require(dplyr)
rxodeTest(
{
.rx <- loadNamespace("RxODE")
for (radi in c(1, 2)) {
.rx$forderForceBase(switch(radi,
TRUE,
FALSE
))
radix <- switch(radi,
"base::order",
"data.table::forder"
)
context(sprintf("Test event Table et(...) sort:%s", radix))
if (requireNamespace("units", quietly = TRUE)) {
library(units)
}
library(dplyr)
et <- et()
test_that("Empty event table check", {
## expect_equal(class(et$env),"rxHidden")
expect_equal(et$nobs, 0L)
expect_equal(et$ndose, 0L)
expect_equal(et$get.EventTable(), NULL)
expect_equal(et$get.dosing(), NULL)
expect_equal(et$get.sampling(), NULL)
})
et <- et(1:10)
test_that("10 sample items", {
expect_equal(et$nobs, 10L)
expect_equal(et$ndose, 0L)
expect_equal(class(et$get.EventTable()), "data.frame")
expect_true(is(et, "rxEt"))
expect_false(et$show["id"])
expect_false(et$show["cmt"])
expect_equal(et$get.dosing(), NULL)
expect_equal(length(et$get.sampling()$time), 10)
})
et <- et(1:10, "matt")
test_that("compartment check", {
expect_equal(et$nobs, 10L)
expect_equal(et$ndose, 0L)
expect_equal(class(et$get.EventTable()), "data.frame")
expect_true(is(et, "rxEt"))
expect_false(et$show["id"])
expect_true(et$show["cmt"])
expect_equal(et$get.dosing(), NULL)
expect_equal(length(et$get.sampling()$time), 10)
})
et <- et(1:10, cmt = 1)
test_that("compartment check", {
expect_equal(et$nobs, 10L)
expect_equal(et$ndose, 0L)
expect_equal(class(et$get.EventTable()), "data.frame")
expect_true(is(et, "rxEt"))
expect_false(et$show["id"])
expect_true(et$show["cmt"])
expect_equal(et$get.dosing(), NULL)
expect_equal(length(et$get.sampling()$time), 10)
expect_true(all(et$cmt == 1L))
})
et1 <- et(1:10, id = 1:10)
test_that("Observation only table check", {
expect_equal(et1$nobs, 100L)
expect_equal(et1$ndose, 0L)
expect_equal(class(et1$get.EventTable()), "data.frame")
expect_true(is(et1, "rxEt"))
expect_true(et1$show["id"])
expect_false(et1$show["cmt"])
expect_equal(et1$get.dosing(), NULL)
expect_equal(length(et1$get.sampling()$time), 100)
})
## now resize down
et2 <- et1 %>% et(id = -(2:10))
test_that("compartment check", {
expect_equal(et2$nobs, 10L)
expect_equal(et2$ndose, 0L)
expect_equal(class(et2$get.EventTable()), "data.frame")
expect_true(is(et, "rxEt"))
expect_true(et2$show["id"])
expect_false(et2$show["cmt"])
expect_equal(et2$get.dosing(), NULL)
expect_equal(length(et2$get.sampling()$time), 10)
})
## now resize back up
et3 <- et2 %>% et(id = 1:10)
test_that("Using simulate with et without windows will warn", {
f1 <- as.data.frame(et3)
f2 <- suppressWarnings({
as.data.frame(simulate(et3))
})
expect_equal(f1$time, f2$time)
expect_warning(simulate(et3))
})
eti <- et(amt = 10) %>% et(id = 2:3)
eti1 <- et(amt = 10, id = 3:4)
eti2 <- et(amt = 10, id = 3)
eti3 <- et(10, id = 3:4)
eti4 <- et(10, id = 3)
eti5 <- et(10) %>% et(id = 2:3)
eti6 <- et(amt = 10) %>% et(id = 2)
eti7 <- et(10) %>% et(id = 2)
eti8 <- et(10, id = 1)
eti9 <- et(10) %>% et(id = 1)
eti10 <- et(amt = 10, id = 1)
eti11 <- et(amt = 10) %>% et(id = 1)
## Now look at windows
eti12 <- et(list(c(10, 11)), id = 1)
eti13 <- et(list(c(10, 11))) %>% et(id = 1)
eti14 <- et(list(c(10, 11)), amt = 10, id = 1)
eti15 <- et(list(c(10, 11)), amt = 10) %>% et(id = 1)
eti16 <- et(list(c(10, 11)), id = 2)
eti17 <- et(list(c(10, 11))) %>% et(id = 2)
eti18 <- et(list(c(10, 11)), amt = 10, id = 2)
eti19 <- et(list(c(10, 11)), amt = 10) %>% et(id = 2)
eti20 <- et(list(c(10, 11)), id = 2:3)
eti21 <- et(list(c(10, 11))) %>% et(id = 2:3)
eti22 <- et(list(c(10, 11)), amt = 10, id = 2:3)
eti23 <- et(list(c(10, 11)), amt = 10) %>% et(id = 2:3)
## Now do it with dosing/sampling windows
test_that("Make sure that et only has IDs 2 and 3.", {
expect_equal(eti$id, 2:3)
expect_equal(eti1$id, 3:4)
expect_equal(eti2$id, 3)
expect_equal(eti3$id, 3:4)
expect_equal(eti4$id, 3)
expect_equal(eti5$id, 2:3)
expect_equal(eti6$id, 2)
expect_equal(eti7$id, 2)
expect_equal(eti8$id, 1)
expect_true(eti8$env$show["id"])
expect_equal(eti9$id, 1)
expect_true(eti9$env$show["id"])
expect_equal(eti10$id, 1)
expect_true(eti10$env$show["id"])
expect_equal(eti11$id, 1)
expect_true(eti11$env$show["id"])
expect_equal(eti12$id, 1)
expect_true(eti12$env$show["id"])
expect_equal(eti13$id, 1)
expect_true(eti13$env$show["id"])
expect_equal(eti14$id, 1)
expect_true(eti14$env$show["id"])
expect_equal(eti15$id, 1)
expect_true(eti15$env$show["id"])
expect_equal(eti16$id, 2)
expect_true(eti16$env$show["id"])
expect_equal(eti17$id, 2)
expect_true(eti17$env$show["id"])
expect_equal(eti18$id, 2)
expect_true(eti18$env$show["id"])
expect_equal(eti19$id, 2)
expect_true(eti19$env$show["id"])
expect_equal(eti20$id, 2:3)
expect_true(eti20$env$show["id"])
expect_equal(eti21$id, 2:3)
expect_true(eti21$env$show["id"])
expect_equal(eti22$id, 2:3)
expect_true(eti22$env$show["id"])
expect_equal(eti23$id, 2:3)
expect_true(eti23$env$show["id"])
})
test_that("Observation only table check", {
expect_equal(et1$nobs, 100L)
expect_equal(et1$ndose, 0L)
expect_equal(class(et1$get.EventTable()), "data.frame")
expect_true(is(et1, "rxEt"))
expect_true(et1$show["id"])
expect_false(et1$show["cmt"])
expect_equal(et1$get.dosing(), NULL)
expect_equal(length(et1$get.sampling()$time), 100)
})
## Check adding different units of time, rate, amt work
if (requireNamespace("units", quietly = TRUE)) {
et3 <- et3 %>% set_units(mg)
## Make sure units are right.
test_that("units tests", {
library(units)
e <- et(amount.units = "mg", time_units = "hr") %>%
add.sampling(seq(0, 24, by = 3)) %>%
add.dosing(1, 3) %>%
et(rate = 3, amt = 2, time = 120)
e2 <- e %>% et(amt = set_units(0.0003, "lb"), time = 0.5)
expect_equal(e2$amt[e2$time == set_units(0.5, hr)], set_units(set_units(0.0003, lb), mg))
e2 <- e %>% et(set_units(30, min))
expect_true(any(e2$time == set_units(0.5, hr)))
e2 <- e %>% et(time = 0.25, rate = set_units(30, ug / min), amt = set_units(4, ug))
tmp <- e2[e2$time == set_units(0.25, hr), ]
expect_equal(set_units(1.8, mg / h), tmp$rate)
expect_equal(set_units(0.004, mg), tmp$amt)
e2 <- e %>% et(time = 0.25, ii = set_units(30, min), amt = 4, addl = 4)
expect_equal(e2$ii[e2$time == set_units(0.25, hr)], set_units(0.5, hr))
## Check importing wrong different ii and time units as well as different rate units work.
e <- et(amount.units = "mg", time_units = "hr") %>%
add.sampling(seq(0, 24, by = 3)) %>%
add.dosing(1, 3) %>%
et(rate = 3, amt = 2, time = 120)
etDf <- as.data.frame(e)
etDf$rate <- set_units(etDf$rate, ug / s)
etDf$ii <- set_units(etDf$ii, min)
et <- et()
et$import.EventTable(etDf)
expect_equal(et$ii, e$ii)
expect_equal(et$rate, e$rate)
})
}
test_that("seq works with wait", {
e1 <- et(amt = 100, ii = 24, addl = 6)
e2 <- et(amt = 200, ii = 24, addl = 6)
e3 <- seq(e1, e2, e1)
e4 <- seq(e1, wait = 72, e2, wait = 72, e1) %>% as.data.frame()
expect_equal(structure(list(
time = c(0, 216, 432),
amt = c(100, 200, 100),
ii = c(24, 24, 24),
addl = c(6L, 6L, 6L),
evid = c(1L, 1L, 1L)
),
class = "data.frame",
row.names = c(NA, -3L)
), e4)
e5 <- etSeq(e1, wait = 72, e2, wait = 72, e1, waitII = "+ii") %>%
as.data.frame()
expect_equal(structure(list(
time = c(0, 240, 480),
amt = c(100, 200, 100),
ii = c(24, 24, 24),
addl = c(6L, 6L, 6L),
evid = c(1L, 1L, 1L)
),
class = "data.frame",
row.names = c(NA, -3L)
), e5)
e1 <- et(amt = 500)
e2 <- et(amt = 250, ii = 24, addl = 4)
expect_equal(
structure(list(
time = c(0, 24),
amt = c(500, 250),
ii = c(0, 24),
addl = c(0L, 4L),
evid = c(1L, 1L)
),
class = "data.frame",
row.names = c(NA, -2L)
),
c(e1, e2) %>% as.data.frame()
)
expect_equal(
structure(list(
time = c(0, 120, 144),
amt = c(250, 500, 250),
ii = c(24, 0, 24),
addl = c(4L, 0L, 4L),
evid = c(1L, 1L, 1L)
),
class = "data.frame",
row.names = c(NA, -3L)
),
c(e2, e1, e2) %>% as.data.frame()
)
e3 <- et(amt = 200)
expect_warning(c(e1, e3))
e4 <- suppressWarnings(c(e1, e3) %>% as.data.frame())
expect_equal(
structure(list(
time = c(0, 24),
amt = c(500, 200),
ii = c(0, 0),
addl = c(0L, 0L),
evid = c(1L, 1L)
),
class = "data.frame",
row.names = c(NA, -2L)
),
e4
)
e4 <- suppressWarnings(c(e1, e3, ii = 12) %>% as.data.frame())
expect_equal(
structure(list(
time = c(0, 12),
amt = c(500, 200),
ii = c(0, 0),
addl = c(0L, 0L),
evid = c(1L, 1L)
),
class = "data.frame",
row.names = c(NA, -2L)
),
e4
)
e1 <- et(amt = 100, ii = 24, addl = 6) %>%
et(seq(0, 2 * 168, by = 0.1))
e2 <- c(e1, e1, samples = "use")
expect_equal(range(e2$time), c(0, 672))
## combine without changing, use rbind
e1 <- et(amt = 100, ii = 24, addl = 6, ID = 1:5)
e2 <- et(amt = 50, ii = 12, addl = 13, ID = 1:3)
e3 <- et(amt = 200, ii = 24, addl = 2, ID = 1:2)
e4 <- rbind(e1, e2, e3)
expect_equal(
e4 %>% select(id, time, amt, ii, addl) %>% as.data.frame(),
structure(list(
id = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 4L, 5L),
time = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
amt = c(100, 50, 200, 100, 50, 200, 100, 50, 100, 100),
ii = c(24, 12, 24, 24, 12, 24, 24, 12, 24, 24),
addl = c(6L, 13L, 2L, 6L, 13L, 2L, 6L, 13L, 6L, 6L)
),
class = "data.frame",
row.names = c(NA, -10L)
)
)
e4 <- rbind(e1, e2, e3, id = "unique")
expect_equal(
e4 %>% select(id, time, amt, ii, addl) %>% as.data.frame(),
structure(list(
id = 1:10,
time = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
amt = c(100, 100, 100, 100, 100, 50, 50, 50, 200, 200),
ii = c(24, 24, 24, 24, 24, 12, 12, 12, 24, 24),
addl = c(6L, 6L, 6L, 6L, 6L, 13L, 13L, 13L, 2L, 2L)
),
class = "data.frame",
row.names = c(NA, -10L)
)
)
})
## FIXME test windows and dur
test_that("no ii throws an error with addl", {
expect_error(et(c(11, 13), amt = 10, addl = 3))
})
## Test Windows
et <- et(list(
c(0, 1),
c(1, 4),
c(4, 8),
c(8, 12),
c(12, 24)
)) %>%
et(amt = 10) %>%
et(c(11, 13), amt = 10, addl = 3, ii = 12)
test_that("Using simulate with et works and gives a different data frame", {
et2 <- as.data.frame(simulate(et))
et1 <- as.data.frame(et)
expect_false(all(et1$time == et2$time))
et3 <- as.data.frame(et)
expect_true(all(et1$time == et3$time))
et$simulate()
et3 <- as.data.frame(et)
expect_false(all(et1$time == et3$time))
})
test_that("Low/High middle tests; i.e windows", {
et2 <- et[which(!is.na(et$low)), ]
expect_true(et$show["low"])
expect_true(et$show["high"])
expect_true(all(et2$time < et2$high))
expect_true(all(et2$time > et2$low))
})
et <- et(list(
c(0, 1),
c(1, 4),
c(4, 8),
c(8, 12),
c(12, 24)
), cmt = 1) %>%
et(amt = 10) %>%
et(c(11, 13), amt = 10, addl = 3, ii = 12)
test_that("Low/High middle tests; i.e windows", {
et2 <- et[which(!is.na(et$low)), ]
expect_true(et$show["low"])
expect_true(et$show["high"])
expect_true(all(et2$time < et2$high))
expect_true(all(et2$time > et2$low))
})
test_that("Window Errors", {
expect_error(et(list(c(1, 0))))
expect_error(et(list(c(0, 1, 2))))
})
context("until is inclusive")
test_that("until is inclusive", {
expect_equal(et(amt = 1, time = 50, until = 57.5, ii = 1.5)$addl, 5)
expect_equal(et(amt = 1, time = 50, until = 57.49999, ii = 1.5)$addl, 4)
expect_equal(et(amt = 1, time = 50, until = 57.50001, ii = 1.5)$addl, 5)
})
context("et Expected errors")
test_that("et errors", {
expect_error(et(list(c(2, 1), c(3, 4)), amt = 3))
expect_error(et(list(c(1, 2), 3, c(1, 2, 3)), amt = 3))
expect_error(et(list(c(1, 2), 3, TRUE), amt = 3))
})
context("et steady state constant infusion")
test_that("et steady state constant infusion", {
expect_error(et(amt = 0, rate = 10, ii = 0, ss = 2))
expect_error(et(amt = 0, rate = 10, ii = 2, ss = 1))
expect_error(et(amt = 0, rate = -2, ii = 0, ss = 1))
expect_error(et(rate = 10, ii = 0, ss = 2))
expect_error(et(rate = 10, ii = 2, ss = 1))
expect_error(et(rate = -2, ii = 0, ss = 1))
t1 <- et(amt = 0, rate = 10, ii = 0, ss = 1) %>% as.data.frame()
t2 <- et(rate = 10, ii = 0, ss = 1) %>% as.data.frame()
expect_equal(t1, t2)
t1 <- et(amt = 0, rate = -1, ii = 0, ss = 1) %>% as.data.frame()
t2 <- et(rate = -1, ii = 0, ss = 1) %>% as.data.frame()
expect_equal(t1, t2)
})
context("et addl")
test_that("et addl expand", {
ev <- et(amt = 3, ii = 24, until = 120)
tmp <- etExpand(ev)
expect_equal(ev$amt, 3)
expect_equal(tmp$time, c(0, 24, 48, 72, 96, 120))
ev$expand()
expect_equal(ev$time, c(0, 24, 48, 72, 96, 120))
})
ev <- et(amt = 3, ii = 24, until = 120) %>% et(amt = 3, rate = dur)
context("conversion to common data frame types")
## test_that("data.table conversion", {
## library(data.table)
## tmp <- data.table(ev)
## expect_equal(names(tmp), c("time", "amt", "rate", "ii", "addl", "evid"))
## expect_false(inherits(tmp$rate, "rxRateDur"))
## expect_false(inherits(tmp$evid, "rxEvid"))
## })
test_that("data.frame conversion", {
tmp <- data.frame(ev)
expect_equal(names(tmp), c("time", "amt", "rate", "ii", "addl", "evid"))
expect_false(inherits(tmp$rate, "rxRateDur"))
expect_false(inherits(tmp$evid, "rxEvid"))
})
test_that("tibble conversion", {
tmp <- tibble::as_tibble(ev)
expect_equal(names(tmp), c("time", "amt", "rate", "ii", "addl", "evid"))
expect_false(inherits(tmp$rate, "rxRateDur"))
expect_false(inherits(tmp$evid, "rxEvid"))
})
}
context("seq() arguments work; See #97")
test_that("seq() args", {
et1 <- et() %>% add.sampling(seq(0, 24, by = 3))
et2 <- et(from = 0, to = 24, by = 3)
expect_equal(et1$time, et2$time)
})
test_that("errors", {
expect_error(et(ii = 12, dosing.interval = 14))
expect_error(et(dose = 4, amt = 3))
expect_error(et(cmt = 1, dosing.to = 3))
expect_error(et(cmt = 1, dose.to = 3))
expect_error(et(cmt = 1, state = 3))
expect_error(et(amt.units = "mg", dose.units = "mg"))
expect_error(et(time.units = "mg", timeUnits = "mg"))
expect_error(et(time = 4, start.time = 5))
expect_error(et(nbr.doses = 4, nbrDoses = 5))
expect_error(et(dur = 4, duration = 5))
})
context("Issue #192 zero dose")
test_that("dose=0 is OK", {
ev1 <- et(amt = 0, time = 10)
ev2 <- eventTable()
ev2$add.dosing(dose = 0, start.time = 10)
expect_equal(ev1, ev2)
})
context("Issue #236 math in to/from")
test_that("Issue #236", {
expect_error(et(from = 0, to = 168 * 2 * 6, length.out = 168 * 2 * 6 + 1), NA)
})
context("Issue #257 -- numeric cmt vectorized")
test_that("Issue #257", {
ds4 <- c(1, 2, 3, 4)
rate <- c(1.5, 2.5, 3.5, 4.5)
expect_error(et() %>% et(amt = ds4, rate = rate, cmt = 4), NA)
})
if (requireNamespace("units", quietly = TRUE)) {
test_that("etRep #313", {
sch1 <- et(timeUnits = "hr") %>%
et(amt = 100, ii = 24, until = set_units(2, "days"))
toto <- rep(sch1, times = 10, wait = set_units(19, "days"))
expect_equal(toto$time, seq(0, by = 504, length.out = 10))
sch1 <- et(timeUnits = "hr") %>%
et(amt = 100, ii = 24, until = set_units(2, "days")) %>%
etExpand()
toto1 <- etExpand(toto)
toto <- expect_warning(rep(sch1, times = 10, wait = set_units(19, "days")))
})
}
test_that("'by' and 'length.out'", {
expect_error(et(0, 3, by = 0.5, length.out = 3))
})
test_that("'amt' and 'time' have different values", {
expect_error(et(amt = c(1, 2), time = c(1, 3, 4)))
})
test_that("'time' with invalid list", {
expect_error(et(time = list(1, 2, 3)))
})
test_that("'is' for RxODE event tables are 'rxEt'", {
ev <- et()
expect_true(is(ev, "rxEt"))
})
},
silent = TRUE,
test = "lvl2"
)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.