View source: R/addTableIntersect.R
addTableIntersectField | R Documentation |
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.
addTableIntersectField(
x,
tableName,
field,
indexDate = "cohort_start_date",
censorDate = NULL,
window = list(c(0, Inf)),
targetDate = startDateColumn(tableName),
order = "first",
nameStyle = "{table_name}_{extra_value}_{window_name}",
name = NULL
)
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. |
order |
which record is considered in case of multiple records (only required for date and days options). |
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. |
table with added columns with intersect information.
cdm <- mockPatientProfiles()
cdm$cohort1 %>%
addTableIntersectField(
tableName = "visit_occurrence",
field = "visit_concept_id",
order = "last",
window = c(-Inf, -1)
)
mockDisconnect(cdm = cdm)
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