Nothing
context("PCCC")
# pccc_col_names <- c(
# "neuromusc", "cvd", "respiratory", "renal", "gi",
# "hemato_immu", "metabolic", "congeni_genetic",
# "malignancy", "neonatal", "tech_dep", "transplant"
# )
test_that("procedure codes work", {
res9 <- comorbid_pccc_pcs(pccc_pts,
icd_name = "icd9_pcs",
return_binary = FALSE
)
expect_true(res9[1, "Neuromusc"])
expect_true(res9[3, "CVD"])
expect_true(res9["11", "Respiratory"])
expect_true(res9[3, "TechDep"])
expect_equal(sum(res9), 4)
res0 <- comorbid_pccc_pcs(pccc_pts,
icd_name = "icd10_pcs",
return_binary = FALSE
)
expect_true(res0["11", "CVD"])
expect_true(res0["10", "Respiratory"])
expect_true(res0[3, 11])
expect_true(res0[3, 4])
expect_true(res0[2, "Transplant"])
expect_equal(sum(res0), 5)
# All ICD-9 procedure codes are numeric, some ICD-10 procedure codes
# are numeric, so best to call functions directly:
pts <- data.frame(encounters = c(100), icd10_pcs = c("0016070"))
icd10_comorbid_pccc_pcs(pts, icd_name = "icd10_pcs")
})
test_that("PCCC dx works", {
res <- icd9_comorbid_pccc_dx(vermont_dx, return_binary = TRUE)
expect_equivalent(
colSums(res[1:1000, ]),
c(82, 270, 50, 119, 55, 39, 313, 30, 128, 7, 129, 21)
)
expect_equal(colnames(res), unlist(unname(names_pccc_abbrev)))
})
test_that("colnames same for both dx and procedure codes", {
expect_warning(
res9d <- comorbid_pccc_dx(pccc_pts, icd_name = "icd9_dx"),
regexp = NA
)
expect_warning(
res0d <- comorbid_pccc_dx(pccc_pts, icd_name = "icd10_dx"),
regexp = NA
)
expect_warning(
res9p <- comorbid_pccc_pcs(pccc_pts, icd_name = "icd9_pcs"),
regexp = NA
)
expect_warning(
res0p <- comorbid_pccc_pcs(pccc_pts, icd_name = "icd10_pcs"),
regexp = NA
)
expect_identical(names(res9d), names(res9p))
expect_identical(names(res9d), names(res0d))
expect_identical(names(res9d), names(res0p))
expect_warning(
res9dd <- icd9_comorbid_pccc_dx(pccc_pts, icd_name = "icd9_dx"),
regexp = NA
)
expect_warning(
res0dd <- icd10_comorbid_pccc_dx(pccc_pts, icd_name = "icd10_dx"),
regexp = NA
)
expect_warning(
res9pp <- icd9_comorbid_pccc_pcs(pccc_pts, icd_name = "icd9_pcs"),
regexp = NA
)
expect_warning(
res0pp <- icd10_comorbid_pccc_pcs(pccc_pts, icd_name = "icd10_pcs"),
regexp = NA
)
expect_identical(names(res9d), names(res9dd))
expect_identical(names(res9d), names(res9pp))
expect_identical(names(res9d), names(res0dd))
expect_identical(names(res9d), names(res0pp))
})
test_that("binary vs logical and df output for PCCC", {
res_bin <- comorbid_pccc_dx(random_test_patients,
return_binary = TRUE, return_df = TRUE
)
res_log <- comorbid_pccc_dx(random_test_patients,
return_binary = FALSE, return_df = TRUE
)
expect_true(all(vapply(res_bin[-1], is.integer, logical(1))))
expect_true(all(vapply(res_log[-1], is.logical, logical(1))))
expect_identical(res_bin, logical_to_binary(res_log))
expect_identical(res_log, binary_to_logical(res_bin))
})
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