tests/testthat/testDataset.R
In Calvagone/campsis: Generic PK/PD Simulation Platform CAMPSIS
library(testthat)
context("Test all methods from the dataset class")
seed <- 1
source(paste0("", "testUtils.R"))
test_that("Set subjects works as expected", {
dataset <- Dataset() %>% setSubjects(3)
expect_equal(dataset %>% length(), 3)
expect_equal(dataset@arms %>% length(), 1)
dataset <- Dataset(2) %>% setSubjects(5)
expect_equal(dataset %>% length(), 5)
expect_equal(dataset@arms %>% length(), 1)
expect_error(Dataset() %>% setSubjects(c(10,20)), regexp="x must be the same length as the number of arms in dataset")
dataset <- Dataset() %>%
add(c(Arm(subjects=5), Arm(subjects=5)))
dataset <- dataset %>%
setSubjects(c(10,20))
expect_equal(dataset@arms@list[[1]] %>% length(), 10)
expect_equal(dataset@arms@list[[2]] %>% length(), 20)
expect_equal(dataset %>% length(), 30)
})
test_that("Add entry, order, filter, getTimes (simple example)", {
dataset <- Dataset()
# Add doses
dataset <- dataset %>% add(Bolus(time=0, amount=100))
dataset <- dataset %>% add(Bolus(time=24, amount=100))
dataset <- dataset %>% add(Bolus(time=48, amount=100))
# Add observations
dataset <- dataset %>% add(Observations(times=seq(0, 48, by=4)))
# Get times
expect_equal(dataset %>% getTimes(), seq(0, 48, by=4))
# Export to RxODE
table1 <- dataset %>% export(dest="RxODE")
expect_equal(nrow(table1), 16)
expect_true(is(table1, "tbl_df"))
# Export to mrgsolve
table2 <- dataset %>% export(dest="mrgsolve")
expect_equal(nrow(table2), 16)
expect_true(is(table2, "tbl_df"))
})
test_that("Two arms example", {
# Create 2 arms
arm1 <- Arm(id=1, subjects=4)
arm2 <- Arm(id=2, subjects=3)
# Add doses in respective arms
arm1 <- arm1 %>% add(Bolus(time=0, amount=100))
arm2 <- arm2 %>% add(Bolus(time=0, amount=200))
# Add observations
obs <- Observations(times=seq(0, 48, by=4))
arm1 <- arm1 %>% add(obs)
arm2 <- arm2 %>% add(obs)
# Create dataset
dataset <- Dataset()
dataset <- dataset %>% add(arm1)
dataset <- dataset %>% add(arm2)
# Total number of subjects
expect_equal(dataset %>% length(), 7)
# Arms number
expect_equal(length(dataset@arms), 2)
# Export to RxODE
table <- dataset %>% export(dest="RxODE")
expect_equal(nrow(table), 98)
# Replace numbers of subjects in second arm
arm2Bis <- dataset@arms %>% getByIndex(2)
arm2Bis@subjects <- as.integer(5)
dataset <- dataset %>% replace(arm2Bis)
# Total number of subjects
expect_equal(dataset %>% length(), 9)
})
test_that("Export using config", {
dataset <- Dataset()
# Add doses
dataset <- dataset %>% add(Bolus(time=0, amount=100))
dataset <- dataset %>% add(Bolus(time=24, amount=100))
dataset <- dataset %>% add(Bolus(time=48, amount=100))
# Add observations
dataset <- dataset %>% add(Observations(times=seq(0, 48, by=10)))
# Export to RxODE
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
expect_true(all(c(1,2) %in% table$CMT))
})
test_that("Export constant covariates work well (N=1, N=2)", {
dataset <- Dataset()
# Add doses
dataset <- dataset %>% add(Bolus(time=0, amount=100))
dataset <- dataset %>% add(Bolus(time=24, amount=100))
dataset <- dataset %>% add(Bolus(time=48, amount=100))
# Add covariate
dataset <- dataset %>% add(Covariate(name="WT", 70))
dataset <- dataset %>% add(Covariate(name="HT", 180))
dataset <- dataset %>% add(EventCovariate(name="DOSE", 100))
expect_equal(dataset %>% getCovariates() %>% getNames(), c("WT", "HT", "DOSE"))
expect_equal(dataset %>% getEventCovariates() %>% getNames(), c("DOSE"))
# Add observations
dataset <- dataset %>% add(Observations(times=seq(0, 48, by=10)))
# Export to RxODE N=1
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
expect_true(all(table$WT==70))
expect_true(all(table$HT==180))
expect_true(all(table$DOSE==100)) # Even if covariate can be adapted by events
# Export to RxODE N=2
arm <- dataset@arms %>% default()
arm@subjects <- as.integer(2)
dataset@arms <- dataset@arms %>% replace(arm)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
expect_true(all(table$WT==70))
expect_true(all(table$HT==180))
expect_true(all(table$DOSE==100)) # Even if covariate can be adapted by events
})
test_that("Export fixed covariates work well (N=3)", {
arm <- Arm(id=1, subjects=3)
# Add doses
arm <- arm %>% add(Bolus(time=0, amount=100))
arm <- arm %>% add(Bolus(time=24, amount=100))
arm <- arm %>% add(Bolus(time=48, amount=100))
# Add covariate
arm <- arm %>% add(Covariate(name="WT", FixedDistribution(values=c(65, 70, 75))))
arm <- arm %>% add(Covariate(name="HT", FixedDistribution(values=c(175, 180, 185))))
# Add observations
arm <- arm %>% add(Observations(times=seq(0, 48, by=10)))
dataset <- Dataset()
dataset <- dataset %>% add(arm)
# Export to RxODE N=1
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
subTable <- table %>% dplyr::select(ID, WT, HT) %>% dplyr::distinct()
expect_equal(subTable, tibble::tibble(ID=c(1,2,3), WT=c(65,70,75), HT=c(175,180,185)))
})
test_that("Export function covariates work well (N=3)", {
arm <- Arm(id=1, subjects=3)
# Add doses
arm <- arm %>% add(Bolus(time=0, amount=100))
arm <- arm %>% add(Bolus(time=24, amount=100))
arm <- arm %>% add(Bolus(time=48, amount=100))
# Add covariate
arm <- arm %>% add(Covariate(name="WT", FunctionDistribution(fun="rnorm", args=list(mean=70, sd=10))))
arm <- arm %>% add(Covariate(name="HT", FunctionDistribution(fun="rnorm", args=list(mean=180, sd=20))))
# Add observations
arm <- arm %>% add(Observations(times=seq(0, 48, by=10)))
dataset <- Dataset()
dataset <- dataset %>% add(arm)
# Export to RxODE N=1
config <- new("dataset_config", def_depot_cmt=as.integer(1), def_obs_cmt=as.integer(2))
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE", seed=1)
subTable <- table %>% dplyr::select(ID, WT, HT) %>% dplyr::distinct() %>% dplyr::mutate(WT=round(WT), HT=round(HT))
expect_equal(subTable, tibble::tibble(ID=c(1,2,3), WT=c(64,72,62), HT=c(212,187,164)))
})
test_that("Export boostrap covariates work well (N=8)", {
arm <- new("arm", id=as.integer(1), subjects=as.integer(8))
# Add doses
arm <- arm %>% add(Bolus(time=0, amount=100))
arm <- arm %>% add(Bolus(time=24, amount=100))
arm <- arm %>% add(Bolus(time=48, amount=100))
# Add covariate
arm <- arm %>% add(Covariate("WT", BootstrapDistribution(data=c(65, 70, 75), random=TRUE, replacement=TRUE)))
arm <- arm %>% add(Covariate("HT", BootstrapDistribution(data=c(175, 180, 185), random=TRUE, replacement=TRUE)))
# Add observations
arm <- arm %>% add(Observations(times=seq(0, 48, by=10)))
dataset <- Dataset()
dataset <- dataset %>% add(arm)
# Export to RxODE
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE", seed=1)
subTable <- table %>% dplyr::select(ID, WT, HT) %>% dplyr::distinct()
expect_equal(subTable, tibble::tibble(ID=c(1,2,3,4,5,6,7,8), WT=c(65,75,65,70,65,75,75,70), HT=c(180,185,185,175,175,175,180,180)))
})
test_that("Export occasions works well - example 1", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 60, by=10)))
# Add occasions
ds <- ds %>% add(Occasion("MY_OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# All OCC values are used because 3 doses
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,3,3,3), 2))
})
test_that("Export occasions works well - example 2", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 60, by=10)))
# Add occasions
ds <- ds %>% add(Occasion("MY_OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Check value 3 is not used (no 3rd dose)
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,2,2), 2))
})
test_that("Export occasions works well - example 3", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(Occasion("MY_OCC", values=c(1,2,4), doseNumbers=c(1,2,4)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# All OCC values are used because 3 doses
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,2,2,2,2,4,4), 2))
})
test_that("Export occasions works well - example 4", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(Occasion("MY_OCC", values=c(2,3,4), doseNumbers=c(2,3,4)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Is this the expected behaviour ? This is arbitrary, for sure
expect_equal(table$MY_OCC, rep(c(0,0,0,0,2,2,2,3,3,3,3,4,4), 2))
})
test_that("Occasion can be added into arms", {
addProtocol <- function(x) {
# Add doses
x <- x %>% add(Bolus(time=0, amount=100))
x <- x %>% add(Bolus(time=24, amount=100))
x <- x %>% add(Bolus(time=48, amount=100))
# Add observations
x <- x %>% add(Observations(times=seq(0, 60, by=10)))
# Add occasions
x <- x %>% add(Occasion("MY_OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
}
arm1 <- Arm(id=1, subjects=1) %>% addProtocol()
arm2 <- Arm(id=2, subjects=1) %>% addProtocol()
ds <- Dataset() %>% add(c(arm1, arm2))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# All OCC values are used because 3 doses
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,3,3,3), 2))
})
test_that("Export IOV works well - example 1", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(IOV("IOV_KA", distribution=NormalDistribution(0, sd=1), doseNumbers=c(3,4)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Arbitrary but OK
expect_equal(round(table$IOV_KA,2), c(0,0,0,0,0,0,0,-0.63,-0.63,-0.63,-0.63,0.18,0.18,0,0,0,0,0,0,0,-0.84,-0.84,-0.84,-0.84,1.60,1.60))
})
test_that("Export IOV works well - example 2", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(IOV("IOV_KA", distribution=NormalDistribution(0, sd=1), doseNumbers=c(1,3)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Arbitrary but OK
expect_equal(round(table$IOV_KA,2), c(-0.63,-0.63,-0.63,-0.63,-0.63,-0.63,-0.63,0.18,0.18,0.18,0.18,0.18,0.18,-0.84,-0.84,-0.84,-0.84,-0.84,-0.84,-0.84,1.60,1.60,1.60,1.60,1.60,1.60))
})
test_that("Replace, delete, find, contains methods works well", {
ds <- Dataset(1)
# Add 3 doses
ds <- ds %>% add(Bolus(time=c(0,24,48), amount=100))
# Add observations
ds <- ds %>% add(Observations(c(1,2,3)))
# Add IOV
ds <- ds %>% add(IOV("IOV_KA", distribution=c(1,2,3)))
# Add occasions
ds <- ds %>% add(Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
# Add covariate
ds <- ds %>% add(Covariate("WT", 0))
# Add dose adaptation
ds <- ds %>% add(DoseAdaptation("AMT*2", compartments=1))
# Double the first dose
updatedDs <- ds %>% replace(Bolus(time=0, amount=200))
expect_true(updatedDs %>% contains(Bolus(time=0, amount=0))) # Only time matters
expect_equal((updatedDs %>% find(Bolus(time=0, amount=0)))@amount, 200)
# Change IOV distribution
updatedDs <- ds %>% replace(IOV("IOV_KA", distribution=c(1,2,3,4)))
expect_true(updatedDs %>% contains(IOV("IOV_KA", 0))) # Only name matters
expect_equal((updatedDs %>% find(IOV("IOV_KA", 0)))@distribution, FixedDistribution(c(1,2,3,4)))
# Change occasion numbers
updatedDs <- ds %>% replace(Occasion("OCC", values=c(1,2), doseNumbers=c(1,2)))
expect_true(updatedDs %>% contains(Occasion("OCC", 0, 0))) # Only name matters
expect_equal((updatedDs %>% find(Occasion("OCC", 0, 0)))@values, c(1,2))
# Change covariate value
updatedDs <- ds %>% replace(Covariate("WT", 1))
expect_true(updatedDs %>% contains(Covariate("WT", 0))) # Only name matters
expect_equal((updatedDs %>% find(Covariate("WT", 0)))@distribution, ConstantDistribution(1))
# Adapt dose adaptation formula
updatedDs <- ds %>% replace(DoseAdaptation("AMT*3", compartments=1))
expect_true(updatedDs %>% contains(DoseAdaptation("", compartments=1))) # Only compartments matters
expect_equal((updatedDs %>% find(DoseAdaptation("", compartments=1)))@formula, "AMT*3")
# Delete the last dose
bolus <- Bolus(time=48, amount=100)
expect_true(ds %>% contains(bolus))
updatedDs <- ds %>% delete(bolus)
expect_false(updatedDs %>% contains(bolus))
# Delete IOV
iov <- IOV("IOV_KA", distribution=c(1,2,3))
expect_true(ds %>% contains(iov))
updatedDs <- ds %>% delete(iov)
expect_false(updatedDs %>% contains(iov))
# Delete occasions
occ <- Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3))
expect_true(ds %>% contains(occ))
updatedDs <- ds %>% delete(occ)
expect_false(updatedDs %>% contains(occ))
# Delete covariate
cov <- Covariate("WT", 0)
expect_true(ds %>% contains(cov))
updatedDs <- ds %>% delete(cov)
expect_false(updatedDs %>% contains(cov))
# Delete observations
obs <- Observations(c(1,2,3))
expect_true(ds %>% contains(obs))
updatedDs <- ds %>% delete(obs)
expect_false(updatedDs %>% contains(obs))
# Delete dose adaptation
doseAdaptation <- DoseAdaptation("", compartments=1)
expect_true(ds %>% contains(doseAdaptation))
updatedDs <- ds %>% delete(doseAdaptation)
expect_false(updatedDs %>% contains(doseAdaptation))
})
test_that("Export works well even if objects are defined in a different order", {
regFilename <- "objects_defined_in_different_order"
arm1 <- Arm(1, subjects=1) %>%
add(Bolus(time=0, amount=1000, compartment=1, ii=24, addl=2)) %>%
add(Observations(times=seq(0,72, by=5))) %>%
add(TimeVaryingCovariate("TVCOV", data.frame(TIME=c(0, 10), VALUE=c(10, 15)))) %>%
add(Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3))) %>%
add(Covariate("BW", 70)) %>%
add(Covariate("HT", 180))
arm2 <- Arm(2, subjects=1) %>%
add(Covariate("HT", 170)) %>%
add(Covariate("BW", 60)) %>%
add(Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3))) %>%
add(TimeVaryingCovariate("TVCOV", data.frame(TIME=c(0, 10), VALUE=c(9, 14)))) %>%
add(Observations(times=seq(0,72, by=5))) %>%
add(Bolus(time=0, amount=2000, compartment=1, ii=24, addl=2))
ds <- Dataset() %>% add(c(arm1, arm2))
table <- ds %>% export(dest="RxODE")
datasetRegressionTest(dataset=ds, seed=1, doseOnly=FALSE,
filename=regFilename)
})
test_that("Any layer added to the multiple-arm dataset apply to each arm.", {
regFilename <- "layer_added_to_multiple_arm_dataset"
arm1 <- Arm(label="10 mg") %>%
add(Bolus(time=0, amount=10))
arm2 <- Arm(label="20 mg") %>%
add(Bolus(time=0, amount=20))
dataset <- Dataset() %>%
add(c(arm1, arm2))
dataset <- dataset %>%
setSubjects(c(4,8))
expect_equal(length(dataset), 12)
dataset <- dataset %>%
add(IOV("IOVKA", distribution=NormalDistribution(0, 1))) %>%
add(Bootstrap(data=data.frame(ID=1:20, BW=70 + 1:20), id="ID", replacement=TRUE)) %>%
add(Observations(1:5))
# Check IOV has been created in arm1
arm1 <- dataset %>% find(Arm(1))
expect_true(!is.null(arm1 %>% find(IOV("IOVKA", distribution=0))))
# Check IOV has been created in arm2
arm2 <- dataset %>% find(Arm(2))
expect_true(!is.null(arm2 %>% find(IOV("IOVKA", distribution=0))))
table <- dataset %>% export(dest="RxODE", seed=1)
datasetRegressionTest(dataset=dataset, seed=1, doseOnly=FALSE,
filename=regFilename)
})
test_that("Boluses/Infusions can now be given at same time and into the same compartment", {
# Now this code is working
dataset <- Dataset() %>%
add(Bolus(time=0, amount=100, compartment=1)) %>%
add(Bolus(time=0, amount=100, compartment=1, ii=24, add=1))
# Amounts have been added
bolusTime0 <- dataset %>%
find(Bolus(time=0, amount=0, compartment=1))
expect_equal(bolusTime0@amount, 100 + 100)
# Check 200 is given at 0, 100 at time 24
expect_true("-> Adm. times (bolus into CMT=1): 0 (200),24 (100)" %in% capture.output(show(dataset)))
# Same code with infusions
dataset <- Dataset() %>%
add(Infusion(time=0, amount=100, compartment=2)) %>%
add(Infusion(time=0, amount=100, compartment=2, ii=24, add=1))
# Infusion amounts have been added
infusionTime0 <- dataset %>%
find(Infusion(time=0, amount=0, compartment=2))
expect_equal(infusionTime0@amount, 100 + 100)
# Check 200 is given at 0, 100 at time 24
expect_true("-> Adm. times (infusion into CMT=2): 0 (200),24 (100)" %in% capture.output(show(dataset)))
# Same code but rate is provided in second infusion
# Not accepted
expect_error(Dataset() %>%
add(Infusion(time=0, amount=100, compartment=2)) %>%
add(Infusion(time=0, amount=100, compartment=2, ii=24, add=1, duration=2)),
regexp="Element 'INFUSION \\[TIME=0, CMT=2\\]' already exists in dataset and has different properties\\. Amounts cannot be added\\.")
# Similar test but with 2 arms
expect_error(Dataset() %>%
add(Arm(subjects=10)) %>%
add(Arm(subjects=10)) %>%
add(Infusion(time=0, amount=100, compartment=2)) %>%
add(Infusion(time=0, amount=100, compartment=2, ii=24, add=1, duration=2)),
regexp="Element 'INFUSION \\[TIME=0, CMT=2\\]' already exists in ARM 1 and has different properties\\. Amounts cannot be added\\.")
# Note that the same error would have been raised in ARM 2 if process was not interrupted.
})
Calvagone/campsis documentation built on April 17, 2024, 5:33 a.m.
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library(testthat)
context("Test all methods from the dataset class")
seed <- 1
source(paste0("", "testUtils.R"))
test_that("Set subjects works as expected", {
dataset <- Dataset() %>% setSubjects(3)
expect_equal(dataset %>% length(), 3)
expect_equal(dataset@arms %>% length(), 1)
dataset <- Dataset(2) %>% setSubjects(5)
expect_equal(dataset %>% length(), 5)
expect_equal(dataset@arms %>% length(), 1)
expect_error(Dataset() %>% setSubjects(c(10,20)), regexp="x must be the same length as the number of arms in dataset")
dataset <- Dataset() %>%
add(c(Arm(subjects=5), Arm(subjects=5)))
dataset <- dataset %>%
setSubjects(c(10,20))
expect_equal(dataset@arms@list[[1]] %>% length(), 10)
expect_equal(dataset@arms@list[[2]] %>% length(), 20)
expect_equal(dataset %>% length(), 30)
})
test_that("Add entry, order, filter, getTimes (simple example)", {
dataset <- Dataset()
# Add doses
dataset <- dataset %>% add(Bolus(time=0, amount=100))
dataset <- dataset %>% add(Bolus(time=24, amount=100))
dataset <- dataset %>% add(Bolus(time=48, amount=100))
# Add observations
dataset <- dataset %>% add(Observations(times=seq(0, 48, by=4)))
# Get times
expect_equal(dataset %>% getTimes(), seq(0, 48, by=4))
# Export to RxODE
table1 <- dataset %>% export(dest="RxODE")
expect_equal(nrow(table1), 16)
expect_true(is(table1, "tbl_df"))
# Export to mrgsolve
table2 <- dataset %>% export(dest="mrgsolve")
expect_equal(nrow(table2), 16)
expect_true(is(table2, "tbl_df"))
})
test_that("Two arms example", {
# Create 2 arms
arm1 <- Arm(id=1, subjects=4)
arm2 <- Arm(id=2, subjects=3)
# Add doses in respective arms
arm1 <- arm1 %>% add(Bolus(time=0, amount=100))
arm2 <- arm2 %>% add(Bolus(time=0, amount=200))
# Add observations
obs <- Observations(times=seq(0, 48, by=4))
arm1 <- arm1 %>% add(obs)
arm2 <- arm2 %>% add(obs)
# Create dataset
dataset <- Dataset()
dataset <- dataset %>% add(arm1)
dataset <- dataset %>% add(arm2)
# Total number of subjects
expect_equal(dataset %>% length(), 7)
# Arms number
expect_equal(length(dataset@arms), 2)
# Export to RxODE
table <- dataset %>% export(dest="RxODE")
expect_equal(nrow(table), 98)
# Replace numbers of subjects in second arm
arm2Bis <- dataset@arms %>% getByIndex(2)
arm2Bis@subjects <- as.integer(5)
dataset <- dataset %>% replace(arm2Bis)
# Total number of subjects
expect_equal(dataset %>% length(), 9)
})
test_that("Export using config", {
dataset <- Dataset()
# Add doses
dataset <- dataset %>% add(Bolus(time=0, amount=100))
dataset <- dataset %>% add(Bolus(time=24, amount=100))
dataset <- dataset %>% add(Bolus(time=48, amount=100))
# Add observations
dataset <- dataset %>% add(Observations(times=seq(0, 48, by=10)))
# Export to RxODE
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
expect_true(all(c(1,2) %in% table$CMT))
})
test_that("Export constant covariates work well (N=1, N=2)", {
dataset <- Dataset()
# Add doses
dataset <- dataset %>% add(Bolus(time=0, amount=100))
dataset <- dataset %>% add(Bolus(time=24, amount=100))
dataset <- dataset %>% add(Bolus(time=48, amount=100))
# Add covariate
dataset <- dataset %>% add(Covariate(name="WT", 70))
dataset <- dataset %>% add(Covariate(name="HT", 180))
dataset <- dataset %>% add(EventCovariate(name="DOSE", 100))
expect_equal(dataset %>% getCovariates() %>% getNames(), c("WT", "HT", "DOSE"))
expect_equal(dataset %>% getEventCovariates() %>% getNames(), c("DOSE"))
# Add observations
dataset <- dataset %>% add(Observations(times=seq(0, 48, by=10)))
# Export to RxODE N=1
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
expect_true(all(table$WT==70))
expect_true(all(table$HT==180))
expect_true(all(table$DOSE==100)) # Even if covariate can be adapted by events
# Export to RxODE N=2
arm <- dataset@arms %>% default()
arm@subjects <- as.integer(2)
dataset@arms <- dataset@arms %>% replace(arm)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
expect_true(all(table$WT==70))
expect_true(all(table$HT==180))
expect_true(all(table$DOSE==100)) # Even if covariate can be adapted by events
})
test_that("Export fixed covariates work well (N=3)", {
arm <- Arm(id=1, subjects=3)
# Add doses
arm <- arm %>% add(Bolus(time=0, amount=100))
arm <- arm %>% add(Bolus(time=24, amount=100))
arm <- arm %>% add(Bolus(time=48, amount=100))
# Add covariate
arm <- arm %>% add(Covariate(name="WT", FixedDistribution(values=c(65, 70, 75))))
arm <- arm %>% add(Covariate(name="HT", FixedDistribution(values=c(175, 180, 185))))
# Add observations
arm <- arm %>% add(Observations(times=seq(0, 48, by=10)))
dataset <- Dataset()
dataset <- dataset %>% add(arm)
# Export to RxODE N=1
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE")
subTable <- table %>% dplyr::select(ID, WT, HT) %>% dplyr::distinct()
expect_equal(subTable, tibble::tibble(ID=c(1,2,3), WT=c(65,70,75), HT=c(175,180,185)))
})
test_that("Export function covariates work well (N=3)", {
arm <- Arm(id=1, subjects=3)
# Add doses
arm <- arm %>% add(Bolus(time=0, amount=100))
arm <- arm %>% add(Bolus(time=24, amount=100))
arm <- arm %>% add(Bolus(time=48, amount=100))
# Add covariate
arm <- arm %>% add(Covariate(name="WT", FunctionDistribution(fun="rnorm", args=list(mean=70, sd=10))))
arm <- arm %>% add(Covariate(name="HT", FunctionDistribution(fun="rnorm", args=list(mean=180, sd=20))))
# Add observations
arm <- arm %>% add(Observations(times=seq(0, 48, by=10)))
dataset <- Dataset()
dataset <- dataset %>% add(arm)
# Export to RxODE N=1
config <- new("dataset_config", def_depot_cmt=as.integer(1), def_obs_cmt=as.integer(2))
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE", seed=1)
subTable <- table %>% dplyr::select(ID, WT, HT) %>% dplyr::distinct() %>% dplyr::mutate(WT=round(WT), HT=round(HT))
expect_equal(subTable, tibble::tibble(ID=c(1,2,3), WT=c(64,72,62), HT=c(212,187,164)))
})
test_that("Export boostrap covariates work well (N=8)", {
arm <- new("arm", id=as.integer(1), subjects=as.integer(8))
# Add doses
arm <- arm %>% add(Bolus(time=0, amount=100))
arm <- arm %>% add(Bolus(time=24, amount=100))
arm <- arm %>% add(Bolus(time=48, amount=100))
# Add covariate
arm <- arm %>% add(Covariate("WT", BootstrapDistribution(data=c(65, 70, 75), random=TRUE, replacement=TRUE)))
arm <- arm %>% add(Covariate("HT", BootstrapDistribution(data=c(175, 180, 185), random=TRUE, replacement=TRUE)))
# Add observations
arm <- arm %>% add(Observations(times=seq(0, 48, by=10)))
dataset <- Dataset()
dataset <- dataset %>% add(arm)
# Export to RxODE
config <- DatasetConfig(defObsCmt=2)
dataset <- dataset %>% add(config)
table <- dataset %>% export(dest="RxODE", seed=1)
subTable <- table %>% dplyr::select(ID, WT, HT) %>% dplyr::distinct()
expect_equal(subTable, tibble::tibble(ID=c(1,2,3,4,5,6,7,8), WT=c(65,75,65,70,65,75,75,70), HT=c(180,185,185,175,175,175,180,180)))
})
test_that("Export occasions works well - example 1", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 60, by=10)))
# Add occasions
ds <- ds %>% add(Occasion("MY_OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# All OCC values are used because 3 doses
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,3,3,3), 2))
})
test_that("Export occasions works well - example 2", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 60, by=10)))
# Add occasions
ds <- ds %>% add(Occasion("MY_OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Check value 3 is not used (no 3rd dose)
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,2,2), 2))
})
test_that("Export occasions works well - example 3", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(Occasion("MY_OCC", values=c(1,2,4), doseNumbers=c(1,2,4)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# All OCC values are used because 3 doses
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,2,2,2,2,4,4), 2))
})
test_that("Export occasions works well - example 4", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(Occasion("MY_OCC", values=c(2,3,4), doseNumbers=c(2,3,4)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Is this the expected behaviour ? This is arbitrary, for sure
expect_equal(table$MY_OCC, rep(c(0,0,0,0,2,2,2,3,3,3,3,4,4), 2))
})
test_that("Occasion can be added into arms", {
addProtocol <- function(x) {
# Add doses
x <- x %>% add(Bolus(time=0, amount=100))
x <- x %>% add(Bolus(time=24, amount=100))
x <- x %>% add(Bolus(time=48, amount=100))
# Add observations
x <- x %>% add(Observations(times=seq(0, 60, by=10)))
# Add occasions
x <- x %>% add(Occasion("MY_OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
}
arm1 <- Arm(id=1, subjects=1) %>% addProtocol()
arm2 <- Arm(id=2, subjects=1) %>% addProtocol()
ds <- Dataset() %>% add(c(arm1, arm2))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# All OCC values are used because 3 doses
expect_equal(table$MY_OCC, rep(c(1,1,1,1,2,2,2,3,3,3), 2))
})
test_that("Export IOV works well - example 1", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(IOV("IOV_KA", distribution=NormalDistribution(0, sd=1), doseNumbers=c(3,4)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Arbitrary but OK
expect_equal(round(table$IOV_KA,2), c(0,0,0,0,0,0,0,-0.63,-0.63,-0.63,-0.63,0.18,0.18,0,0,0,0,0,0,0,-0.84,-0.84,-0.84,-0.84,1.60,1.60))
})
test_that("Export IOV works well - example 2", {
ds <- Dataset(2)
# Add doses
ds <- ds %>% add(Bolus(time=0, amount=100))
ds <- ds %>% add(Bolus(time=24, amount=100))
ds <- ds %>% add(Bolus(time=48, amount=100))
ds <- ds %>% add(Bolus(time=72, amount=100))
# Add observations
ds <- ds %>% add(Observations(times=seq(0, 80, by=10)))
# Add occasions (skip occasion on dose 3)
ds <- ds %>% add(IOV("IOV_KA", distribution=NormalDistribution(0, sd=1), doseNumbers=c(1,3)))
# Export to RxODE
table <- ds %>% export(dest="RxODE", seed=1)
# Arbitrary but OK
expect_equal(round(table$IOV_KA,2), c(-0.63,-0.63,-0.63,-0.63,-0.63,-0.63,-0.63,0.18,0.18,0.18,0.18,0.18,0.18,-0.84,-0.84,-0.84,-0.84,-0.84,-0.84,-0.84,1.60,1.60,1.60,1.60,1.60,1.60))
})
test_that("Replace, delete, find, contains methods works well", {
ds <- Dataset(1)
# Add 3 doses
ds <- ds %>% add(Bolus(time=c(0,24,48), amount=100))
# Add observations
ds <- ds %>% add(Observations(c(1,2,3)))
# Add IOV
ds <- ds %>% add(IOV("IOV_KA", distribution=c(1,2,3)))
# Add occasions
ds <- ds %>% add(Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3)))
# Add covariate
ds <- ds %>% add(Covariate("WT", 0))
# Add dose adaptation
ds <- ds %>% add(DoseAdaptation("AMT*2", compartments=1))
# Double the first dose
updatedDs <- ds %>% replace(Bolus(time=0, amount=200))
expect_true(updatedDs %>% contains(Bolus(time=0, amount=0))) # Only time matters
expect_equal((updatedDs %>% find(Bolus(time=0, amount=0)))@amount, 200)
# Change IOV distribution
updatedDs <- ds %>% replace(IOV("IOV_KA", distribution=c(1,2,3,4)))
expect_true(updatedDs %>% contains(IOV("IOV_KA", 0))) # Only name matters
expect_equal((updatedDs %>% find(IOV("IOV_KA", 0)))@distribution, FixedDistribution(c(1,2,3,4)))
# Change occasion numbers
updatedDs <- ds %>% replace(Occasion("OCC", values=c(1,2), doseNumbers=c(1,2)))
expect_true(updatedDs %>% contains(Occasion("OCC", 0, 0))) # Only name matters
expect_equal((updatedDs %>% find(Occasion("OCC", 0, 0)))@values, c(1,2))
# Change covariate value
updatedDs <- ds %>% replace(Covariate("WT", 1))
expect_true(updatedDs %>% contains(Covariate("WT", 0))) # Only name matters
expect_equal((updatedDs %>% find(Covariate("WT", 0)))@distribution, ConstantDistribution(1))
# Adapt dose adaptation formula
updatedDs <- ds %>% replace(DoseAdaptation("AMT*3", compartments=1))
expect_true(updatedDs %>% contains(DoseAdaptation("", compartments=1))) # Only compartments matters
expect_equal((updatedDs %>% find(DoseAdaptation("", compartments=1)))@formula, "AMT*3")
# Delete the last dose
bolus <- Bolus(time=48, amount=100)
expect_true(ds %>% contains(bolus))
updatedDs <- ds %>% delete(bolus)
expect_false(updatedDs %>% contains(bolus))
# Delete IOV
iov <- IOV("IOV_KA", distribution=c(1,2,3))
expect_true(ds %>% contains(iov))
updatedDs <- ds %>% delete(iov)
expect_false(updatedDs %>% contains(iov))
# Delete occasions
occ <- Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3))
expect_true(ds %>% contains(occ))
updatedDs <- ds %>% delete(occ)
expect_false(updatedDs %>% contains(occ))
# Delete covariate
cov <- Covariate("WT", 0)
expect_true(ds %>% contains(cov))
updatedDs <- ds %>% delete(cov)
expect_false(updatedDs %>% contains(cov))
# Delete observations
obs <- Observations(c(1,2,3))
expect_true(ds %>% contains(obs))
updatedDs <- ds %>% delete(obs)
expect_false(updatedDs %>% contains(obs))
# Delete dose adaptation
doseAdaptation <- DoseAdaptation("", compartments=1)
expect_true(ds %>% contains(doseAdaptation))
updatedDs <- ds %>% delete(doseAdaptation)
expect_false(updatedDs %>% contains(doseAdaptation))
})
test_that("Export works well even if objects are defined in a different order", {
regFilename <- "objects_defined_in_different_order"
arm1 <- Arm(1, subjects=1) %>%
add(Bolus(time=0, amount=1000, compartment=1, ii=24, addl=2)) %>%
add(Observations(times=seq(0,72, by=5))) %>%
add(TimeVaryingCovariate("TVCOV", data.frame(TIME=c(0, 10), VALUE=c(10, 15)))) %>%
add(Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3))) %>%
add(Covariate("BW", 70)) %>%
add(Covariate("HT", 180))
arm2 <- Arm(2, subjects=1) %>%
add(Covariate("HT", 170)) %>%
add(Covariate("BW", 60)) %>%
add(Occasion("OCC", values=c(1,2,3), doseNumbers=c(1,2,3))) %>%
add(TimeVaryingCovariate("TVCOV", data.frame(TIME=c(0, 10), VALUE=c(9, 14)))) %>%
add(Observations(times=seq(0,72, by=5))) %>%
add(Bolus(time=0, amount=2000, compartment=1, ii=24, addl=2))
ds <- Dataset() %>% add(c(arm1, arm2))
table <- ds %>% export(dest="RxODE")
datasetRegressionTest(dataset=ds, seed=1, doseOnly=FALSE,
filename=regFilename)
})
test_that("Any layer added to the multiple-arm dataset apply to each arm.", {
regFilename <- "layer_added_to_multiple_arm_dataset"
arm1 <- Arm(label="10 mg") %>%
add(Bolus(time=0, amount=10))
arm2 <- Arm(label="20 mg") %>%
add(Bolus(time=0, amount=20))
dataset <- Dataset() %>%
add(c(arm1, arm2))
dataset <- dataset %>%
setSubjects(c(4,8))
expect_equal(length(dataset), 12)
dataset <- dataset %>%
add(IOV("IOVKA", distribution=NormalDistribution(0, 1))) %>%
add(Bootstrap(data=data.frame(ID=1:20, BW=70 + 1:20), id="ID", replacement=TRUE)) %>%
add(Observations(1:5))
# Check IOV has been created in arm1
arm1 <- dataset %>% find(Arm(1))
expect_true(!is.null(arm1 %>% find(IOV("IOVKA", distribution=0))))
# Check IOV has been created in arm2
arm2 <- dataset %>% find(Arm(2))
expect_true(!is.null(arm2 %>% find(IOV("IOVKA", distribution=0))))
table <- dataset %>% export(dest="RxODE", seed=1)
datasetRegressionTest(dataset=dataset, seed=1, doseOnly=FALSE,
filename=regFilename)
})
test_that("Boluses/Infusions can now be given at same time and into the same compartment", {
# Now this code is working
dataset <- Dataset() %>%
add(Bolus(time=0, amount=100, compartment=1)) %>%
add(Bolus(time=0, amount=100, compartment=1, ii=24, add=1))
# Amounts have been added
bolusTime0 <- dataset %>%
find(Bolus(time=0, amount=0, compartment=1))
expect_equal(bolusTime0@amount, 100 + 100)
# Check 200 is given at 0, 100 at time 24
expect_true("-> Adm. times (bolus into CMT=1): 0 (200),24 (100)" %in% capture.output(show(dataset)))
# Same code with infusions
dataset <- Dataset() %>%
add(Infusion(time=0, amount=100, compartment=2)) %>%
add(Infusion(time=0, amount=100, compartment=2, ii=24, add=1))
# Infusion amounts have been added
infusionTime0 <- dataset %>%
find(Infusion(time=0, amount=0, compartment=2))
expect_equal(infusionTime0@amount, 100 + 100)
# Check 200 is given at 0, 100 at time 24
expect_true("-> Adm. times (infusion into CMT=2): 0 (200),24 (100)" %in% capture.output(show(dataset)))
# Same code but rate is provided in second infusion
# Not accepted
expect_error(Dataset() %>%
add(Infusion(time=0, amount=100, compartment=2)) %>%
add(Infusion(time=0, amount=100, compartment=2, ii=24, add=1, duration=2)),
regexp="Element 'INFUSION \\[TIME=0, CMT=2\\]' already exists in dataset and has different properties\\. Amounts cannot be added\\.")
# Similar test but with 2 arms
expect_error(Dataset() %>%
add(Arm(subjects=10)) %>%
add(Arm(subjects=10)) %>%
add(Infusion(time=0, amount=100, compartment=2)) %>%
add(Infusion(time=0, amount=100, compartment=2, ii=24, add=1, duration=2)),
regexp="Element 'INFUSION \\[TIME=0, CMT=2\\]' already exists in ARM 1 and has different properties\\. Amounts cannot be added\\.")
# Note that the same error would have been raised in ARM 2 if process was not interrupted.
})
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