tests/testthat/test-long.R
In dylanrussellmd/nsqipr: Interact with NSQIP data via R
testthat::test_that("make_reop_long works", {
x <- data.table::data.table(caseid = c(1,2,3,4),
reoperation1 = c(TRUE, TRUE, FALSE, NA),
retorpodays = c(10, 7, NA, NA),
reoporcpt1 = c("44005", "37211", NA, NA),
retorrelated = c(TRUE, TRUE, NA, NA),
reoporicd91 = c("K56.69","T82.868A", NA, NA),
reopor1icd101 = c("K56.59", "T82.868A", NA, NA),
reoperation2 = c(TRUE, TRUE, FALSE, NA),
retor2podays = c(10, 7, NA, NA),
reopor2cpt1 = c("44005", "37211", NA, NA),
retor2related = c(TRUE, TRUE, NA, NA),
reopor2icd91 = c("K56.69","T82.868A", NA, NA),
reopor2icd101 = c("K56.59", "T82.868A", NA, NA),
reoperation3 = c(TRUE, TRUE, FALSE, NA),
retor3podays = c(10, 7, NA, NA),
reopor3cpt1 = c("44005", "37211", NA, NA),
retor3related = c(TRUE, TRUE, NA, NA),
reopor3icd91 = c("K56.69","T82.868A", NA, NA),
reopor3icd101 = c("K56.59", "T82.868A", NA, NA))
y <- data.table::data.table(caseid = c(1, 1, 1, 2, 2, 2, 3, 3, 3),
nreoperation = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L),
reoperation = c(TRUE,TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE),
retorpodays = c(10, 10, 10, 7, 7, 7, NA, NA, NA),
reoporcpt = c("44005", "44005", "44005", "37211", "37211", "37211", NA, NA, NA),
retorrelated = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, NA, NA, NA),
reoporicd9 = c("K56.69", "K56.69", "K56.69", "T82.868A", "T82.868A", "T82.868A", NA, NA, NA),
reoporicd10 = c("K56.59", "K56.59", "K56.59", "T82.868A", "T82.868A", "T82.868A", NA, NA, NA))
testthat::expect_equal(make_reop_long(x), y)
testthat::expect_equal(make_reop_long(x, TRUE), y[-7:-9, ])
testthat::expect_null(make_reop_long(data.table::data.table()))
})
testthat::test_that("make_readm_long works", {
x <- data.table::data.table(caseid = c(1,2,3,4),
readmission1 = c(TRUE, TRUE, FALSE, NA),
readmpodays1 = c(10, 7, NA, NA),
readmrelated1 = c(TRUE, FALSE, NA, NA),
readmsuspreason1 = c("Reason", "Reason", NA, NA),
readmrelicd91 = c("111", "222", NA, NA),
readmrelicd101 = c("1111","2222", NA, NA),
unplannedreadmission1 = c(TRUE, FALSE, NA, NA),
readmunrelsusp1 = c("Reason", NA, NA, NA),
readmunrelicd91 = c("111", NA, NA, NA),
readmunrelicd101 = c("1111",NA,NA,NA),
readmission2 = c(TRUE, NA, FALSE, NA),
readmpodays2 = c(10, 7, NA, NA),
readmrelated2 = c(TRUE, FALSE, NA, NA),
readmsuspreason2 = c("Reason", "Reason", NA, NA),
readmrelicd92 = c("111", "222", NA, NA),
readmrelicd102 = c("1111","2222", NA, NA),
unplannedreadmission2 = c(TRUE, FALSE, NA, NA),
readmunrelsusp2 = c("Reason", NA, NA, NA),
readmunrelicd92 = c("111", NA, NA, NA),
readmunrelicd102 = c("1111",NA,NA,NA),
readmission3 = c(TRUE, TRUE, FALSE, NA),
readmpodays3 = c(10, 7, NA, NA),
readmrelated3 = c(TRUE, FALSE, NA, NA),
readmsuspreason3 = c("Reason", "Reason", NA, NA),
readmrelicd93 = c("111", "222", NA, NA),
readmrelicd103 = c("1111","2222", NA, NA),
unplannedreadmission3 = c(TRUE, FALSE, NA, NA),
readmunrelsusp3 = c("Reason", NA, NA, NA),
readmunrelicd93 = c("111", NA, NA, NA),
readmunrelicd103 = c("1111",NA,NA,NA),
readmission4 = c(TRUE, TRUE, FALSE, NA),
readmpodays4 = c(10, 7, NA, NA),
readmrelated4 = c(TRUE, FALSE, NA, NA),
readmsuspreason4 = c("Reason", "Reason", NA, NA),
readmrelicd94 = c("111", "222", NA, NA),
readmrelicd104 = c("1111","2222", NA, NA),
unplannedreadmission4 = c(TRUE, FALSE, NA, NA),
readmunrelsusp4 = c("Reason", NA, NA, NA),
readmunrelicd94 = c("111", NA, NA, NA),
readmunrelicd104 = c("1111",NA,NA,NA),
readmission5 = c(TRUE, TRUE, FALSE, NA),
readmpodays5 = c(10, 7, NA, NA),
readmrelated5 = c(TRUE, FALSE, NA, NA),
readmsuspreason5 = c("Reason", "Reason", NA, NA),
readmrelicd95 = c("111", "222", NA, NA),
readmrelicd105 = c("1111","2222", NA, NA),
unplannedreadmission5 = c(TRUE, FALSE, NA, NA),
readmunrelsusp5 = c("Reason", NA, NA, NA),
readmunrelicd95 = c("111", NA, NA, NA),
readmunrelicd105 = c("1111",NA,NA,NA))
y <- data.table::data.table(caseid = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3),
nreadmission = c(1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L),
readmission = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE),
readmpodays = c(10, 10, 10, 10, 10, 7, 7, 7, 7, NA, NA, NA, NA, NA),
unplannedreadmission = c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, NA, NA, NA, NA, NA),
readmrelated = c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, NA, NA, NA, NA, NA),
readmsuspreason = c("Reason", "Reason", "Reason", "Reason", "Reason", "Reason", "Reason", "Reason", "Reason", NA, NA, NA, NA, NA),
readmunrelsusp = c("Reason", "Reason", "Reason", "Reason", "Reason", NA, NA, NA, NA, NA, NA, NA, NA, NA),
readmrelicd9 = c("111", "111", "111", "111", "111", "222", "222", "222", "222", NA, NA, NA, NA, NA),
readmrelicd10 = c("1111", "1111", "1111", "1111", "1111", "2222", "2222", "2222", "2222", NA, NA, NA, NA, NA),
readmunrelicd9 = c("111", "111", "111", "111", "111", NA, NA, NA, NA, NA, NA, NA, NA, NA),
readmunrelicd10 = c("1111", "1111", "1111", "1111", "1111", NA, NA, NA, NA, NA, NA, NA, NA, NA))
testthat::expect_equal(make_readm_long(x), y)
testthat::expect_equal(make_readm_long(x, TRUE), y[-10:-14, ])
testthat::expect_null(make_readm_long(data.table::data.table()))
})
testthat::test_that("make_anesthes_other_long works", {
x <- data.table::data.table(caseid = c(1,2,3,4),
anesthes_other = c("General","General, Spinal", "General, Spinal, MAC/IV Sedation", NA))
y <- data.table::data.table(caseid = c(1, 2, 2, 3, 3, 3),
nanesthes_other = c(1L, 1L, 2L, 1L, 2L, 3L),
anesthes_other = factor(c("General", "General", "Spinal", "General", "Spinal", "Monitored anesthesia care"),
levels = c("Epidural","General","Local","Monitored anesthesia care","None","Other","Regional","Spinal")))
testthat::expect_equal(make_anesthes_other_long(x), y)
testthat::expect_null(make_anesthes_other_long(data.table::data.table()))
})
testthat::test_that("make_cpt_long works",{
x <- data.table::data.table(caseid = 4914509L, cpt = "49650", othercpt1 = "38900",
othercpt2 = "75952", othercpt3 = "36245", othercpt4 = "49020",
othercpt5 = "43999", othercpt6 = "38900", othercpt7 = "44955",
othercpt8 = "22216", othercpt9 = "44005", othercpt10 = "11046",
concpt1 = "58661", concpt2 = "44380", concpt3 = "37236",
concpt4 = "44388", concpt5 = "19361", concpt6 = "19330",
concpt7 = "15274", concpt8 = "35701", concpt9 = "22848",
concpt10 = "35761", prncptx = "FLAP ISLAND PEDICLE ANATOMIC NAMED AXIAL ARTERY",
otherproc1 = "LAPS PROCTECTOMY ABDOMINOPERINEAL W/COLOSTOMY",
otherproc2 = "LAPAROSCOPY RADICAL NEPHRECTOMY", otherproc3 = "CYSTECTOMY PARTIAL SIMPLE",
otherproc4 = NA, otherproc5 = "DERMAL AUTOGRAFT TRUNK/ARM/LEG 1ST 100 CM",
otherproc6 = "CLOSURE RECTOVESICAL FISTULA", otherproc7 = "INTRAOP SENTINEL LYMPH NODE ID W/DYE INJECTION",
otherproc8 = "ALLOGRAFT FOR SPINE SURGERY ONLY MORSELIZED",
otherproc9 = "POSTERIOR SEGMENTAL INSTRUMENTATION 3-6 VRT SEG",
otherproc10 = NA, concurr1 = "RPR UMBILICAL HERNIA AGE 5 YRS/> INCARCERATED",
concurr2 = NA, concurr3 = "REPAIR FIRST ABDOMINAL WALL HERNIA",
concurr4 = "MUSC MYOCUTANEOUS/FASCIOCUTANEOUS FLAP TRUNK",
concurr5 = "MASTOPEXY", concurr6 = "REMOVAL MAMMARY IMPLANT MATERIAL",
concurr7 = "SUTURE NERVE REQ XTNSV MOBIL/TRPOS NERVE", concurr8 = "SPLIT AGRFT F/S/N/H/F/G/M/D GT 1ST 100 CM/</1 %",
concurr9 = "SEVERING TARSORRHAPHY", concurr10 = NA, workrvu = 26.32,
otherwrvu1 = 15.31, otherwrvu2 = 21.15, otherwrvu3 = 4.49,
otherwrvu4 = 12.8, otherwrvu5 = 34.58, otherwrvu6 = 3.02,
otherwrvu7 = 1.9, otherwrvu8 = 3.73, otherwrvu9 = NA,
otherwrvu10 = NA, conwrvu1 = 7.08, conwrvu2 = 15.85,
conwrvu3 = 0.8, conwrvu4 = 12.8, conwrvu5 = 11.35,
conwrvu6 = 0, conwrvu7 = 12.92, conwrvu8 = 16.42, conwrvu9 = 0.8,
conwrvu10 = 1.44)
y <- data.table::data.table(caseid = c(4914509L, 4914509L, 4914509L, 4914509L,
4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L,
4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L,
4914509L, 4914509L, 4914509L),
nproc = 1:21,
cpt = c("49650", "38900", "75952", "36245", "49020", "43999", "38900", "44955", "22216", "44005", "11046", "58661", "44380", "37236", "44388", "19361", "19330", "15274", "35701", "22848", "35761"),
proc = c("FLAP ISLAND PEDICLE ANATOMIC NAMED AXIAL ARTERY", "LAPS PROCTECTOMY ABDOMINOPERINEAL W/COLOSTOMY", "LAPAROSCOPY RADICAL NEPHRECTOMY", "CYSTECTOMY PARTIAL SIMPLE", NA, "DERMAL AUTOGRAFT TRUNK/ARM/LEG 1ST 100 CM",
"CLOSURE RECTOVESICAL FISTULA", "INTRAOP SENTINEL LYMPH NODE ID W/DYE INJECTION", "ALLOGRAFT FOR SPINE SURGERY ONLY MORSELIZED", "POSTERIOR SEGMENTAL INSTRUMENTATION 3-6 VRT SEG",
NA, "RPR UMBILICAL HERNIA AGE 5 YRS/> INCARCERATED", NA, "REPAIR FIRST ABDOMINAL WALL HERNIA", "MUSC MYOCUTANEOUS/FASCIOCUTANEOUS FLAP TRUNK", "MASTOPEXY",
"REMOVAL MAMMARY IMPLANT MATERIAL", "SUTURE NERVE REQ XTNSV MOBIL/TRPOS NERVE", "SPLIT AGRFT F/S/N/H/F/G/M/D GT 1ST 100 CM/</1 %", "SEVERING TARSORRHAPHY", NA),
workrvu = c(26.32, 15.31, 21.15, 4.49, 12.8, 34.58, 3.02, 1.9, 3.73, NA, NA, 7.08, 15.85, 0.8, 12.8, 11.35, 0, 12.92, 16.42, 0.8, 1.44),
primarysurg = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE))
testthat::expect_equal(make_cpt_long(x), y)
testthat::expect_null(make_cpt_long(data.table::data.table()))
})
testthat::test_that("make_pan_percdrainage_long works", {
x <- data.table::data.table(caseid = 1:15,
pan_percdrainage = c("Yes-other", "Yes-bile", "Yes-pus",
"Yes-amylase-rich fluid", "Yes-amylase-rich fluid,Yes-pus",
"Yes-bile,Yes-other", "Yes-amylase-rich fluid,Yes-pus,Yes-other",
"Yes-amylase-rich fluid,Yes-bile,Yes-other", "Yes-pus,Yes-bile",
"Yes-pus,Yes-other", "Yes-amylase-rich fluid,Yes-pus,Yes-bile",
"Yes-amylase-rich fluid,Yes-other", "Yes-amylase-rich fluid,Yes-pus,Yes-bile,Yes-other",
"Yes-amylase-rich fluid,Yes-bile", "Yes-pus,Yes-bile,Yes-other"))
make_pan_percdrainage_cols(x)
y <- data.table::data.table(caseid = c(1L, 2L, 3L, 4L, 5L, 5L, 6L,6L, 7L, 7L, 7L, 8L, 8L, 8L, 9L, 9L, 10L, 10L,
11L, 11L, 11L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L, 15L, 15L, 15L),
npercdrainage = c(1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,
1L, 2L, 1L, 2L, 3L, 1L, 2L, 1L, 2L, 3L, 4L, 1L, 2L, 1L, 2L, 3L),
percdrainage = c("Yes-other", "Yes-bile", "Yes-pus", "Yes-amylase-rich fluid",
"Yes-amylase-rich fluid", "Yes-pus", "Yes-bile", "Yes-other",
"Yes-amylase-rich fluid", "Yes-pus", "Yes-other", "Yes-amylase-rich fluid",
"Yes-bile", "Yes-other", "Yes-pus", "Yes-bile", "Yes-pus", "Yes-other",
"Yes-amylase-rich fluid", "Yes-pus", "Yes-bile", "Yes-amylase-rich fluid",
"Yes-other", "Yes-amylase-rich fluid", "Yes-pus", "Yes-bile", "Yes-other",
"Yes-amylase-rich fluid", "Yes-bile", "Yes-pus", "Yes-bile", "Yes-other"))
testthat::expect_equal(make_pan_percdrainage_long(x), y)
testthat::expect_null(make_pan_percdrainage_long(data.table::data.table()))
})
testthat::test_that("make_amylase_long works", {
x <- data.table::data.table(caseid = 1:30,
pan_amylase_pod1 = c(NA, 3439L, 8817L, 6082L, 9805L, 7159L, 5389L, 7994L, 9258L,
6324L, 3610L, 9366L, 2870L, 4513L, 9146L, 1895L, 5985L, 5463L,
1045L, 1032L, 8639L, 9672L, 5401L, 6309L, 3063L, 7331L, 8368L, 1341L, 3158L, 9575L),
pan_amylase_pod230 = c(NA, 5829L, 7374L, 8896L, 8113L, 1529L, 3858L, 7262L, 4652L, 2942L, 3474L,
4057L, 5721L, 5126L, 4818L, 4812L, 8941L, 1135L, 3906L, 7273L, 3748L,
5734L, 3663L, 3659L, 2371L, 8570L, 8137L, 1887L, 9045L, 3509L),
damylase = c(NA, 29L, 19L, 20L, 30L, 27L, 3L, 15L, 9L, 22L, 4L, 25L, 23L, 2L, 24L, 21L, 13L,
18L, 28L, 10L, 11L, 5L, 16L, 8L, 26L, 7L, 6L, 12L, 17L, 14L))
y <- data.table::data.table(caseid = c(2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L,
11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L,
18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L,
26L, 26L, 27L, 27L, 28L, 28L, 29L, 29L, 30L, 30L),
pod = c(1, 29, 1, 19, 1, 20, 1, 30, 1, 27, 1, 3, 1, 15, 1, 9, 1, 22, 1, 4, 1, 25, 1,
23, 1, 2, 1, 24, 1, 21, 1, 13, 1, 18, 1, 28, 1, 10, 1, 11, 1, 5, 1, 16, 1, 8,
1, 26, 1, 7, 1, 6, 1, 12, 1, 17, 1, 14),
amylase = c(3439L, 5829L, 8817L, 7374L, 6082L, 8896L, 9805L, 8113L, 7159L, 1529L,
5389L, 3858L, 7994L, 7262L, 9258L, 4652L, 6324L, 2942L, 3610L, 3474L,
9366L, 4057L, 2870L, 5721L, 4513L, 5126L, 9146L, 4818L, 1895L, 4812L,
5985L, 8941L, 5463L, 1135L, 1045L, 3906L, 1032L, 7273L, 8639L, 3748L,
9672L, 5734L, 5401L, 3663L, 6309L, 3659L, 3063L, 2371L, 7331L, 8570L,
8368L, 8137L, 1341L, 1887L, 3158L, 9045L, 9575L, 3509L))
testthat::expect_equal(make_amylase_long(x), y)
testthat::expect_null(make_amylase_long(data.table::data.table()))
})
dylanrussellmd/nsqipr documentation built on Oct. 13, 2023, 11:01 a.m.
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testthat::test_that("make_reop_long works", {
x <- data.table::data.table(caseid = c(1,2,3,4),
reoperation1 = c(TRUE, TRUE, FALSE, NA),
retorpodays = c(10, 7, NA, NA),
reoporcpt1 = c("44005", "37211", NA, NA),
retorrelated = c(TRUE, TRUE, NA, NA),
reoporicd91 = c("K56.69","T82.868A", NA, NA),
reopor1icd101 = c("K56.59", "T82.868A", NA, NA),
reoperation2 = c(TRUE, TRUE, FALSE, NA),
retor2podays = c(10, 7, NA, NA),
reopor2cpt1 = c("44005", "37211", NA, NA),
retor2related = c(TRUE, TRUE, NA, NA),
reopor2icd91 = c("K56.69","T82.868A", NA, NA),
reopor2icd101 = c("K56.59", "T82.868A", NA, NA),
reoperation3 = c(TRUE, TRUE, FALSE, NA),
retor3podays = c(10, 7, NA, NA),
reopor3cpt1 = c("44005", "37211", NA, NA),
retor3related = c(TRUE, TRUE, NA, NA),
reopor3icd91 = c("K56.69","T82.868A", NA, NA),
reopor3icd101 = c("K56.59", "T82.868A", NA, NA))
y <- data.table::data.table(caseid = c(1, 1, 1, 2, 2, 2, 3, 3, 3),
nreoperation = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L),
reoperation = c(TRUE,TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE),
retorpodays = c(10, 10, 10, 7, 7, 7, NA, NA, NA),
reoporcpt = c("44005", "44005", "44005", "37211", "37211", "37211", NA, NA, NA),
retorrelated = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, NA, NA, NA),
reoporicd9 = c("K56.69", "K56.69", "K56.69", "T82.868A", "T82.868A", "T82.868A", NA, NA, NA),
reoporicd10 = c("K56.59", "K56.59", "K56.59", "T82.868A", "T82.868A", "T82.868A", NA, NA, NA))
testthat::expect_equal(make_reop_long(x), y)
testthat::expect_equal(make_reop_long(x, TRUE), y[-7:-9, ])
testthat::expect_null(make_reop_long(data.table::data.table()))
})
testthat::test_that("make_readm_long works", {
x <- data.table::data.table(caseid = c(1,2,3,4),
readmission1 = c(TRUE, TRUE, FALSE, NA),
readmpodays1 = c(10, 7, NA, NA),
readmrelated1 = c(TRUE, FALSE, NA, NA),
readmsuspreason1 = c("Reason", "Reason", NA, NA),
readmrelicd91 = c("111", "222", NA, NA),
readmrelicd101 = c("1111","2222", NA, NA),
unplannedreadmission1 = c(TRUE, FALSE, NA, NA),
readmunrelsusp1 = c("Reason", NA, NA, NA),
readmunrelicd91 = c("111", NA, NA, NA),
readmunrelicd101 = c("1111",NA,NA,NA),
readmission2 = c(TRUE, NA, FALSE, NA),
readmpodays2 = c(10, 7, NA, NA),
readmrelated2 = c(TRUE, FALSE, NA, NA),
readmsuspreason2 = c("Reason", "Reason", NA, NA),
readmrelicd92 = c("111", "222", NA, NA),
readmrelicd102 = c("1111","2222", NA, NA),
unplannedreadmission2 = c(TRUE, FALSE, NA, NA),
readmunrelsusp2 = c("Reason", NA, NA, NA),
readmunrelicd92 = c("111", NA, NA, NA),
readmunrelicd102 = c("1111",NA,NA,NA),
readmission3 = c(TRUE, TRUE, FALSE, NA),
readmpodays3 = c(10, 7, NA, NA),
readmrelated3 = c(TRUE, FALSE, NA, NA),
readmsuspreason3 = c("Reason", "Reason", NA, NA),
readmrelicd93 = c("111", "222", NA, NA),
readmrelicd103 = c("1111","2222", NA, NA),
unplannedreadmission3 = c(TRUE, FALSE, NA, NA),
readmunrelsusp3 = c("Reason", NA, NA, NA),
readmunrelicd93 = c("111", NA, NA, NA),
readmunrelicd103 = c("1111",NA,NA,NA),
readmission4 = c(TRUE, TRUE, FALSE, NA),
readmpodays4 = c(10, 7, NA, NA),
readmrelated4 = c(TRUE, FALSE, NA, NA),
readmsuspreason4 = c("Reason", "Reason", NA, NA),
readmrelicd94 = c("111", "222", NA, NA),
readmrelicd104 = c("1111","2222", NA, NA),
unplannedreadmission4 = c(TRUE, FALSE, NA, NA),
readmunrelsusp4 = c("Reason", NA, NA, NA),
readmunrelicd94 = c("111", NA, NA, NA),
readmunrelicd104 = c("1111",NA,NA,NA),
readmission5 = c(TRUE, TRUE, FALSE, NA),
readmpodays5 = c(10, 7, NA, NA),
readmrelated5 = c(TRUE, FALSE, NA, NA),
readmsuspreason5 = c("Reason", "Reason", NA, NA),
readmrelicd95 = c("111", "222", NA, NA),
readmrelicd105 = c("1111","2222", NA, NA),
unplannedreadmission5 = c(TRUE, FALSE, NA, NA),
readmunrelsusp5 = c("Reason", NA, NA, NA),
readmunrelicd95 = c("111", NA, NA, NA),
readmunrelicd105 = c("1111",NA,NA,NA))
y <- data.table::data.table(caseid = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3),
nreadmission = c(1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L),
readmission = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE),
readmpodays = c(10, 10, 10, 10, 10, 7, 7, 7, 7, NA, NA, NA, NA, NA),
unplannedreadmission = c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, NA, NA, NA, NA, NA),
readmrelated = c(TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, NA, NA, NA, NA, NA),
readmsuspreason = c("Reason", "Reason", "Reason", "Reason", "Reason", "Reason", "Reason", "Reason", "Reason", NA, NA, NA, NA, NA),
readmunrelsusp = c("Reason", "Reason", "Reason", "Reason", "Reason", NA, NA, NA, NA, NA, NA, NA, NA, NA),
readmrelicd9 = c("111", "111", "111", "111", "111", "222", "222", "222", "222", NA, NA, NA, NA, NA),
readmrelicd10 = c("1111", "1111", "1111", "1111", "1111", "2222", "2222", "2222", "2222", NA, NA, NA, NA, NA),
readmunrelicd9 = c("111", "111", "111", "111", "111", NA, NA, NA, NA, NA, NA, NA, NA, NA),
readmunrelicd10 = c("1111", "1111", "1111", "1111", "1111", NA, NA, NA, NA, NA, NA, NA, NA, NA))
testthat::expect_equal(make_readm_long(x), y)
testthat::expect_equal(make_readm_long(x, TRUE), y[-10:-14, ])
testthat::expect_null(make_readm_long(data.table::data.table()))
})
testthat::test_that("make_anesthes_other_long works", {
x <- data.table::data.table(caseid = c(1,2,3,4),
anesthes_other = c("General","General, Spinal", "General, Spinal, MAC/IV Sedation", NA))
y <- data.table::data.table(caseid = c(1, 2, 2, 3, 3, 3),
nanesthes_other = c(1L, 1L, 2L, 1L, 2L, 3L),
anesthes_other = factor(c("General", "General", "Spinal", "General", "Spinal", "Monitored anesthesia care"),
levels = c("Epidural","General","Local","Monitored anesthesia care","None","Other","Regional","Spinal")))
testthat::expect_equal(make_anesthes_other_long(x), y)
testthat::expect_null(make_anesthes_other_long(data.table::data.table()))
})
testthat::test_that("make_cpt_long works",{
x <- data.table::data.table(caseid = 4914509L, cpt = "49650", othercpt1 = "38900",
othercpt2 = "75952", othercpt3 = "36245", othercpt4 = "49020",
othercpt5 = "43999", othercpt6 = "38900", othercpt7 = "44955",
othercpt8 = "22216", othercpt9 = "44005", othercpt10 = "11046",
concpt1 = "58661", concpt2 = "44380", concpt3 = "37236",
concpt4 = "44388", concpt5 = "19361", concpt6 = "19330",
concpt7 = "15274", concpt8 = "35701", concpt9 = "22848",
concpt10 = "35761", prncptx = "FLAP ISLAND PEDICLE ANATOMIC NAMED AXIAL ARTERY",
otherproc1 = "LAPS PROCTECTOMY ABDOMINOPERINEAL W/COLOSTOMY",
otherproc2 = "LAPAROSCOPY RADICAL NEPHRECTOMY", otherproc3 = "CYSTECTOMY PARTIAL SIMPLE",
otherproc4 = NA, otherproc5 = "DERMAL AUTOGRAFT TRUNK/ARM/LEG 1ST 100 CM",
otherproc6 = "CLOSURE RECTOVESICAL FISTULA", otherproc7 = "INTRAOP SENTINEL LYMPH NODE ID W/DYE INJECTION",
otherproc8 = "ALLOGRAFT FOR SPINE SURGERY ONLY MORSELIZED",
otherproc9 = "POSTERIOR SEGMENTAL INSTRUMENTATION 3-6 VRT SEG",
otherproc10 = NA, concurr1 = "RPR UMBILICAL HERNIA AGE 5 YRS/> INCARCERATED",
concurr2 = NA, concurr3 = "REPAIR FIRST ABDOMINAL WALL HERNIA",
concurr4 = "MUSC MYOCUTANEOUS/FASCIOCUTANEOUS FLAP TRUNK",
concurr5 = "MASTOPEXY", concurr6 = "REMOVAL MAMMARY IMPLANT MATERIAL",
concurr7 = "SUTURE NERVE REQ XTNSV MOBIL/TRPOS NERVE", concurr8 = "SPLIT AGRFT F/S/N/H/F/G/M/D GT 1ST 100 CM/</1 %",
concurr9 = "SEVERING TARSORRHAPHY", concurr10 = NA, workrvu = 26.32,
otherwrvu1 = 15.31, otherwrvu2 = 21.15, otherwrvu3 = 4.49,
otherwrvu4 = 12.8, otherwrvu5 = 34.58, otherwrvu6 = 3.02,
otherwrvu7 = 1.9, otherwrvu8 = 3.73, otherwrvu9 = NA,
otherwrvu10 = NA, conwrvu1 = 7.08, conwrvu2 = 15.85,
conwrvu3 = 0.8, conwrvu4 = 12.8, conwrvu5 = 11.35,
conwrvu6 = 0, conwrvu7 = 12.92, conwrvu8 = 16.42, conwrvu9 = 0.8,
conwrvu10 = 1.44)
y <- data.table::data.table(caseid = c(4914509L, 4914509L, 4914509L, 4914509L,
4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L,
4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L, 4914509L,
4914509L, 4914509L, 4914509L),
nproc = 1:21,
cpt = c("49650", "38900", "75952", "36245", "49020", "43999", "38900", "44955", "22216", "44005", "11046", "58661", "44380", "37236", "44388", "19361", "19330", "15274", "35701", "22848", "35761"),
proc = c("FLAP ISLAND PEDICLE ANATOMIC NAMED AXIAL ARTERY", "LAPS PROCTECTOMY ABDOMINOPERINEAL W/COLOSTOMY", "LAPAROSCOPY RADICAL NEPHRECTOMY", "CYSTECTOMY PARTIAL SIMPLE", NA, "DERMAL AUTOGRAFT TRUNK/ARM/LEG 1ST 100 CM",
"CLOSURE RECTOVESICAL FISTULA", "INTRAOP SENTINEL LYMPH NODE ID W/DYE INJECTION", "ALLOGRAFT FOR SPINE SURGERY ONLY MORSELIZED", "POSTERIOR SEGMENTAL INSTRUMENTATION 3-6 VRT SEG",
NA, "RPR UMBILICAL HERNIA AGE 5 YRS/> INCARCERATED", NA, "REPAIR FIRST ABDOMINAL WALL HERNIA", "MUSC MYOCUTANEOUS/FASCIOCUTANEOUS FLAP TRUNK", "MASTOPEXY",
"REMOVAL MAMMARY IMPLANT MATERIAL", "SUTURE NERVE REQ XTNSV MOBIL/TRPOS NERVE", "SPLIT AGRFT F/S/N/H/F/G/M/D GT 1ST 100 CM/</1 %", "SEVERING TARSORRHAPHY", NA),
workrvu = c(26.32, 15.31, 21.15, 4.49, 12.8, 34.58, 3.02, 1.9, 3.73, NA, NA, 7.08, 15.85, 0.8, 12.8, 11.35, 0, 12.92, 16.42, 0.8, 1.44),
primarysurg = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE))
testthat::expect_equal(make_cpt_long(x), y)
testthat::expect_null(make_cpt_long(data.table::data.table()))
})
testthat::test_that("make_pan_percdrainage_long works", {
x <- data.table::data.table(caseid = 1:15,
pan_percdrainage = c("Yes-other", "Yes-bile", "Yes-pus",
"Yes-amylase-rich fluid", "Yes-amylase-rich fluid,Yes-pus",
"Yes-bile,Yes-other", "Yes-amylase-rich fluid,Yes-pus,Yes-other",
"Yes-amylase-rich fluid,Yes-bile,Yes-other", "Yes-pus,Yes-bile",
"Yes-pus,Yes-other", "Yes-amylase-rich fluid,Yes-pus,Yes-bile",
"Yes-amylase-rich fluid,Yes-other", "Yes-amylase-rich fluid,Yes-pus,Yes-bile,Yes-other",
"Yes-amylase-rich fluid,Yes-bile", "Yes-pus,Yes-bile,Yes-other"))
make_pan_percdrainage_cols(x)
y <- data.table::data.table(caseid = c(1L, 2L, 3L, 4L, 5L, 5L, 6L,6L, 7L, 7L, 7L, 8L, 8L, 8L, 9L, 9L, 10L, 10L,
11L, 11L, 11L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L, 15L, 15L, 15L),
npercdrainage = c(1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L,
1L, 2L, 1L, 2L, 3L, 1L, 2L, 1L, 2L, 3L, 4L, 1L, 2L, 1L, 2L, 3L),
percdrainage = c("Yes-other", "Yes-bile", "Yes-pus", "Yes-amylase-rich fluid",
"Yes-amylase-rich fluid", "Yes-pus", "Yes-bile", "Yes-other",
"Yes-amylase-rich fluid", "Yes-pus", "Yes-other", "Yes-amylase-rich fluid",
"Yes-bile", "Yes-other", "Yes-pus", "Yes-bile", "Yes-pus", "Yes-other",
"Yes-amylase-rich fluid", "Yes-pus", "Yes-bile", "Yes-amylase-rich fluid",
"Yes-other", "Yes-amylase-rich fluid", "Yes-pus", "Yes-bile", "Yes-other",
"Yes-amylase-rich fluid", "Yes-bile", "Yes-pus", "Yes-bile", "Yes-other"))
testthat::expect_equal(make_pan_percdrainage_long(x), y)
testthat::expect_null(make_pan_percdrainage_long(data.table::data.table()))
})
testthat::test_that("make_amylase_long works", {
x <- data.table::data.table(caseid = 1:30,
pan_amylase_pod1 = c(NA, 3439L, 8817L, 6082L, 9805L, 7159L, 5389L, 7994L, 9258L,
6324L, 3610L, 9366L, 2870L, 4513L, 9146L, 1895L, 5985L, 5463L,
1045L, 1032L, 8639L, 9672L, 5401L, 6309L, 3063L, 7331L, 8368L, 1341L, 3158L, 9575L),
pan_amylase_pod230 = c(NA, 5829L, 7374L, 8896L, 8113L, 1529L, 3858L, 7262L, 4652L, 2942L, 3474L,
4057L, 5721L, 5126L, 4818L, 4812L, 8941L, 1135L, 3906L, 7273L, 3748L,
5734L, 3663L, 3659L, 2371L, 8570L, 8137L, 1887L, 9045L, 3509L),
damylase = c(NA, 29L, 19L, 20L, 30L, 27L, 3L, 15L, 9L, 22L, 4L, 25L, 23L, 2L, 24L, 21L, 13L,
18L, 28L, 10L, 11L, 5L, 16L, 8L, 26L, 7L, 6L, 12L, 17L, 14L))
y <- data.table::data.table(caseid = c(2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L,
11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L,
18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L,
26L, 26L, 27L, 27L, 28L, 28L, 29L, 29L, 30L, 30L),
pod = c(1, 29, 1, 19, 1, 20, 1, 30, 1, 27, 1, 3, 1, 15, 1, 9, 1, 22, 1, 4, 1, 25, 1,
23, 1, 2, 1, 24, 1, 21, 1, 13, 1, 18, 1, 28, 1, 10, 1, 11, 1, 5, 1, 16, 1, 8,
1, 26, 1, 7, 1, 6, 1, 12, 1, 17, 1, 14),
amylase = c(3439L, 5829L, 8817L, 7374L, 6082L, 8896L, 9805L, 8113L, 7159L, 1529L,
5389L, 3858L, 7994L, 7262L, 9258L, 4652L, 6324L, 2942L, 3610L, 3474L,
9366L, 4057L, 2870L, 5721L, 4513L, 5126L, 9146L, 4818L, 1895L, 4812L,
5985L, 8941L, 5463L, 1135L, 1045L, 3906L, 1032L, 7273L, 8639L, 3748L,
9672L, 5734L, 5401L, 3663L, 6309L, 3659L, 3063L, 2371L, 7331L, 8570L,
8368L, 8137L, 1341L, 1887L, 3158L, 9045L, 9575L, 3509L))
testthat::expect_equal(make_amylase_long(x), y)
testthat::expect_null(make_amylase_long(data.table::data.table()))
})
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