inst/doc/event.R

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

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

## -----------------------------------------------------------------------------
library(PatientProfiles)
library(dplyr)
library(omock)
library(CohortConstructor)
library(CodelistGenerator)

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

## -----------------------------------------------------------------------------
codelist <- getDrugIngredientCodes(
  cdm = cdm,
  name = "acetaminophen",
  nameStyle = "{concept_name}"
)
cdm$my_cohort <- conceptCohort(
  cdm = cdm,
  conceptSet = codelist,
  name = "my_cohort"
) |>
  requireIsFirstEntry()
codelist <- list(osteoarthritis = 80180L, diverticular_disease = 4266809L)
cdm$conditions <- conceptCohort(
  cdm = cdm,
  conceptSet = codelist,
  name = "conditions"
)

## -----------------------------------------------------------------------------
cohort_event_days <- cdm$my_cohort |>
  addCohortEventDays(
    targetCohortTable = "conditions",
    indexDate = "cohort_start_date",
    order = "first",
    window = list(next_year = c(0, 365))
  )

cohort_event_days |>
  glimpse()

## -----------------------------------------------------------------------------
cohort_event_days |>
  group_by(event_next_year) |>
  summarise(
    n = n(),
    median_days = median(days_next_year)
  ) |>
  collect()

## -----------------------------------------------------------------------------
cohort_event_date <- cdm$my_cohort |>
  addCohortEventDate(
    targetCohortTable = "conditions",
    indexDate = "cohort_start_date",
    order = "last",
    window = list(previous_year = c(-365, 0))
  )

cohort_event_date |>
  glimpse()

## -----------------------------------------------------------------------------
concept_event_days <- cdm$my_cohort |>
  addConceptEventDays(
    conceptSet = codelist,
    order = "first",
    window = list(next_event = c(0, Inf))
  )

concept_event_days |>
  glimpse()

## -----------------------------------------------------------------------------
cdm$my_cohort |>
  addConceptEventDays(
    conceptSet = codelist,
    order = "first",
    window = list("next" = c(0, Inf)),
    multipleEvents = NULL
  ) |>
  group_by(event_next) |>
  summarise(n = n()) |>
  collect()

## -----------------------------------------------------------------------------
cdm$my_cohort |>
  addConceptEventDays(
    conceptSet = codelist,
    order = "first",
    window = list("next" = c(0, Inf)),
    multipleEvents = TRUE
  ) |>
  group_by(event_next) |>
  summarise(n = n()) |>
  collect()

## -----------------------------------------------------------------------------
cdm$my_cohort |>
  addConceptEventDays(
    conceptSet = codelist,
    order = "first",
    window = list("next" = c(0, Inf)),
    multipleEvents = c("osteoarthritis", "diverticular_disease")
  ) |>
  group_by(event_next) |>
  summarise(n = n()) |>
  collect()

## -----------------------------------------------------------------------------
events_in_two_directions <- cdm$my_cohort |>
  addCohortEventDays(
    targetCohortTable = "conditions",
    order = "first",
    window = list(
      before = c(-365, 0),
      after = c(0, 365)
    )
  )

events_in_two_directions |>
  glimpse()