tests/testthat/test-sas.R

In jackwasey/icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

context("SAS format file data interpretation")

test_that("basic SAS VALUE declarations can be read into an R list", {
  # general format from my n=1 sample seems to be:
  # VALUE somename numbers, "ranges"-"ranges", ranges-ranges = "mappinname"
  result <- sas_format_extract('VALUE JACK 12345 = "TESTTHAT"')
  expect_equal(result, list(JACK = list(TESTTHAT = "12345")))
  result <- sas_format_extract('VALUE JACK 12345, 22222 = "TESTTHAT"')
  expect_equal(result, list(JACK = list(TESTTHAT = c("12345", "22222"))))
  result <- sas_format_extract('VALUE TESTTHAT 100-102 = "YES"')
  expect_equal(result, list(TESTTHAT = list("YES" = "100-102")))
  expect_equal(
    sas_format_extract('VALUE $RFRMSOMETHING 100-102 = "HTN" 103,104 = "CHF"'),
    list("$RFRMSOMETHING" = list(HTN = "100-102", CHF = c("103", "104")))
  )
  result <- sas_format_extract(c(
    'VALUE $RFRMSOMETHING 100-102 = "HTN" 103,104 = "CHF";\n',
    ' VALUE otherstuff 105 = "YES"'
  ))
  expect_equal(result, list(
    "$RFRMSOMETHING" = list(
      HTN = "100-102",
      CHF = c("103", "104")
    ),
    otherstuff = list("YES" = "105")
  ))
  result <- sas_format_extract(c(
    '   VALUE $RFRMSOMETHING 100-102 = "HTN" 103,104 = "CHF";',
    'VALUE  otherstuff   105   =  "  Y E S " '
  ))
  expect_equal(result, list(
    "$RFRMSOMETHING" = list(
      HTN = "100-102",
      CHF = c("103", "104")
    ),
    otherstuff = list("YES" = "105")
  ))
})

test_that("groups of SAS assignments can be extracted", {
  # this is a single assignment, but of the form of sub-part of
  # multi-assignment, so we should handle it.
  expect_equal(
    sas_parse_assignments('"123" = "YES"'),
    list(YES = "123")
  )
  expect_equal(
    sas_parse_assignments('"123-456" = "YES"'),
    list(YES = "123-456")
  )
  expect_equal(
    sas_parse_assignments('123-456 = "YES"'),
    list(YES = "123-456")
  )
  expect_equal(
    sas_parse_assignments(
      paste(
        '"41511"-"41519", "4160 "-"4169 ","4179 " = "PULMCIRC"',
        '"5571 ","5579 ", "V434 "= "PERIVASC"'
      )
    ),
    list(
      PULMCIRC = c("41511-41519", "4160-4169", "4179"),
      PERIVASC = c("5571", "5579", "V434")
    )
  )
})

test_that("read LET string declarations from SAS code", {
  res_list <- sas_extract_let_strings(
    "\t%LET DC16=%STR('196','197','198','199');      "
  )
  expect_is(res_list, "list")
  expect_true(all(vapply(res_list, length, integer(1))))
  expect_true(all(vapply(res_list, is.character, logical(1))))
  expect_true(names(res_list) == "DC16")
  expect_equal(res_list[[1]], c("196", "197", "198", "199"))
  res_list <- sas_extract_let_strings(c(
    "\t%LET DC16=%STR('196','197','198','199');      ",
    "\t%LET DC17=%STR('042','043','044');"
  ))
  expect_equal(res_list[["DC16"]], c("196", "197", "198", "199"))
  expect_equal(res_list[["DC17"]], c("042", "043", "044"))
  expect_equal(
    sas_extract_let_strings(
      "\t%LET LBL16=%STR(Metastatic Carcinoma);"
    )[["LBL16"]],
    "Metastatic Carcinoma"
  )
  expect_equal(
    sas_extract_let_strings('\t%LET ABC=%STR("123");")[["ABC"]]'),
    list(ABC = "123")
  )
})