ramses-antibiotics / ramses-package

R Package for Data-Driven Antimicrobial Stewardship & Surveillance in Hospitals
https://ramses-antibiotics.web.app/
GNU General Public License v3.0
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therapy_timeline looking for dates in inpatient_diagnoses #103

Closed peterdutey closed 2 years ago

peterdutey commented 2 years ago

The test dataset has episode_start and episode_end in it and incorrectly letting the .therapy_timeline_get_diagnoses() function pass tests even though validate_inpatient_diagnoses() does not mandate start/end dates.

.therapy_timeline_get_diagnoses() should be changed


> therapy_timeline(TherapyEpisode(ramses_db,  xxx))
Error in `dplyr::mutate()`:
! Problem while computing `diagnosis_episode_end = dplyr::lag(.data$episode_end, n = 1, order_by =
  .data$episode_start)`.
Caused by error in `.data$episode_start`:
! Column `episode_start` not found in `.data`.
Run `rlang::last_error()` to see where the error occurred.

Backtrace:
     x
  1. +-Ramses::therapy_timeline(TherapyEpisode(ramses_db, xxx))
  2. +-Ramses::therapy_timeline(TherapyEpisode(ramses_db, xxx))
  3. | \-Ramses .local(x, ...)
  4. |   \-Ramses:::.therapy_timeline_create(...)
  5. |     \-Ramses:::.therapy_timeline_get_diagnoses(input_patient)
  6. |       \-... %>% ...
  7. +-dplyr::summarise(...)
  8. +-dplyr::group_by(...)
  9. +-dplyr::select(., -.data$diagnosis_episode_end)
 10. +-dplyr::mutate(., grp = max(.data$grp))
 11. +-dplyr::group_by(., .data$patient_id, .data$icd_code, .data$prim_diag)
 12. +-dplyr::mutate(...)
 13. +-dplyr::ungroup(.)
 14. +-dplyr::mutate(...)
 15. +-dplyr:::mutate.data.frame(...)
 16. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
 17. |   +-base::withCallingHandlers(...)
 18. |   \-mask$eval_all_mutate(quo)
 19. +-dplyr::lag(.data$episode_end, n = 1, order_by = .data$episode_start)
 20. +-episode_start
 21. +-rlang:::`$.rlang_data_pronoun`(.data, episode_start)
 22. | \-rlang:::data_pronoun_get(...)
 23. \-rlang:::abort_data_pronoun(x, call = y)
 24.   \-rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
 25. ```