tests/testthat/test-time_after_x.R
In qPharmetra/PMDatR: Pharmacometric Data Management in R
context("time-after")
describe("time after criteria works", {
# real world type example
it("after event flag", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 100, 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- c(0, 24, 240, 242)
expect_equal(time_after_criteria(input,"TAEV", EVID == 2)$TAEV, output)
})
it("before first event flag should be zero", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 2, 0, 0.5,
1, "01/11/2017 12:00", "A", 100, 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- c(0, 0, 0, 2)
expect_equal(time_after_criteria(input,"TAEV", EVID == 2)$TAEV, output)
})
})
describe("time after first dose works", {
# real world type example
it("works for time after first dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 0, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 4, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output=c(0, 8, 24, 74, 240, 242, 244)
expect_equal(time_after_first_dose(input)$TAFD, output)
expect_equal(time_after_first_dose(input, .criteria=AMT>0)$TAFD, output-24)
expect_equal(time_after_first_dose(input, .name = "tafd")$tafd, output)
input <- input %>% rename(ELTM=TIME)
expect_equal(time_after_first_dose(input,.time="ELTM")$TAFD, output)
})
it("can select different baseline (EVID==4)", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 0, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 4, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output=c(-240, -232, -216, -166, 0, 2, 4)
expect_equal(time_after_first_dose(input,.time="TIME", .criteria=EVID==4)$TAFD, output)
})
it("works for time after dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_after_dose(input)$TAD, c(0, 8, 0, 0, 0))
})
# it("works for time after dose with excluded dose", {
# input <- tibble::tribble(
# ~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE, EXCL,
# 1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3, 1,
# 1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3, 0,
# 1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5, 0,
# 1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5, 0,
# 1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5, 0
# ) %>% dplyr::mutate(
# TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
# )
# expect_equal(time_after_dose(input, .excl=EXCL==1)$TAD, c(0, 8, 0, 2, 4))
# })
it("works for time after dose with expanding addl", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 0, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 4, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_after_dose(input)$TAD, c(0, 8, 0, 2, 0, 0, 0))
expect_equal(time_after_dose(input, .criteria = AMT>0)$TAD, c(0, 8, 0, 2, 0, 2, 4))
})
it("works for time after dose with expanding addl and ADDL=NA in obs", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 0, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 4, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = iso_to_posix(TIME),
ADDL = ifelse(EVID!=1,NA,ADDL)
)
expect_equal(time_after_dose(input)$TAD, c(0, 8, 0, 2, 0, 0, 0))
expect_equal(time_after_dose(input, .criteria = AMT>0)$TAD, c(0, 8, 0, 2, 0, 2, 4))
})
it("works for time after dose with expanding addl and predose obs giving negative TAD", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 09:15", "A", 0 , 0, 0, 0, 0.3,
1, "01/01/2017 09:45", "A", 0 , 0, 0, 0, 0.3,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 0, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 0, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 4, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = iso_to_posix(TIME)
)
expect_equal(time_after_dose(input)$TAD,
c(-.75, -.25, 0, 8, 0, 2, 0, 0, 0))
expect_equal(time_after_dose(input, .criteria = AMT>0)$TAD,
c(-.75, -.25, 0, 8, 0, 2, 0, 2, 4))
})
it("works for time of first dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_of_first_dose(input)$FDDTTM, rep(input$TIME[1],7))
})
it("works for time of first dose with addnl criteria", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_of_first_dose(input,"FDDTTM",AMT>0 & II>0)$FDDTTM, rep(input$TIME[3],7))
})
})
describe("relative time works", {
# real world type example
it("works creating RTIME column", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(relative_time(input)$RTIME, c(0, 8, 24, 74, 240, 242, 244))
})
it("works to overwrite TIME column", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(relative_time(input, .name = "TIME")$TIME, c(0, 8, 24, 74, 240, 242, 244))
})
})
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context("time-after")
describe("time after criteria works", {
# real world type example
it("after event flag", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 100, 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- c(0, 24, 240, 242)
expect_equal(time_after_criteria(input,"TAEV", EVID == 2)$TAEV, output)
})
it("before first event flag should be zero", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 2, 0, 0.5,
1, "01/11/2017 12:00", "A", 100, 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output <- c(0, 0, 0, 2)
expect_equal(time_after_criteria(input,"TAEV", EVID == 2)$TAEV, output)
})
})
describe("time after first dose works", {
# real world type example
it("works for time after first dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 0, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 4, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output=c(0, 8, 24, 74, 240, 242, 244)
expect_equal(time_after_first_dose(input)$TAFD, output)
expect_equal(time_after_first_dose(input, .criteria=AMT>0)$TAFD, output-24)
expect_equal(time_after_first_dose(input, .name = "tafd")$tafd, output)
input <- input %>% rename(ELTM=TIME)
expect_equal(time_after_first_dose(input,.time="ELTM")$TAFD, output)
})
it("can select different baseline (EVID==4)", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 0, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 4, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
output=c(-240, -232, -216, -166, 0, 2, 4)
expect_equal(time_after_first_dose(input,.time="TIME", .criteria=EVID==4)$TAFD, output)
})
it("works for time after dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_after_dose(input)$TAD, c(0, 8, 0, 0, 0))
})
# it("works for time after dose with excluded dose", {
# input <- tibble::tribble(
# ~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE, EXCL,
# 1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3, 1,
# 1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3, 0,
# 1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5, 0,
# 1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5, 0,
# 1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5, 0
# ) %>% dplyr::mutate(
# TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
# )
# expect_equal(time_after_dose(input, .excl=EXCL==1)$TAD, c(0, 8, 0, 2, 4))
# })
it("works for time after dose with expanding addl", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 0, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 4, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_after_dose(input)$TAD, c(0, 8, 0, 2, 0, 0, 0))
expect_equal(time_after_dose(input, .criteria = AMT>0)$TAD, c(0, 8, 0, 2, 0, 2, 4))
})
it("works for time after dose with expanding addl and ADDL=NA in obs", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 0, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 4, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = iso_to_posix(TIME),
ADDL = ifelse(EVID!=1,NA,ADDL)
)
expect_equal(time_after_dose(input)$TAD, c(0, 8, 0, 2, 0, 0, 0))
expect_equal(time_after_dose(input, .criteria = AMT>0)$TAD, c(0, 8, 0, 2, 0, 2, 4))
})
it("works for time after dose with expanding addl and predose obs giving negative TAD", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 09:15", "A", 0 , 0, 0, 0, 0.3,
1, "01/01/2017 09:45", "A", 0 , 0, 0, 0, 0.3,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 0, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 0, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 4, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = iso_to_posix(TIME)
)
expect_equal(time_after_dose(input)$TAD,
c(-.75, -.25, 0, 8, 0, 2, 0, 0, 0))
expect_equal(time_after_dose(input, .criteria = AMT>0)$TAD,
c(-.75, -.25, 0, 8, 0, 2, 0, 2, 4))
})
it("works for time of first dose", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_of_first_dose(input)$FDDTTM, rep(input$TIME[1],7))
})
it("works for time of first dose with addnl criteria", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(time_of_first_dose(input,"FDDTTM",AMT>0 & II>0)$FDDTTM, rep(input$TIME[3],7))
})
})
describe("relative time works", {
# real world type example
it("works creating RTIME column", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(relative_time(input)$RTIME, c(0, 8, 24, 74, 240, 242, 244))
})
it("works to overwrite TIME column", {
input <- tibble::tribble(
~ID, ~TIME, ~TRT, ~AMT, ~II, ~EVID, ~ADDL, ~CRE,
1, "01/01/2017 10:00", "A", 100, 0, 1, 0, 0.3,
1, "01/01/2017 18:00", "A", 0 , 0, 2, 0, 0.3,
1, "01/02/2017 10:00", "A", 100, 24, 1, 8, 0.2,
1, "01/04/2017 12:00", "A", 0 , 24, 2, 0, 0.2,
1, "01/11/2017 10:00", "A", 100, 0, 1, 0, 0.5,
1, "01/11/2017 12:00", "A", 0 , 0, 1, 0, 0.5,
1, "01/11/2017 14:00", "A", 0 , 0, 1, 0, 0.5
) %>% dplyr::mutate(
TIME = as.POSIXct(anytime::anytime(TIME, tz = "UTC", asUTC = TRUE), origin = "1970-01-01")
)
expect_equal(relative_time(input, .name = "TIME")$TIME, c(0, 8, 24, 74, 240, 242, 244))
})
})
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