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X-DataInitiative / SCALPEL-Extraction

SCALPEL extraction library to fetch concepts from flattened SNDS
BSD 3-Clause "New" or "Revised" License
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Cnam 458 fracture severity update #252

Closed ysebiat closed 4 years ago

ysebiat commented 4 years ago

The new flattening renders the previous algorithm for severity obsolete, at it was using the fact that it was a cartesian product. This update corrects this by adding the adequate events, mainly Fracture Surgeries and Deaths.

This also corrects a bug in the Fracture algorithm. The bug was responsible for aggressively deleting fractures where the patient, after a first visit for a fracture, came back to have an act that is not considered a fracture such as plaster removal. The previous implementation deleted both, which is not the expected behaviour as we want to keep the first incident as a fracture event.

codecov[bot] commented 4 years ago

Codecov Report

Merging #252 into develop will increase coverage by 0.23%. The diff coverage is 95.91%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #252      +/-   ##
===========================================
+ Coverage    93.30%   93.53%   +0.23%     
===========================================
  Files          218      218              
  Lines         2526     2585      +59     
  Branches        72       41      -31     
===========================================
+ Hits          2357     2418      +61     
+ Misses         169      167       -2
Impacted Files Coverage Δ
...nique/cmap/cnam/study/fall/fractures/Surgery.scala 100.00% <ø> (ø)
...dy/fall/extractors/FallHospitalStayExtractor.scala 66.66% <66.66%> (ø)
.../cnam/etl/transformers/interaction/ExposureN.scala 100.00% <100.00%> (ø)
...ers/interaction/InteractionTransformerConfig.scala 100.00% <100.00%> (ø)
...ers/interaction/NLevelInteractionTransformer.scala 100.00% <100.00%> (ø)
...chnique/cmap/cnam/study/fall/FallMainExtract.scala 99.34% <100.00%> (+0.07%) :arrow_up:
...nique/cmap/cnam/study/fall/FallMainTransform.scala 99.11% <100.00%> (+0.02%) :arrow_up:
...nique/cmap/cnam/study/fall/config/FallConfig.scala 100.00% <100.00%> (ø)
...map/cnam/study/fall/extractors/ActsExtractor.scala 90.00% <100.00%> (+6.66%) :arrow_up:
...nam/study/fall/extractors/DiagnosisExtractor.scala 100.00% <100.00%> (ø)
... and 9 more

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