tests/testthat/setup.R

In phers: Calculate Phenotype Risk Scores

library('data.table')
library('foreach')
library('qs')
library('BEDMatrix')
library('survival')
registerDoSEQ()


snapshot = function(xObs, path) {
  if (file.exists(path)) {
    xExp = qs::qread(path)
  } else {
    qs::qsave(xObs, path)
    xExp = xObs}
  return(xExp)}
dataDir = 'data'


# data for unit test
icdTest = data.table(
  person_id = c(1, rep(2L, 3), 3, rep(4L, 3)),
  icd = c('001', '002', '003', '005', '002', '004', '005', '006'),
  flag = 9,
  occurrence_age = c(rep(10, 6), c(10, 11)))

demosTest = data.table(
  person_id = 1:4,
  sex = c('female', 'male', 'female', 'male'),
  first_age = seq(20, 23),
  last_age = seq(25, 28))

phecodeOccurrencesTest = data.table(
  person_id = c(1, rep(2L, 2), 3, 4),
  phecode = c('001', '002', '003', '002', '004'),
  occurrence_age = rep(10, 5))
setkey(phecodeOccurrencesTest)

phecodeOccurrencesLLTest = data.table(
  person_id = c(1, rep(2L, 2), 3, 4),
  phecode = c('001', '002', '003', '002', '004'),
  num_occurrences = rep(1, 5))
setkey(phecodeOccurrencesLLTest)

phecodeOccurrencesCoxTest = data.table(
  person_id = c(1, rep(2L, 2), 3, 4),
  phecode = c('001', '002', '003', '002', '004'),
  occurrence_age = seq(22, 26))
setkey(phecodeOccurrencesCoxTest)

phecodeOccurrencesPreCalcTest = data.table(
  person_id = c(1, rep(2L, 2), 3, 4),
  phecode = c('700', '200', '300', '200', '500'))
setkey(phecodeOccurrencesPreCalcTest)

dxIcdTest = data.table(disease_id = 1, icd = c('005', '006'), flag = 9)

diseasePhecodeMapTest = data.table(
  disease_id = 1, phecode = c('001', '002', '003'))
setkey(diseasePhecodeMapTest)

scoresTest = data.table(
  person_id = rep(1:6, 2), disease_id = c(rep(1, 6), rep(2, 6)),
  score = c(5, 3, 4, 1, 0.5, 0, 2, 1, 0, 1, 2, 0.5))

demosTest2 = data.table(
  person_id = 1:6,
  sex = c('female', 'male', 'female', 'male', 'female', 'male'))
formTest = ~ sex