawalonoski
    jawalonoski committed Feb 24, 2023
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  2. Fix gender specific BIC code.

    @jawalonoski
    jawalonoski committed Feb 24, 2023
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  3. ESRD tuning for coverage start date.

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Commits on Feb 27, 2023

  1. Remove temporary output file.

    @jawalonoski
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  2. Merge pull request #1248 from synthetichealth/entitlement_codes 

    Medicare eligibility and entitlements
    @jawalonoski
    jawalonoski authored Feb 27, 2023
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Commits on Feb 28, 2023

  1. Truncate provider UPIN, PIN and NUM fields to their defined max lengths.

    @hadleynet
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  2. Check provider pin lengths on input.

    @jawalonoski
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  3. Merge pull request #1256 from synthetichealth/bfd_field_lengths 

    Truncate provider UPIN, PIN and NUM fields to their defined max lengths.
    @jawalonoski
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Commits on Mar 2, 2023

  1. Update various drug costs that drive higher than expected BFD clainm … 

    …costs
    @hadleynet
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  2. Additional cost updates.

    @jawalonoski
    jawalonoski committed Mar 2, 2023
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  3. Change prescriptions to administrations.

    @jawalonoski
    jawalonoski committed Mar 2, 2023
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  4. Remove duplicate rows from costs.

    @jawalonoski
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  5. Add provider finder restricted to Medicare.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Mar 2, 2023
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  6. Update PRVDR_NUM fields.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Mar 2, 2023
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  7. Update additional medication costs.

    @jawalonoski
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  8. Merge pull request #1258 from synthetichealth/update_med_costs 

    Update various drug costs that drive higher than expected BFD clainm …
    @jawalonoski
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  9. basics of US Core 5 support

    @dehall
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  10. update code displays where not matching a preferred display

    @dehall
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  11. test fixes alongside US Core 5

    @dehall
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Commits on Mar 6, 2023

  1. calculate age by UTC, not local time

    @dehall
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  2. Person.getSymptoms now returns a sorted list

    @dehall
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  3. new flag to only generate a single person by seed

    @dehall
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Commits on Mar 7, 2023

  1. address review feedback

    @dehall
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Commits on Mar 8, 2023

  1. Repair inpatient encounter reason codes.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Mar 8, 2023
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  2. Adjustments based on comments.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Mar 8, 2023
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  3. Fix broken costs test.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Mar 8, 2023
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Commits on Mar 9, 2023

  1. workaround for validation error

    @dehall
    dehall committed Mar 9, 2023
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  2. add uscore 5 structure definitions

    @dehall
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  3. remove workaround for us core codesystem

    @dehall
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Commits on Mar 13, 2023

  1. Fix ethnicity display in clinical notes.

    @jawalonoski
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Commits on Mar 18, 2023

  1. new generators; not guaranteed to work (yet)

    @awatson1978
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Commits on Mar 19, 2023

  1. simulation configs - will probably run and fail

    @awatson1978
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Commits on Mar 20, 2023

  1. heck; the graphs seem to be kind of working

    @awatson1978
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Commits on Mar 22, 2023

  1. Handle occasional Provenance Provider/Organization reference issues.

    @jawalonoski
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  2. Merge pull request #1259 from synthetichealth/uscore5 

    US Core 5, plus code fixes
    @jawalonoski
    jawalonoski authored Mar 22, 2023
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  3. bump github action version 

    all previous versions of this action were removed by the owner when v0.2.1 was pushed a few days ago... not ideal
    @dehall
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  4. Merge pull request #1275 from synthetichealth/bump-version 

    Bump github action version on Deploy
    @jawalonoski
    jawalonoski authored Mar 22, 2023
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  5. updated readme

    @awatson1978
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  6. Merge pull request #1269 from synthetichealth/note_fix 

    Fix ethnicity display in clinical notes.
    @jawalonoski
    jawalonoski authored Mar 22, 2023
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Commits on Mar 27, 2023

  1. Add reasons to encounters.

    @hadleynet
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  2. Add reason for immunotherapy encounters

    @hadleynet
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  3. Undo unintended code change

    @hadleynet
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  4. Additional encounter reasons

    @hadleynet
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  5. And yet more encounter reasons

    @hadleynet
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  6. Additional batch of encounter reasons

    @hadleynet
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  7. Additional encounter reasons

    @hadleynet
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Commits on Mar 31, 2023

  1. Final set of module updates to add reasons to encounters

    @hadleynet
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Commits on Apr 3, 2023

  1. Merge pull request #1262 from synthetichealth/more_repro_fixes 

    Additional reproducibility fixes, plus a "single person seed" feature
    @jawalonoski
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Commits on Apr 10, 2023

  1. Added priorities to payers

    @RobertScalfani
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  2. Added ACA, priority, max out of pocket to plans

    @RobertScalfani
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  3. Simplified PayerManager logic, added new payer/plan implementations

    @RobertScalfani
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  4. Simplified health insurance module enrollment periods

    @RobertScalfani
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  5. Simplified and updated plan finder logic for new plan implementation

    @RobertScalfani
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  6. Remoed planrecord from coveragerecord, simplified both

    @RobertScalfani
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  7. Improved claim stability, added new methods that hide its properties … 

    …better
    @RobertScalfani
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  8. Updated Person to be compatible with new coverage implementation

    @RobertScalfani
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  9. Updated exporters to use new Claim accessors

    @RobertScalfani
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  10. Added new insurance plan/payer/eligbilty fields and rows

    @RobertScalfani
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Commits on Apr 11, 2023

  1. Removed attribute-based person constructor

    @RobertScalfani
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  2. Added payer tests

    @RobertScalfani
    RobertScalfani committed Apr 11, 2023
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  3. Test Fixes

    @RobertScalfani
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  4. checkstyle fixes

    @RobertScalfani
    RobertScalfani committed Apr 11, 2023
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Commits on Apr 12, 2023

  1. Added new tests

    @RobertScalfani
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  2. Fixed sonatype error

    @RobertScalfani
    RobertScalfani committed Apr 12, 2023
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  3. Merge pull request #1273 from synthetichealth/encounter_reasons 

    Add reasons to encounters
    @jawalonoski
    jawalonoski authored Apr 12, 2023
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  4. Test fixes

    @RobertScalfani
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Commits on Apr 17, 2023

  1. Fixes for employment condition and stress level 

    Previously, the SDoH HSRN submodule would change employment condition
every wellness visit, even if the actual condition did not change.

This change keeps the same condition across wellness visits of the
status does not change.

There was a similar problem with stress level. That is also fixed by
this change.
    @eedrummer @hadleynet
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  2. WIP: Working on a more realiztic simulation of unemployment

    @eedrummer @hadleynet
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  3. Test for the employment model

    @eedrummer @hadleynet
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  4. WIP: Tweaks to try to get county unemployment levels right

    @eedrummer @hadleynet
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  5. WIP: Employment stats looking good. Somehow breaks BB2RIFExporter

    @eedrummer @hadleynet
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  6. Fixing Sonatype Lift identified possible NPE issue

    @eedrummer @hadleynet
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Commits on Apr 18, 2023

  1. Added plan endyear that supports future endyears

    @RobertScalfani
    RobertScalfani committed Apr 18, 2023
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  2. Updated claim values, fixed secondary payer csv export

    @RobertScalfani
    RobertScalfani committed Apr 18, 2023
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Commits on Apr 21, 2023

  1. change endyear to use max int value

    @RobertScalfani
    RobertScalfani committed Apr 21, 2023
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  2. Fixed end year issue

    @RobertScalfani
    RobertScalfani committed Apr 21, 2023
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Commits on Apr 24, 2023

  1. Moved payer validity check sooner

    @RobertScalfani
    RobertScalfani committed Apr 24, 2023
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Commits on Apr 26, 2023

  1. WIP of US Core 5 test fixes for CI

    @dehall
    dehall committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. bring in some tricks from when USCore 4 was added

    @dehall
    dehall committed Apr 27, 2023
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  2. converted payers/plans to lists instead of sets

    @RobertScalfani
    RobertScalfani committed Apr 27, 2023
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Commits on Apr 28, 2023

  1. Changed payers to use LinkedHashMap for ordering, fixed Java11 issue

    @RobertScalfani
    RobertScalfani committed Apr 28, 2023
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  2. Merge pull request #1279 from synthetichealth/improved-enrollments 

    Enrollment Improvements
    @jawalonoski
    jawalonoski authored Apr 28, 2023
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  3. Update BFD inpatient exporter to ensure line item totals match claim … 

    …totals
    @hadleynet
    hadleynet committed Apr 28, 2023
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  4. Fix Sonatype warnings

    @hadleynet
    hadleynet committed Apr 28, 2023
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  5. Update BFD outpatient exporter to make line item financials add up to… 

    … match claim totals. Factor out common code from inpatient and outpatient into base class.
    @hadleynet
    hadleynet committed Apr 28, 2023
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  6. Add tests to ensure HHA claim line charges and payments add up to cla… 

    …im totals
    @hadleynet
    hadleynet committed Apr 28, 2023
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  7. Add tests to ensure SNF claim line charges and payments add up to cla… 

    …im totals
    @hadleynet
    hadleynet committed Apr 28, 2023
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  8. Update BFD hospice exporter to ensure line item costs sum to claim le… 

    …vel cost.
    @hadleynet
    hadleynet committed Apr 28, 2023
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  9. Fix BFD inpatient and outpatient exporter claim payment values. Addit… 

    …ional hospice exporter testing.
    @hadleynet
    hadleynet committed Apr 28, 2023
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  10. Remove redundant lines in Outpatient exporter. Increase number of gen… 

    …erated patients in BFD exporter tests to ensure HHA file is created (necessitated by rebase on master)
    @hadleynet
    hadleynet committed Apr 28, 2023
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  11. Merge pull request #1278 from synthetichealth/bfd_claim_totals 

     BFD Exporter Updates
    @jawalonoski
    jawalonoski authored Apr 28, 2023
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Commits on May 1, 2023

  1. fixes to homelessness module

    @dehall
    dehall committed May 1, 2023
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  2. one more valueset

    @dehall
    dehall committed May 1, 2023
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  3. Merge pull request #1286 from synthetichealth/fix_uscore5 

    Fix CI test failures due to US Core 5 artifacts
    @jawalonoski
    jawalonoski authored May 1, 2023
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Commits on May 2, 2023

  1. CSV sort patient expenses and payer transitions by time.

    @jawalonoski
    jawalonoski committed May 2, 2023
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Commits on May 5, 2023

  1. add survey link to readme

    @dehall
    dehall authored May 5, 2023
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  2. Merge pull request #1290 from synthetichealth/survey-link-readme 

    Add survey link to readme
    @dehall
    dehall authored May 5, 2023
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Commits on May 10, 2023

  1. Claims CSV contains invalid uuids

    Simon Schiff committed May 10, 2023
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Commits on May 16, 2023

  1. Merge pull request #1291 from SimonUzL/master 

    Claims CSV contains invalid uuids
    @jawalonoski
    jawalonoski authored May 16, 2023
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Commits on May 24, 2023

  1. update survey URL in readme

    @dehall
    dehall authored May 24, 2023
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Commits on May 25, 2023

  1. Merge pull request #1288 from synthetichealth/csv_ordering 

    CSV sort patient expenses and payer transitions by time.
    @jawalonoski
    jawalonoski authored May 25, 2023
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  2. rework how physiology sbml is loaded to support running from JAR

    @dehall
    dehall committed May 25, 2023
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Commits on May 30, 2023

  1. Merge pull request #1299 from synthetichealth/physiology_jar_fix 

    Fix physiology simulations when running from JAR
    @jawalonoski
    jawalonoski authored May 30, 2023
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Commits on Jun 6, 2023

  1. Replace weirdly encoded characters.

    @jawalonoski
    jawalonoski committed Jun 6, 2023
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  2. Adjust patient residence codes.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Jun 6, 2023
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  3. Fix typo in comment.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Jun 6, 2023
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  4. Adjust residence code.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Jun 6, 2023
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  5. Stop exporting the BFD beneficiary history file

    @hadleynet
    hadleynet committed Jun 6, 2023
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Commits on Jun 7, 2023

  1. Fix 'Person does not have insurance at time' export error and use pre… 

    …tty_print config option.
    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Jun 7, 2023
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  2. XML and JSON exporters can now control pretty printing.

    @jawalonoski @hadleynet
    jawalonoski authored and hadleynet committed Jun 7, 2023
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  3. Merge pull request #1309 from synthetichealth/remove_bfd_bene_history 

    Remove BFD beneficiary history file
    @jawalonoski
    jawalonoski authored Jun 7, 2023
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Commits on Jun 8, 2023

  1. Small tweak to add symptom information to the JSON export

    @eedrummer
    eedrummer committed Jun 8, 2023
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  2. Merge pull request #1311 from synthetichealth/json-export-symptoms 

    Small tweak to add symptom information to the JSON export
    @jawalonoski
    jawalonoski authored Jun 8, 2023
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Commits on Jun 9, 2023

  1. Add symptom unit tests.

    @jawalonoski
    jawalonoski committed Jun 9, 2023
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  2. Fix random CCDA export issue with super encounter.

    @jawalonoski
    jawalonoski committed Jun 9, 2023
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Commits on Jun 13, 2023

  1. Merge pull request #1312 from synthetichealth/symptoms 

    Symptoms
    @eedrummer
    eedrummer authored Jun 13, 2023
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  2. Fix #1313

    @jawalonoski
    jawalonoski committed Jun 13, 2023
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Commits on Jun 14, 2023

  1. BFD inpatient exporter updates. Ensure claim totals match sum of line… 

    … items, always have a total charge line item, improve mapping from procedure code to revenue center.
    @hadleynet
    hadleynet committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. sync

    @awatson1978
    awatson1978 committed Jun 15, 2023
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  2. updated models; synthea runs again

    @awatson1978
    awatson1978 committed Jun 15, 2023
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  3. Merge pull request #1315 from synthetichealth/bfd_inpatient_rev_center 

    BFD inpatient exporter updates
    @jawalonoski
    jawalonoski authored Jun 15, 2023
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Commits on Jun 16, 2023

  1. Merge pull request #1314 from synthetichealth/esrd 

    Resolve weirdness of ESRD diagnosis and transplant interaction
    @eedrummer
    eedrummer authored Jun 16, 2023
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  2. 3.2.0 release

    @hadleynet
    hadleynet committed Jun 16, 2023
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  3. v3.2.1-SNAPSHOT start

    @hadleynet
    hadleynet committed Jun 16, 2023
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  4. Fix the uberJar classifier so the publish task works properly

    @hadleynet
    hadleynet committed Jun 16, 2023
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Commits on Jun 22, 2023

  1. Fix SDOH address category.

    @jawalonoski
    jawalonoski committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. Refactor bfd outpatient exporter in prep for revised revenue center m… 

    …apping. Will now always emit a total charge line item.
    @hadleynet
    hadleynet committed Jun 23, 2023
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Commits on Jun 26, 2023

  1. Add new mapping file for outpatient HCPCS code to revenue center

    @hadleynet
    hadleynet committed Jun 26, 2023
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Commits on Jun 28, 2023

  1. Set blank HCPCS code for outpatient total charge line items

    @hadleynet
    hadleynet committed Jun 28, 2023
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  2. Merge pull request #1321 from synthetichealth/bfd_outpatient_rev_center 

    Outpatient Revenue Center Updates
    @jawalonoski
    jawalonoski authored Jun 28, 2023
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Commits on Jul 3, 2023

  1. Update BFD HHA exporter to support PPS codes and improve HCPCS to rev… 

    …enue center mapping
    @hadleynet
    hadleynet committed Jul 3, 2023
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Commits on Jul 11, 2023

  1. wearables module with fitness data

    @awatson1978
    awatson1978 committed Jul 11, 2023
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  2. wearables module with fitness data

    @awatson1978
    awatson1978 committed Jul 11, 2023
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Commits on Jul 13, 2023

  1. revert synthea.properties.physiology.state.enabled back to false

    @awatson1978
    awatson1978 committed Jul 13, 2023
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Commits on Jul 14, 2023

  1. Remove debug code, fix field mapping table to remove total charge rev… 

    … center from random selected values.
    @hadleynet
    hadleynet committed Jul 14, 2023
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  2. Merge pull request #1318 from synthetichealth/sdoh_fix 

    Fix SDOH address category.
    @jawalonoski
    jawalonoski authored Jul 14, 2023
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Commits on Jul 17, 2023

  1. Update src/main/java/org/mitre/synthea/export/rif/BB2RIFExporter.java 

    Co-authored-by: sonatype-lift[bot] <37194012+sonatype-lift[bot]@users.noreply.github.com>
    @jawalonoski @sonatype-lift
    jawalonoski and sonatype-lift[bot] authored Jul 17, 2023
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  2. Merge pull request #1328 from synthetichealth/bfd_hha_rev_center 

    Update BFD HHA Exporter
    @jawalonoski
    jawalonoski authored Jul 17, 2023
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Commits on Jul 20, 2023

  1. .idea added to .gitignore

    @awatson1978
    awatson1978 committed Jul 20, 2023
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  2. cleaning up whitespace

    @awatson1978
    awatson1978 committed Jul 20, 2023
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  3. removed .bkup files

    @awatson1978
    awatson1978 committed Jul 20, 2023
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  4. updated wearables remarks

    @awatson1978
    awatson1978 committed Jul 20, 2023
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Commits on Jul 23, 2023

  1. Merge branch 'wearables' of https://github.com/synthetichealth/synthea … 

    …into wearables
    @awatson1978
    awatson1978 committed Jul 23, 2023
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  2. exporter.ndjson.export; exporter.fhir.personal_data

    @awatson1978
    awatson1978 committed Jul 23, 2023
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  3. updates to build.gradle to support latest APIs

    @awatson1978
    awatson1978 committed Jul 23, 2023
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  4. wearable device; sedentary condition; baseline encounter start/end

    @awatson1978
    awatson1978 committed Jul 23, 2023
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  5. Merge branch 'bugfix-gradle-build-errors' into wearables-plus-gradle-… 

    …bugfix
    @awatson1978
    awatson1978 committed Jul 23, 2023
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Commits on Jul 24, 2023

  1. PO2ART graphs generated in main patient cohort with LOINC

    @awatson1978
    awatson1978 committed Jul 24, 2023
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Commits on Jul 26, 2023

  1. wearables_circadian

    @awatson1978
    awatson1978 committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. menstrual cycle module; still has errors

    @awatson1978
    awatson1978 committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. menstrual cycle module; still has errors

    @awatson1978
    awatson1978 committed Jul 28, 2023
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Commits on Aug 2, 2023

  1. menstrual_cycle.json works consistently

    @awatson1978
    awatson1978 committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. reset synthea.properties

    @awatson1978
    awatson1978 committed Aug 3, 2023
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