inst/doc/demographics.R

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

## ----message= FALSE, warning=FALSE--------------------------------------------
library(PatientProfiles)
library(duckdb)
library(dplyr)

cdm <- mockPatientProfiles(numberIndividuals = 10000)

cdm$person |>
  dplyr::glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$observation_period |>
  dplyr::glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence <- cdm$condition_occurrence |>
  addAge(indexDate = "condition_start_date")

cdm$condition_occurrence |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence <- cdm$condition_occurrence |>
  addAge(
    indexDate = "condition_start_date",
    ageGroup = list(
      "0 to 17" = c(0, 17),
      "18 to 65" = c(18, 65),
      ">= 66" = c(66, Inf)
    )
  )

cdm$condition_occurrence |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence <- cdm$condition_occurrence |>
  addAge(
    indexDate = "condition_start_date",
    ageName = "age_from_year_of_birth",
    ageMissingMonth = 1,
    ageMissingDay = 1,
    ageImposeMonth = TRUE,
    ageImposeDay = TRUE
  )

cdm$condition_occurrence |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence <- cdm$condition_occurrence |>
  addSex()

cdm$condition_occurrence |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence <- cdm$condition_occurrence |>
  addInObservation(indexDate = "condition_start_date") |>
  addPriorObservation(indexDate = "condition_start_date") |>
  addFutureObservation(indexDate = "condition_start_date")

cdm$condition_occurrence |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence |>
  addInObservation(
    indexDate = "condition_start_date",
    window = c(-180, 30)
  ) |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$condition_occurrence |>
  addInObservation(
    indexDate = "condition_start_date",
    window = c(365, Inf),
    completeInterval = FALSE
  ) |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$cohort1 |>
  glimpse()

cdm$cohort1 <- cdm$cohort1 |>
  addAge(ageGroup = list(
    "0 to 17" = c(0, 17),
    "18 to 65" = c(18, 65),
    ">= 66" = c(66, Inf)
  )) |>
  addSex() |>
  addInObservation() |>
  addPriorObservation() |>
  addFutureObservation()

cdm$cohort1 |>
  glimpse()

## ----message= FALSE, warning=FALSE--------------------------------------------
cdm$cohort2 |>
  glimpse()

tictoc::tic()
cdm$cohort2 |>
  addAge(ageGroup = list(
    "0 to 17" = c(0, 17),
    "18 to 65" = c(18, 65),
    ">= 66" = c(66, Inf)
  )) |>
  addSex() |>
  addInObservation() |>
  addPriorObservation() |>
  addFutureObservation()
tictoc::toc()

tictoc::tic()
cdm$cohort2 |>
  addDemographics(
    age = TRUE,
    ageName = "age",
    ageGroup = list(
      "0 to 17" = c(0, 17),
      "18 to 65" = c(18, 65),
      ">= 66" = c(66, Inf)
    ),
    sex = TRUE,
    sexName = "sex",
    priorObservation = TRUE,
    priorObservationName = "prior_observation",
    futureObservation = FALSE,
  ) |>
  glimpse()
tictoc::toc()