inst/doc/table-intersect.R

In PatientProfiles: Identify Characteristics of Patients in the OMOP Common Data Model

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----warning = FALSE, message = FALSE-----------------------------------------
library(CodelistGenerator)
library(PatientProfiles)
library(dplyr)
library(CohortConstructor)
library(ggplot2)
library(omock)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")

cdm$ankle_sprain <- conceptCohort(
  cdm = cdm,
  name = "ankle_sprain",
  conceptSet = list("ankle_sprain" = 81151)
)
cdm$ankle_sprain

cdm$ankle_sprain |>
  addTableIntersectFlag(
    tableName = "condition_occurrence",
    window = c(-30, -1)
  ) |>
  glimpse()

## -----------------------------------------------------------------------------
cdm$ankle_sprain |>
  addTableIntersectFlag(
    tableName = "drug_exposure",
    indexDate = "cohort_start_date",
    targetStartDate = "drug_exposure_start_date",
    targetEndDate = "drug_exposure_end_date",
    window = c(-30, -1)
  ) |>
  glimpse()

## -----------------------------------------------------------------------------
cdm$ankle_sprain |>
  addTableIntersectFlag(
    tableName = "drug_exposure",
    indexDate = "cohort_start_date",
    window = c(-30, -1)
  ) |>
  glimpse()

## -----------------------------------------------------------------------------
cdm$ankle_sprain |>
  addTableIntersectCount(
    tableName = "drug_exposure",
    indexDate = "cohort_start_date",
    window = c(-180, -1)
  ) |>
  glimpse()

cdm$ankle_sprain |>
  addTableIntersectDate(
    tableName = "drug_exposure",
    indexDate = "cohort_start_date",
    order = "last",
    window = c(-180, -1)
  ) |>
  glimpse()


cdm$ankle_sprain |>
  addTableIntersectDate(
    tableName = "drug_exposure",
    indexDate = "cohort_start_date",
    order = "last",
    window = c(-180, -1)
  ) |>
  glimpse()

## -----------------------------------------------------------------------------
acetaminophen_cs <- getDrugIngredientCodes(
  cdm = cdm,
  name = c("acetaminophen")
)

cdm$acetaminophen_records <- cdm$drug_exposure |>
  filter(drug_concept_id %in% !!acetaminophen_cs[[1]]) |>
  compute()

cdm$ankle_sprain |>
  addTableIntersectFlag(
    tableName = "acetaminophen_records",
    indexDate = "cohort_start_date",
    targetStartDate = "drug_exposure_start_date",
    targetEndDate = "drug_exposure_end_date",
    window = c(-Inf, Inf)
  ) |>
  glimpse()

## -----------------------------------------------------------------------------
cdm$proc_or_meas <- union_all(
  cdm$procedure_occurrence |>
    select("person_id",
      "record_date" = "procedure_date"
    ),
  cdm$measurement |>
    select("person_id",
      "record_date" = "measurement_date"
    )
) |>
  compute()

cdm$ankle_sprain |>
  addTableIntersectFlag(
    tableName = "proc_or_meas",
    indexDate = "cohort_start_date",
    targetStartDate = "record_date",
    targetEndDate = "record_date",
    window = c(0, 0)
  ) |>
  glimpse()