Nothing
library(testthat)
context("Test all methods from the parameters class")
source(paste0("", "testUtils.R"))
test_that("Write/Read THETA's", {
file <- paste0(testFolder, "write/parameters/")
# Read THETA's
theta1 <- Theta(name="CL", index=1, value=5, fix=TRUE)
theta2 <- Theta(name="KA", index=2, value=1, fix=TRUE)
theta3 <- Theta(name="V", index=3, value=80, fix=TRUE)
thetas <- Parameters() %>% add(theta1) %>% add(theta2) %>% add(theta3)
thetas %>% write(file=file)
# Write THETA's
thetas2 <- read.parameters(paste0(file, "theta.csv"), type="theta")
# Check we can retrieve the exact same list
expect_equal(thetas, thetas2)
})
test_that("Add/contains methods", {
theta1 <- Theta(name="CL", index=1, value=5, fix=TRUE)
theta2 <- Theta(name="KA", index=2, value=1, fix=TRUE)
thetas <- Parameters() %>% add(theta1) %>% add(theta2)
expect_true(thetas %>% contains(Theta(name="CL")))
expect_false(thetas %>% contains(Theta(name="V")))
thetas <- thetas %>% add(Theta(name="V"))
expect_true(thetas %>% contains(Theta(name="V")))
})
test_that("GetByIndex, find & select method work well", {
p <- Parameters()
p <- p %>% add(Theta())
p <- p %>% add(Theta())
p <- p %>% add(Theta())
p <- p %>% add(Omega())
p <- p %>% add(Omega())
p <- p %>% add(Sigma())
# Search by index
expect_equal(p %>% getByIndex(Theta(index=3)), Theta(index=3))
expect_equal(p %>% getByIndex(Omega(index=1, index2=1)), Omega(index=1, index2=1))
expect_equal(p %>% getByIndex(Sigma(index=1, index2=1)), Sigma(index=1, index2=1))
# Or equivalently using find
expect_equal(p %>% find(Theta(index=3)), Theta(index=3))
expect_equal(p %>% find(Omega(index=1, index2=1)), Omega(index=1, index2=1))
expect_equal(p %>% find(Sigma(index=1, index2=1)), Sigma(index=1, index2=1))
p <- p %>% select("theta")
expect_equal(p %>% length(), 3)
# Check there is no conflict with dplyr::select
df <- data.frame(ID=c(1,2,3), ID2=c(3,4,5))
df <- df %>% select(ID)
expect_false("ID2" %in% colnames(df))
})
test_that("Sort method", {
sigma1 <- Sigma(index=1, index2=1, value=1)
omega2 <- Omega(index=2, index2=2, value=1)
omega1 <- Omega(index=1, index2=1, value=1)
theta2 <- Theta(index=2, value=1)
theta1 <- Theta(index=1, value=1)
params <- Parameters() %>% add(c(sigma1, omega2, omega1, theta2, theta1))
orderedParams <- params %>% sort()
expectedParams <- Parameters() %>% add(c(theta1, theta2, omega1, omega2, sigma1))
expect_equal(orderedParams, expectedParams)
})
test_that("Disable method (IIV/RUV)", {
model <- model_suite$testing$nonmem$advan4_trans4
model <- model %>% disable("IIV")
expect_equal((model@parameters %>% find(Omega(name="KA")))@value, 0)
expect_equal((model@parameters %>% find(Omega(name="CL")))@value, 0)
expect_equal((model@parameters %>% find(Omega(name="V2")))@value, 0)
expect_equal((model@parameters %>% find(Omega(name="V3")))@value, 0)
expect_equal((model@parameters %>% find(Omega(name="Q")))@value, 0)
expect_equal((model@parameters %>% find(Sigma(name="PROP")))@value, 0.025)
model <- model %>% disable("RUV")
expect_equal((model@parameters %>% find(Sigma(name="PROP")))@value, 0)
expect_error(model %>% disable("SOMETHING"), regexp="Only these variabilities can be disabled")
})
test_that("Disable method (VARCOV)", {
model <- model_suite$testing$other$my_model1
expect_equal(model@parameters@varcov %>% length(), 49) # 7*7 matrix
model <- model %>% disable("VARCOV")
expect_equal(model@parameters@varcov %>% length(), 0)
})
test_that("Disable method (VARCOV_OMEGA & VARCOV_SIGMA)", {
model <- model_suite$testing$other$my_model1
expect_equal(model@parameters@varcov %>% length(), 49) # 7*7 matrix
model <- model %>% disable("VARCOV_OMEGA")
expect_equal(model@parameters@varcov %>% length(), 25) # 2 OMEGA's removed
model <- model %>% disable("VARCOV_SIGMA")
expect_equal(model@parameters@varcov %>% length(), 16) # 1 SIGMA removed
# All at once
model <- model_suite$testing$other$my_model1
model <- model %>% disable(c("VARCOV_OMEGA", "VARCOV_SIGMA"))
expect_equal(model@parameters@varcov %>% length(), 16)
})
test_that("Disable method (IOV)", {
model <- read.campsis(paste0(testFolder, "custom/", "model1_omega_fixed"))
model <- model %>% disable("IOV")
omega4 <- model@parameters %>% getByIndex(Omega(index=4, index2=4))
expect_true(omega4@value != 0)
omega5 <- model@parameters %>% getByIndex(Omega(index=5, index2=5))
expect_true(omega5@value == 0)
omega6 <- model@parameters %>% getByIndex(Omega(index=6, index2=6))
expect_true(omega6@value == 0)
})
test_that("Fix omega method is working", {
# 'Unfix' OMEGA matrix
original_model <- read.campsis(paste0(testFolder, "custom/", "model1_omega_fixed"))
list <- original_model@parameters@list %>% purrr::map(.f=function(x) {
if (is(x, "omega")) {
if(isTRUE(x@same)) {
x@value <- as.numeric(NA)
}
x@same <- as.logical(NA)
}
return(x)
})
model_not_fixed <- original_model
model_not_fixed@parameters@list <- list
# Fix OMEGA
model_fixed <- model_not_fixed
model_fixed@parameters <- model_fixed@parameters %>% fixOmega()
expect_equal(original_model, model_fixed)
})
test_that("Name column is optional", {
model <- read.campsis(paste0(testFolder, "custom/", "advan1_trans1_no_name"))
names <- (model@parameters %>% select("theta"))@list %>% purrr::map_chr(.f=~.x@name)
expect_true(all(is.na(names)))
})
test_that("THETA indexes validation", {
# 2 THETAS OK
theta1 <- Theta(index=1, value=0)
theta2 <- Theta(index=2, value=0)
thetas <- Parameters() %>% add(theta1) %>% add(theta2)
expect_equal(thetas %>% length(), 2)
expect_true(validObject(thetas))
# Wrong starting index
thetas <- Parameters() %>% add(Theta(index=2, value=0))
expect_error(validObject(thetas))
# NA value
thetas <- Parameters() %>% add(Theta(index=1, value=NA))
expect_error(validObject(thetas))
# Index 2 missing
theta1 <- Theta(index=1, value=0)
theta2 <- Theta(index=3, value=0)
thetas <- Parameters() %>% add(theta1) %>% add(theta2)
expect_equal(thetas %>% length(), 2)
expect_error(validObject(thetas))
})
test_that("OMEGA indexes validation", {
# 2 OMEGA OK
omega1 <- Omega(index=1, index2=1, value=0)
omega2 <- Omega(index=2, index2=2, value=0)
omegas <- Parameters() %>% add(omega1) %>% add(omega2)
expect_equal(omegas %>% length(), 2)
expect_true(validObject(omegas))
# Wrong starting index
omegas <- Parameters() %>% add(Omega(index=2, index2=2, value=0))
expect_error(validObject(omegas))
# NA value
omegas <- Parameters() %>% add(Omega(index=1, index2=1, value=NA))
expect_error(validObject(omegas))
# Index 2 missing
omega1 <- Omega(index=1, index2=1, value=0)
omega2 <- Omega(index=3, index2=3, value=0)
omegas <- Parameters() %>% add(omega1) %>% add(omega2)
expect_equal(omegas %>% length(), 2)
expect_error(validObject(omegas))
})
test_that("SIGMA indexes validation", {
# 2 SIGMA OK
sigma1 <- Sigma(index=1, index2=1, value=0)
sigma2 <- Sigma(index=2, index2=2, value=0)
sigmas <- Parameters() %>% add(sigma1) %>% add(sigma2)
expect_equal(sigmas %>% length(), 2)
expect_true(validObject(sigmas))
# Wrong starting index
sigmas <- Parameters() %>% add(Sigma(index=2, index2=2, value=0))
expect_error(validObject(sigmas))
# NA value
sigmas <- Parameters() %>% add(Sigma(index=1, index2=1, value=NA))
expect_error(validObject(sigmas))
# Index 2 missing
sigma1 <- Sigma(index=1, index2=1, value=0)
sigma2 <- Sigma(index=3, index2=3, value=0)
sigmas <- Parameters() %>% add(sigma1) %>% add(sigma2)
expect_equal(sigmas %>% length(), 2)
expect_error(validObject(sigmas))
})
test_that("Add parameters with NA indexes", {
# Thetas
parameters <- Parameters()
parameters <- parameters %>% add(Theta(value=0))
parameters <- parameters %>% add(Theta(value=0))
parameters <- parameters %>% add(Theta(value=0))
expect_equal(parameters %>% getByIndex(Theta(index=1)) %>% length(), 1)
expect_equal(parameters %>% getByIndex(Theta(index=2)) %>% length(), 1)
expect_equal(parameters %>% getByIndex(Theta(index=3)) %>% length(), 1)
expect_true(validObject(parameters))
# Omegas
parameters <- Parameters()
parameters <- parameters %>% add(Omega(value=0))
parameters <- parameters %>% add(Omega(value=0))
parameters <- parameters %>% add(Omega(value=0))
expect_equal(parameters %>% getByIndex(Omega(index=1, index2=1)) %>% length(), 1)
expect_equal(parameters %>% getByIndex(Omega(index=2, index2=2)) %>% length(), 1)
expect_equal(parameters %>% getByIndex(Omega(index=3, index2=3)) %>% length(), 1)
expect_true(validObject(parameters))
# Sigmas
parameters <- Parameters()
parameters <- parameters %>% add(Sigma(value=0))
parameters <- parameters %>% add(Sigma(value=0))
parameters <- parameters %>% add(Sigma(value=0))
expect_equal(parameters %>% getByIndex(Sigma(index=1, index2=1)) %>% length(), 1)
expect_equal(parameters %>% getByIndex(Sigma(index=2, index2=2)) %>% length(), 1)
expect_equal(parameters %>% getByIndex(Sigma(index=3, index2=3)) %>% length(), 1)
expect_true(validObject(parameters))
})
test_that("Replace parameters without specifying the index", {
# Thetas
parameters <- Parameters()
parameters <- parameters %>% add(Theta(name="X1", value=0))
parameters <- parameters %>% add(Theta(name="X2", value=0))
parameters <- parameters %>% add(Theta(name="X3", value=0))
parameters <- parameters %>% replace(Theta(name="X1", value=10))
expect_equal((parameters %>% find(Theta(name="X1")))@value, 10)
# Omegas
parameters <- Parameters()
parameters <- parameters %>% add(Omega(name="X1", value=0))
parameters <- parameters %>% add(Omega(name="X2", value=0))
parameters <- parameters %>% add(Omega(name="X3", value=0))
parameters <- parameters %>% replace(Omega(name="X1", value=10))
expect_equal((parameters %>% find(Omega(name="X1")))@value, 10)
# Sigmas
parameters <- Parameters()
parameters <- parameters %>% add(Sigma(name="X1", value=0))
parameters <- parameters %>% add(Sigma(name="X2", value=0))
parameters <- parameters %>% add(Sigma(name="X3", value=0))
parameters <- parameters %>% replace(Sigma(name="X1", value=10))
expect_equal((parameters %>% find(Sigma(name="X1")))@value, 10)
})
test_that("Add all method works well", {
# Use c() operator and add
parameters1 <- Parameters()
parameters1 <- parameters1 %>% add(c(Theta(value=0), Theta(value=0), Theta(value=0)))
expect_equal(parameters1 %>% length(), 3)
# Use list() operator and add
parameters2 <- Parameters()
parameters2 <- parameters2 %>% add(list(Theta(value=0), Theta(value=0), Theta(value=0)))
expect_equal(parameters2 %>% length(), 3)
expect_equal(parameters1, parameters2)
})
test_that("Max index on empty list works and returns an integer", {
parameters <- Parameters()
index <- parameters %>% maxIndex()
expect_true(is.integer(index))
expect_equal(index, 0)
})
test_that("Parameters encoded with locale 'French' (semi-colon used as delimiter in CSV file) can be read properly", {
# Model with parameters that were saved into CSV files on laptop with locale French
# This model correspond to advan1_trans1
model <- read.campsis(paste0(testFolder, "custom/", "csv_locale_french"))
# Let's compare it with original model from model library
expect_equal(model, model_suite$testing$nonmem$advan1_trans1)
})
test_that("Standardise method works as expected", {
params1 <- Parameters() %>%
add(Omega(name="CL", value=0.2, type="sd")) %>%
add(Omega(name="V", value=0.3^2, type="var")) %>%
add(Omega(name="CL_V", index=1, index2=2, value=0.25, type="cor"))
params2 <- Parameters() %>%
add(Omega(name="CL", value=0.2, type="sd")) %>%
add(Omega(name="V", value=0.3^2, type="var")) %>%
add(Omega(name="CL_V", index=1, index2=2, value=0.015, type="covar"))
params_expected <- Parameters() %>%
add(Omega(name="CL", value=0.2^2, type="var")) %>%
add(Omega(name="V", value=0.3^2, type="var")) %>%
add(Omega(name="CL_V", index=1, index2=2, value=0.015, type="covar"))
expect_equal(params1 %>% standardise(), params_expected)
expect_equal(params2 %>% standardise(), params_expected)
})
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