Map OMOP data to inpatient_episodes table

[razekmh]

Extract data from the example OMOP data to fill the inpatient_episodes table from the validate article. This is a split from #17

Please feel free to assign yourself to the issue. Please the respective branch for development.

[AngharadGreen]

• For this issue I have used the updated OMOK v0.3.0 to generate OMOP mockVisitOccurrence and mockProcedureOccurrence tables as these tables can be mapped to the RAMSES inpatient_episodes table.
• For the RAMSES inpatient_episodes table the variables admission_method, last_episode_in_encounter, consultant_code and main_specialty_code are difficult to map to the OMOP CDM - I am looking into this in more detail to determine what OMOP tables would be appropriate to map to, as these variables must not contain missing data.

[AngharadGreen]

Mapping synthetic data from OMOK to the Ramses inpatient_episodes table

I put together a summary presentation going over mapping OMOP CDM to the data frame accepted by Ramses Mapping OMOP to rameses.pptx

This summary diagram shows how the inpatient_episodes table could map to the data within OMOP:

Following this summary I will now try to reproduce the inpatient_episodes table from data generated from OMOK:

library(Ramses)
library(omock)
library(dplyr)
library(AMR)
library(DBI)

# Connect to ramses local database

ramses_db <- connect_local_database("ramses-db.duckdb")

# View and check structure of the ramses inpatient_episodes table
View(inpatient_episodes)
str(inpatient_episodes)

# generate mock OMOP data from OMOK v0.3.0

cdm <- mockCdmReference() |>
  mockPerson(nPerson = 10) |>
  mockObservationPeriod() |>
  mockConditionOccurrence() |>
  mockDrugExposure() |>
  mockMeasurement() |>
  mockDeath() |>
  mockProcedureOccurrence() |>
  mockObservation() |>
  mockVisitOccurrence() |>
  mockVocabularyTables()

#Extract the visit_occurrence table from mock omok database
omop_visit_occurrence <- cdm$visit_occurrence

#View and check structure of the omop_visit_occurrence table
View(omop_visit_occurrence)
str(omop_visit_occurrence)


#Extract the procedure_occurrence table from mock omok database
omop_procedure_occurrence <- cdm$procedure_occurrence

#View and check structure of the omop_procedure_occurence table
View(omop_procedure_occurrence)
str(omop_procedure_occurrence)

#Merge dataframes omop_visit_occurrence and omop_procedure_occurrence based on column visit_occurrence_id

Merged_df <- merge(omop_visit_occurrence, omop_procedure_occurrence, by="visit_occurrence_id")
View(Merged_df)

# If need to save this use write.csv(Merged_df,'Merged_df.csv', row.names = FALSE)

# Map OMOP fields to RAMSES fields

omop_to_ramses_inpatient_episodes <- Merged_df %>%
  transmute(
    #Mapping OMOP visit_occurrence_table person_id to RAMSES patient_id
    patient_id = person_id.x,
    #Mapping OMOP visit_occurrence_table visit_occurrence_id to RAMSES encounter_id
    encounter_id = visit_occurrence_id,
    #Mapping OMOP visit_occurrence_table visit_start_date to RAMSES admission_date
    admission_date = visit_start_date,
    #Mapping OMOP visit_occurrence_table visit_end_date to RAMSES discharge_date
    discharge_date = visit_end_date,
    #Mapping OMOP procedure_occurrence_table procedure_occurrence_id to RAMSES episode_number 
    episode_number = procedure_occurrence_id,
    #Mapping OMOP procedure_occurrence_table procedure_date to RAMSES episode_start
    episode_start = procedure_date,
    #Mapping OMOP procedure_occurrence_table procedure_end_date to RAMSES episode_end
    episode_end = procedure_end_date)

# The ramses columns admission_method, last_episode_in_encounter, consultant_code and main_specialty_code are not easily mapped to OMOP data from OMOCK so synthetic data will be added here for now: 

# Add in column admission_method to omop_to_ramses_inpatient_episodes
omop_to_ramses_inpatient_episodes$admission_method <- c("1", "2", "1", "1", "2", "1", "2", "1", "2", "1", "1", "1", "2", "2", "2", "2", "1", "1", "1", "1", "1", "2", "1", "1", "2", "1", "2", "1", "2", "1", "1", "1", "2", "2", "2", "2", "1", "1", "1", "1", "1", "2", "1", "1", "2", "1", "2", "1", "2", "1")

# Add in column last_episode_in_encounter to omop_to_ramses_inpatient_episodes
omop_to_ramses_inpatient_episodes$last_episode_in_encounter <- c("2", "2", "1", "2", "1", "2", "2", "2", "1", "1", "1", "1", "2", "2", "2", "2", "1", "2", "1", "2", "2", "2", "1", "2", "1", "2", "2", "2", "1", "1", "1", "1", "2", "2", "2", "2", "1", "2", "1", "2", "2", "2", "1", "2", "1", "2", "2", "2", "1", "1")

# Add in column consultant_code omop_to_ramses_inpatient_episodes
omop_to_ramses_inpatient_episodes$consultant_code <- c("C1000003", "C1000004", "C1000005", "C1000006", "C1000007", "C1000008", "C1000009", "C1000010", "C1000011", "C1000012", "C1000013", "C1000014", "C1000015", "C1000016", "C1000017", "C1000018", "C1000019", "C1000020", "C1000021", "C1000022", "C1000023", "C1000024", "C1000025", "C1000026", "C1000027", "C1000028", "C1000029", "C1000030", "C1000031", "C1000032", "C1000033", "C1000034", "C1000035", "C1000036", "C1000037", "C1000038", "C1000039", "C1000040", "C1000041", "C1000042", "C1000043", "C1000044", "C1000045", "C1000046", "C1000047", "C1000048", "C1000049", "C1000050", "C1000051", "C1000052")

# Add in column main_specialty_code to omop_to_ramses_inpatient_episodes
omop_to_ramses_inpatient_episodes$main_specialty_code <- c("100", "101", "107", "110", "120", "130", "140", "141", "142", "143", "145", "146", "147", "148", "149", "150", "160", "170", "171", "191", "180", "190", "192", "200", "300", "301", "302", "303", "304", "305", "310", "311", "312", "313", "314", "315", "317", "320", "321", "325", "326", "330", "340", "350", "352", "360", "361", "370", "371", "400")

#View and check structure of the omop_to_ramses_inpatient_episodes
View(omop_to_ramses_inpatient_episodes)
str(omop_to_ramses_inpatient_episodes)

#Extract the person table from mock omok database
omop_person <- cdm$person

#View and check structure of the omop_person table
View(omop_person)
str(omop_person)

omop_to_ramses_person <- omop_person %>%
  transmute(
    #Mapping OMOP visit_occurrence_table person_id to RAMSES patient_id
    patient_id = person_id)

#View and check structure of the omop_person table
View(omop_to_ramses_person)
str(omop_to_ramses_person)

#Validate omop_to_ramses_inpatient_episodes
validate_inpatient_episodes(patients = omop_to_ramses_person,
                            episodes = omop_to_ramses_inpatient_episodes)

[1] FALSE
Warning messages:
1: Some `episodes` fall outside hospitalisation dates. 
2: Total bed days calculated from `episodes` does notmatch admission duration.
 Bed days may be incorrect. 
3: Some hospital encounters have gaps between `episodes`.
Bed days may be underestimated. 
4: Hospital `episodes` must not overlap.

[AngharadGreen]

I will now use the new OMOP extract to map to the Ramses inpatient_episodes table

• The in_patient_episodes table represents a set of simulated records of finished consultant episodes for 202 patients, detailing all dates and times of admission, discharge, episode start and end, clinician, and clinical specialty.
• Ramses is designed around the notion of hospital encounters identified by variable encounter_id, which correspond to the window from the time a patient is admitted to the time a patient is discharged.
• In addition, Ramses use subdivisions of hospital encounters called episodes of care, which designate a continuous period of inpatient care under the responsibility of a department, specialty, or clinical team.
• All hospital encounters consist of at least one episode of care.
• Episodes of care are used to calculate bed-days as well as rates of infection, prescribing and other stewardship metrics for individual specialties and teams of clinicians.
• Hospital encounters and episodes of care are recorded in a single table in which every row corresponds to one episode of care.
• Dates of admissions and episode start/end must be valid:

1. there must be no overlap between admissions or between episodes
2. there must be no gap between episodes in an admission.

Ramses	OMOP
patient_id	person_id
encounter_id	visit_occurrence_id (visit_occurrence)
admission_method
admission_date	visit_start_date (visit occurrence)
discharge_date	visit_end_date (visit_occurrence)
episode_number	procedure_occurrence_id (procedure_occurrence)
last_episode_in_encounter
episode_start	procedure_date
episode_end
consultant_code
main_specialty_code

Ramses also relies on validate_inpatient_episodes