Intersecting the cohort with columns of an OMOP table of user's choice. It will add an extra column to the cohort, indicating the intersected entries with the target columns in a window of the user's choice.

Usage

addTableIntersectField(
  x,
  tableName,
  field,
  indexDate = "cohort_start_date",
  censorDate = NULL,
  window = list(c(0, Inf)),
  targetDate = startDateColumn(tableName),
  inObservation = TRUE,
  order = "first",
  allowDuplicates = FALSE,
  nameStyle = "{table_name}_{extra_value}_{window_name}",
  name = NULL
)

Arguments

x: Table with individuals in the cdm.
tableName: Name of the table to intersect with. Options: visit_occurrence, condition_occurrence, drug_exposure, procedure_occurrence, device_exposure, measurement, observation, drug_era, condition_era, specimen, episode.
field: The columns from the table in tableName to intersect over. For example, if the user uses visit_occurrence in tableName then for field the possible options include visit_occurrence_id, visit_concept_id, visit_type_concept_id.
indexDate: Variable in x that contains the date to compute the intersection.
censorDate: whether to censor overlap events at a specific date or a column date of x.
window: window to consider events in when intersecting with the chosen column.
targetDate: The dates in the target columns in tableName that the user may want to restrict to.
inObservation: If TRUE only records inside an observation period will be considered.
order: which record is considered in case of multiple records (only required for date and days options).
allowDuplicates: Whether to allow multiple records with same conceptSet, person_id and targetDate. If switched to TRUE, the created new columns (field) will be collapsed to a character vector separated by `;` to account for multiple values per person.
nameStyle: naming of the added column or columns, should include required parameters.
name: Name of the new table, if NULL a temporary table is returned.

Value

table with added columns with intersect information.

Examples

# \donttest{
library(PatientProfiles)

cdm <- mockPatientProfiles(source = "duckdb")

cdm$cohort1 |>
  addTableIntersectField(
    tableName = "visit_occurrence",
    field = "visit_concept_id",
    order = "last",
    window = c(-Inf, -1)
  )
#> # Source:   table<og_138_1757798578> [?? x 5]
#> # Database: DuckDB 1.3.3-dev231 [unknown@Linux 6.11.0-1018-azure:R 4.5.1/:memory:]
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                   <int>      <int> <date>            <date>         
#>  1                    3          8 1997-01-29        2004-04-29     
#>  2                    2          2 1974-01-03        1976-12-04     
#>  3                    3          6 1964-01-23        1983-05-19     
#>  4                    3          7 1964-01-06        1965-01-31     
#>  5                    2          1 1989-12-08        1996-11-01     
#>  6                    1          9 1933-03-25        1935-04-11     
#>  7                    1          5 1966-08-22        1971-05-23     
#>  8                    2          3 1920-06-29        1931-05-25     
#>  9                    2         10 1924-07-01        1939-07-26     
#> 10                    1          4 1928-11-08        1935-09-12     
#> # ℹ 1 more variable: visit_occurrence_visit_concept_id_minf_to_m1 <int>

# }