tests/testthat/test.NHSReadV3.child_codes.R

In rcfree/rclinconcept: A package for loading and querying clinical concept dictionaries in R

library(testthat)
if(!is_sqlite_available()) {
  return(NA)
}
exp_h3_readcodes<-c("H3122", "H312z", "H3y..", "H3y0.", "H3z..", "H4641", "Hyu31",
                    "X101i", "X101l", "X101m", "X102z", "Xa35l", "XaEIV", "XaEIW",
                    "XaEIY", "XaIND", "XaN4a", "XaZd1")

dict<-setup_test_dict("NHSReadV3",T)

context("READ V3 child code retrieval functions")

# test_that("get_child_codes returns all READ v3 descendent rows when default parameters",{
#   obs_children<-get_child_codes(dict,"H3...")
#   expect_equal(length(obs_children),18)
#   obs_row1<-as.list(obs_children[1,])
#   obs_row1$term_198<-NULL
#   exp_row1<-list(read_code = "H3122", term="Acute exacerbation of chronic obstructive airways disease",term_30 = "Acute exacerbation of COAD",
#                  term_60 = "Acute exacerbation of chronic obstructive airways disease", term_id = "Y106q", desc_type = "P", synonym = "0",
#                  status = "C")
#   expect_equal(obs_row1,exp_row1)
#
#   row18<-as.list(obs_children[18,])
#   expect_equal(list(read_code = "XaZd1", term = "Acute non-infective exacerbation of chronic obstructive pulmonary disease",term_30 = "Acut non-infect exacerbat COPD",
#                   term_60 = "Acute non-infective exacerbation of COPD", term_198 = "Acute non-infective exacerbation of chronic obstructive pulmonary disease",
#                     term_id = "Yavfv", desc_type="P", synonym = "0", status = "C"),row18)
# })
test_that("get_child_codes returns all READ v3 descendent codes when default parameters",{
  skip_if_not(is_sqlite_available(),"SQLite must be installed to run these tests")
  skip_on_cran()
  expect_child_codes(dict,"H3...",exp_h3_readcodes)
  expect_child_codes(dict,"H31..",c("H310.","XE0YM","X101j","H31y1","H3122","H3121","H312z","H31y.","H31z.","XE0ZN","H310z","XaZd1","Xa35l","H3y0.","X101i","H31yz","X101k","H311.","H311z","H313."))
  expect_child_codes(dict,"H32..",c("X101n","H3200","H3201","H3202","H320z","H32y2","H321.","H322.","H32y.","H32z.","H32y0","Hyu30","XE0YO","XE0YP","XE0YN","H32yz","X101o","X101p","H320.","H582.","X101q","X101r","XaIQg","H4640"))
})

test_that("get_child_codes returns filtered READ v3 descendent codes when immediate_children flag",{
  expect_child_codes(dict,"H3...",c("H3122", "H312z", "H3y..", "H3z..", "Hyu31", "X101l", "XaEIV",
                                    "XaEIW", "XaEIY", "XaIND", "XaN4a"),immediate=T)
  expect_child_codes(dict,"H31..",c("H310.", "H3121", "H3122", "H312z", "H31y.", "H31y1", "H31z.",
                                    "X101j", "XE0YM", "XE0ZN"),immediate=T)
  expect_child_codes(dict,"H32..",c("H321.", "H322.", "H32y.", "H32y2", "H32z.", "X101n"),immediate=T)
})

test_that("get_child_codes returns filtered READ v3 descendent codes when current_only flag",{
  skip_if_not(is_sqlite_available(),"SQLite must be installed to run these tests")
  skip_on_cran()
  expect_child_codes(dict,"H3...",c("H3122", "H4641", "X101l", "X101m", "X102z", "Xa35l", "XaIND",
                                    "XaZd1"),current=T)
  expect_child_codes(dict,"H31..",c("H310.","H3122","H31y1","X101j","X101k","Xa35l","XaZd1","XE0YM"),current=T)
  expect_child_codes(dict,"H32..",c("H320.", "H321.", "H322.", "H32y2", "H582.", "X101n", "X101o",
                                   "X101p", "X101q", "X101r", "XaIQg"),current=T)
})

test_that("get_child_codes returns filtered READ v3 descendent codes when immediate_children and current_only flag",{
  skip_if_not(is_sqlite_available(),"SQLite must be installed to run these tests")
  skip_on_cran()
  expect_child_codes(dict,"H3...",c("H3122", "X101l", "XaIND"),immediate=T,current=T)
  expect_child_codes(dict,"H31..",c("H310.", "H3122", "H31y1", "X101j", "XE0YM"),immediate=T,current=T)
  expect_child_codes(dict,"H32..",c("H321.", "H322.", "H32y2", "X101n"),immediate=T,current=T)
})

rcc_disconnect(dict)