tests/testthat/test-addl.R
In qPharmetra/PMDatR: Pharmacometric Data Management in R
context("addl")
describe("get_addl_dosing works as expected for QD", {
# real world type example
ex_dat1 <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "12/14/2016 09:00", "A", 100, "ONCE", FALSE, 0, 1,
1, "12/21/2016 10:12", "A", 100, "QD", FALSE, 24, 1,
1, "01/01/2017 10:00", "A", 0, "QD", TRUE, 24, 2,
1, "01/11/2017 07:33", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
# structure of ex_dat1 should be the following, with TIME set to UTC
# # A tibble: 4 × 9
# ID TIME TRT AMT FREQ MEX MEX__ II EVID
#<dbl> <dttm> <chr> <dbl> <chr> <chr> <dbl> <dbl> <dbl>
# 1 2016-12-14 09:00:00 A 100 ONCE Y 0 0 1
# 1 2016-12-21 10:12:00 A 100 QD Y 0 24 1
# 1 2017-01-01 00:00:00 A 0 QD N 1 24 2
# 1 2017-01-11 07:33:00 A 100 QD Y 0 24 1
it("works for simple QD dosing", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/02/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 8,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 2", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "06/12/2017 08:30", "A", 100, "QD", FALSE, 24, 1,
1, "08/21/2017 21:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2017-06-12 08:30:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2017-06-12 21:00:00", "A", 100, "QD", FALSE, 24, 1, 69,
1, "2017-08-21 21:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 3", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 21:00", "A", 100, "QD", FALSE, 24, 1,
1, "11/16/2016 08:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 21:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-19 08:00:00", "A", 100, "QD", FALSE, 24, 1, 27,
1, "2016-11-16 08:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 4, dose too close", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 08:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 10:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 08:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 5, time slightly > II", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 10:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for less simple QD dosing 6, actual doses within II of eachother", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/10/2017 11:10", "A", 100, "QD", FALSE, 24, 1,
1, "02/05/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "02/06/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "02/07/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "03/07/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "03/08/2017 14:00", "A", 100, "QD", FALSE, 24, 1,
1, "03/09/2017 09:30", "A", 100, "QD", FALSE, 24, 1,
1, "04/29/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "04/30/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "05/01/2017 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/10/2017 11:10", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/11/2017 00:00", "A", 100, "QD", FALSE, 24, 1, 24,
1, "02/05/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "02/06/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "02/07/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "02/08/2017 00:00", "A", 100, "QD", FALSE, 24, 1, 26,
1, "03/07/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/07/2017 14:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/08/2017 14:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/09/2017 09:30", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/10/2017 00:00", "A", 100, "QD", FALSE, 24, 1, 49,
1, "04/29/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "04/30/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "05/01/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing, dose at II/2", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 12:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 12:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 12:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing, dose at II/2 tol now at .51", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 12:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 12:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=.51), output)
})
it("zero tolerance with dose at II, tol=0", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=.0), output)
})
it("zero tolerance with dose at II + delta, tol=0", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 00:01", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 00:01:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 00:01:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=.0), output)
})
it("QD Dose at 2*II, tol=1", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/19/2016 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-19 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=1), output)
})
it("QD Dose at 2*II, tol=0", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/19/2016 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 24, 1, 1,
1, "2016-10-19 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=0), output)
})
it("works for QD with single missing dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "01/05/2017 10:00", "A", 0, "QD", TRUE, 24, 1,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/02/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 2,
1, "01/05/2017 10:00", "A", 0, "QD", TRUE, 0, 1, 0,
1, "01/06/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 4,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for QD with single missing dose at a different time", {
# given a dosing time of a missed dose that does NOT correspond with the next dose time,
# the time should not be adjusted to match. The 7:00 time should be
# preserved, even though the next dose time is 10:00
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "01/05/2017 07:00", "A", 0, "QD", TRUE, 24, 1,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/02/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 2,
1, "01/05/2017 07:00", "A", 0, "QD", TRUE, 0, 1, 0,
1, "01/06/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 4,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
})
describe("get_addl_dosing works as expected for BID", {
it("works for simple BID dosing", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 18,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple BID dosing 2, too close", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/01/2017 17:59", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 17:59", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple BID dosing 2, just far enough", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/01/2017 18:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 06:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 18:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID with single missing dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 6,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/05/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 10,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID with multiple non-consecutive missing doses", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~MEX__, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 12, 1,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 1, 12, 1,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 1, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 12, 1,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 6,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/05/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 3,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/08/2017 10:00", "A", 100, "BID", FALSE, 12, 1, 5,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID where next dose sequence time is different than previous", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 12, 1,
1, "01/08/2017 09:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 09:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 21:00", "A", 100, "BID", FALSE, 12, 1, 11,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/08/2017 09:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/08/2017 21:00", "A", 100, "BID", FALSE, 12, 1, 4,
1, "01/11/2017 09:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID where no future doses are in the next SEQ", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 11,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/08/2017 10:00", "A", 100, "BID", FALSE, 12, 1, 5,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
})
qPharmetra/PMDatR documentation built on April 7, 2024, 5:42 p.m.
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context("addl")
describe("get_addl_dosing works as expected for QD", {
# real world type example
ex_dat1 <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "12/14/2016 09:00", "A", 100, "ONCE", FALSE, 0, 1,
1, "12/21/2016 10:12", "A", 100, "QD", FALSE, 24, 1,
1, "01/01/2017 10:00", "A", 0, "QD", TRUE, 24, 2,
1, "01/11/2017 07:33", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
# structure of ex_dat1 should be the following, with TIME set to UTC
# # A tibble: 4 × 9
# ID TIME TRT AMT FREQ MEX MEX__ II EVID
#<dbl> <dttm> <chr> <dbl> <chr> <chr> <dbl> <dbl> <dbl>
# 1 2016-12-14 09:00:00 A 100 ONCE Y 0 0 1
# 1 2016-12-21 10:12:00 A 100 QD Y 0 24 1
# 1 2017-01-01 00:00:00 A 0 QD N 1 24 2
# 1 2017-01-11 07:33:00 A 100 QD Y 0 24 1
it("works for simple QD dosing", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/02/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 8,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 2", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "06/12/2017 08:30", "A", 100, "QD", FALSE, 24, 1,
1, "08/21/2017 21:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2017-06-12 08:30:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2017-06-12 21:00:00", "A", 100, "QD", FALSE, 24, 1, 69,
1, "2017-08-21 21:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 3", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 21:00", "A", 100, "QD", FALSE, 24, 1,
1, "11/16/2016 08:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 21:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-19 08:00:00", "A", 100, "QD", FALSE, 24, 1, 27,
1, "2016-11-16 08:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 4, dose too close", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 08:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 10:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 08:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing 5, time slightly > II", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 10:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for less simple QD dosing 6, actual doses within II of eachother", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/10/2017 11:10", "A", 100, "QD", FALSE, 24, 1,
1, "02/05/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "02/06/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "02/07/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "03/07/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "03/08/2017 14:00", "A", 100, "QD", FALSE, 24, 1,
1, "03/09/2017 09:30", "A", 100, "QD", FALSE, 24, 1,
1, "04/29/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "04/30/2017 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "05/01/2017 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/10/2017 11:10", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/11/2017 00:00", "A", 100, "QD", FALSE, 24, 1, 24,
1, "02/05/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "02/06/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "02/07/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "02/08/2017 00:00", "A", 100, "QD", FALSE, 24, 1, 26,
1, "03/07/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/07/2017 14:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/08/2017 14:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/09/2017 09:30", "A", 100, "QD", FALSE, 0, 1, 0,
1, "03/10/2017 00:00", "A", 100, "QD", FALSE, 24, 1, 49,
1, "04/29/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "04/30/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "05/01/2017 00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing, dose at II/2", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 12:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 12:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 12:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple QD dosing, dose at II/2 tol now at .51", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 12:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 12:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=.51), output)
})
it("zero tolerance with dose at II, tol=0", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=.0), output)
})
it("zero tolerance with dose at II + delta, tol=0", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/18/2016 00:01", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 00:01:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 00:01:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=.0), output)
})
it("QD Dose at 2*II, tol=1", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/19/2016 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-18 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-19 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=1), output)
})
it("QD Dose at 2*II, tol=0", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "10/17/2016 00:00", "A", 100, "QD", FALSE, 24, 1,
1, "10/19/2016 00:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "2016-10-17 00:00:00", "A", 100, "QD", FALSE, 24, 1, 1,
1, "2016-10-19 00:00:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input, .tolII=0), output)
})
it("works for QD with single missing dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "01/05/2017 10:00", "A", 0, "QD", TRUE, 24, 1,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/02/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 2,
1, "01/05/2017 10:00", "A", 0, "QD", TRUE, 0, 1, 0,
1, "01/06/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 4,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for QD with single missing dose at a different time", {
# given a dosing time of a missed dose that does NOT correspond with the next dose time,
# the time should not be adjusted to match. The 7:00 time should be
# preserved, even though the next dose time is 10:00
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 24, 1,
1, "01/05/2017 07:00", "A", 0, "QD", TRUE, 24, 1,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 24, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0,
1, "01/02/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 2,
1, "01/05/2017 07:00", "A", 0, "QD", TRUE, 0, 1, 0,
1, "01/06/2017 10:00", "A", 100, "QD", FALSE, 24, 1, 4,
1, "01/11/2017 10:00", "A", 100, "QD", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
})
describe("get_addl_dosing works as expected for BID", {
it("works for simple BID dosing", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 18,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple BID dosing 2, too close", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/01/2017 17:59", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 17:59", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for simple BID dosing 2, just far enough", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/01/2017 18:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 00:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 06:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 18:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID with single missing dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 6,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/05/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 10,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID with multiple non-consecutive missing doses", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~MEX__, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 12, 1,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 1, 12, 1,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 1, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 12, 1,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 6,
1, "01/05/2017 10:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/05/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 3,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/08/2017 10:00", "A", 100, "BID", FALSE, 12, 1, 5,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID where next dose sequence time is different than previous", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 12, 1,
1, "01/08/2017 09:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 09:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 21:00", "A", 100, "BID", FALSE, 12, 1, 11,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/08/2017 09:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/08/2017 21:00", "A", 100, "BID", FALSE, 12, 1, 4,
1, "01/11/2017 09:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
it("works for BID where no future doses are in the next SEQ", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 12, 1,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 12, 1,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 12, 1
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~FREQ, ~MEX, ~II, ~EVID, ~ADDL,
1, "01/01/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/01/2017 22:00", "A", 100, "BID", FALSE, 12, 1, 11,
1, "01/07/2017 22:00", "A", 0, "BID", TRUE, 0, 1, 0,
1, "01/08/2017 10:00", "A", 100, "BID", FALSE, 12, 1, 5,
1, "01/11/2017 10:00", "A", 100, "BID", FALSE, 0, 1, 0,
1, "01/11/2017 22:00", "A", 100, "BID", FALSE, 0, 1, 0
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(get_addl_dosing(input), output)
})
})
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