View source: R/addConceptIntersect.R
addConceptIntersectFlag | R Documentation |
It creates column to indicate the flag overlap information between a table and a concept
addConceptIntersectFlag(
x,
conceptSet,
indexDate = "cohort_start_date",
censorDate = NULL,
window = list(c(0, Inf)),
targetStartDate = "event_start_date",
targetEndDate = "event_end_date",
inObservation = TRUE,
nameStyle = "{concept_name}_{window_name}",
name = NULL
)
x |
Table with individuals in the cdm. |
conceptSet |
Concept set list. |
indexDate |
Variable in x that contains the date to compute the intersection. |
censorDate |
whether to censor overlap events at a date column of x |
window |
window to consider events in. |
targetStartDate |
Event start date to use for the intersection. |
targetEndDate |
Event end date to use for the intersection. |
inObservation |
If TRUE only records inside an observation period will be considered. |
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 overlap information
library(PatientProfiles)
cdm <- mockPatientProfiles()
concept <- dplyr::tibble(
concept_id = c(1125315),
domain_id = "Drug",
vocabulary_id = NA_character_,
concept_class_id = "Ingredient",
standard_concept = "S",
concept_code = NA_character_,
valid_start_date = as.Date("1900-01-01"),
valid_end_date = as.Date("2099-01-01"),
invalid_reason = NA_character_
) %>%
dplyr::mutate(concept_name = paste0("concept: ", .data$concept_id))
cdm <- CDMConnector::insertTable(cdm, "concept", concept)
result <- cdm$cohort1 %>%
addConceptIntersectFlag(
conceptSet = list("acetaminophen" = 1125315)
) %>%
dplyr::collect()
mockDisconnect(cdm = cdm)
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