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Create Event IDs from Patient-Level Data

Source: R/prep_events.R
prep_create_event_ids.Rd

Converts patient-level isolate data to event-level data by grouping repeat cultures from the same infection episode.

Usage

prep_create_event_ids(
  data,
  patient_col = "patient_id",
  date_col = "date_of_culture",
  organism_col = "organism_normalized",
  specimen_col = "specimen_type",
  antibiotic_col = "antibiotic_name",
  value_col = "antibiotic_value",
  gap_days = 14,
  culture_col = "id_organisminfo",
  admission_col = "date_of_admission",
  keep_event_culture = c("all", "closest_to_admission")
)

Arguments

data

Data frame (long format – one row per antibiotic test).

patient_col

Patient ID column. Default "patient_id".

date_col

Culture date column. Default "date_of_culture".

organism_col

Organism column. Default "organism_normalized".

specimen_col

Specimen type column. Default "specimen_type".

antibiotic_col

Antibiotic name column. Default "antibiotic_name".

value_col

Susceptibility result column (S/I/R). Default "antibiotic_value".

gap_days

Days threshold: gap > gap_days triggers a new event. Default 14.

culture_col

Culture/isolate identifier column. When present, same-day cultures from the same site and organism are evaluated separately before duplicate culture removal. Default "id_organisminfo".

admission_col

Admission date column. Used when keep_event_culture is "closest_to_admission". Default "date_of_admission".

keep_event_culture

Character. "all" keeps all culture rows after assigning event IDs. "closest_to_admission" keeps all antibiotic rows from only the culture date closest to admission within each event/organism/site. Default "all".

Value

Original data frame with event_id column added.

Details

Event classification rules (in order of precedence):

| Scenario | Result | |—————————————————–|—————–| | Different body sites (any date) | Separate events | | Same site, same day, same organism, same ABG | One event | | Same site, same day, same organism, diff ABG | Separate events | | Same site, same organism, within gap_days, same ABG | Same event | | Same site, same organism, within gap_days, ABG changed | New event | | Same site, same organism, after > gap_days | New event | | Same site, same day, different organisms | Separate events |

Event IDs are numbered GLOBALLY per patient in chronological order.