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Create summariseConceptCounts() #37

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martaalcalde opened this issue Jul 23, 2024 · 2 comments
Closed

Create summariseConceptCounts() #37

martaalcalde opened this issue Jul 23, 2024 · 2 comments
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@martaalcalde
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  • Stratify by age and sex
@martaalcalde martaalcalde added this to the Sprint 23/07-2/08 milestone Jul 23, 2024
@catalamarti
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discuss differences with summariseCodeUse if any. options:

  • reexport summariseCodeUse
  • move summariseCodeUse to omopSketch
  • include in a vignette summariseCodeUse

Do we want to stratify by year and age/sex at the same time?

@martaalcalde martaalcalde modified the milestones: Sprint 23/07-2/08, Release 0.1 Aug 8, 2024
@martaalcalde
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martaalcalde commented Sep 6, 2024

(Please @catalamarti confirm)

Decided with Marti that we would proceed as:

  • copy summariseCodeUse() from CodelistGenerator package
summariseCodeUse(
  x,
  cdm,
  CountBy = c("record", "person"),
  byConcept = TRUE,
  byYear = FALSE,
  bySex = FALSE,
  ageGroup = NULL
)
  • if x is not specified, all the codes in the concept table are summarised
  • modify the arguments so they fit the standard of omopSketch
  • Currently, the previous function doesn't allow for multiple strata at the same time (i.e., if you stratify by sex and year, it is stratified as women & overall, male & overall, overall & 1997, etc -> change it so strata is mixed

Once this is done, we will proceed with issue #70

@martaalcalde martaalcalde removed this from the Release 0.1 milestone Sep 6, 2024
@KimLopezGuell KimLopezGuell self-assigned this Sep 12, 2024
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