Nothing
library(testthat)
context("Test parameter S4 objects")
test_that("Working THETA parameter", {
theta1 <- Theta(name="CL", index=1, fix=TRUE, value=4)
expect_equal(theta1@name, "CL")
expect_equal(theta1@index, 1)
expect_equal(theta1@fix, TRUE)
expect_equal(theta1 %>% getName, "THETA_CL")
})
test_that("THETA parameter, default name", {
theta1 <- Theta(index=1, fix=TRUE, value=4)
expect_equal(theta1@name, as.character(NA))
})
test_that("Invalid OMEGA parameters raise an error", {
expect_error(Omega(name="CL_V", index=1, index2=2, value=0.25, type="corr"),
regexp="Type should be one of: 'var', 'sd', 'covar', 'cor', 'cv' or 'cv%'")
expect_error(Omega(name="CL_V", index=1, index2=2, value=0.25, type="var"),
regexp="Parameter type must be 'covar' or 'cor' \\(index:1, index2:2\\)")
})
test_that("Check incorrect length of parameter", {
expect_error(Theta(name=c("CL", "CL"), index=1, fix=TRUE, value=4))
})
test_that("isDial method", {
omega2_2 <- Omega(name="CL", index=2, index2=2, fix=TRUE, value=0.2)
expect_true(isDiag(omega2_2))
omega1_2 <- Omega(name="CL", index=1, index2=2, fix=TRUE, value=0.2)
expect_false(isDiag(omega1_2))
})
test_that("getNONMEMName method", {
theta1 <- Theta(name="CL", index=1)
expect_equal(theta1 %>% getNONMEMName(), "THETA(1)")
omega1_2 <- Omega(name="CL", index=1, index2=2)
expect_equal(omega1_2 %>% getNONMEMName(), "OMEGA(1,2)")
sigma1_2 <- Sigma(name="CL", index=1, index2=2)
expect_equal(sigma1_2 %>% getNONMEMName(), "SIGMA(1,2)")
})
test_that("OMEGA index2 can't be NA", {
# Missing index2 argument
expect_error(Omega(index=1))
# Missing index2 argument
expect_error(Omega(index=1, index2=NA))
})
test_that("As.data.frame method", {
theta1 <- Theta(name="CL", index=1)
df <- theta1 %>% as.data.frame(row.names=character(), optional=F)
expect_equal(data.frame(name="CL", index=1, value=as.numeric(NA), fix=FALSE,
label=as.character(NA), unit=as.character(NA), comment=as.character(NA)), df)
})
test_that("Standardise method works as expected", {
# Type not valid
expect_error(Omega(index=1, index2=1, value=117, type="cv%%"))
# Value in CV%
omega <- Omega(index=1, index2=1, value=117, type="cv%")
omega_ <- omega %>% standardise()
expect_equal(round(omega_@value, 2), 0.86)
# Value in CV
omega <- Omega(index=1, index2=1, value=1.17, type="cv")
omega_ <- omega %>% standardise()
expect_equal(round(omega_@value, 2), 0.86)
# Value in sd
omega <- Omega(index=1, index2=1, value=0.2, type="sd")
omega_ <- omega %>% standardise()
expect_equal(omega_@value, 0.04)
# Co-variance (covar)
omega <- Omega(index=1, index2=2, value=0.2, type="covar")
omega_ <- omega %>% standardise()
expect_equal(omega, omega_) # No change
# Correlation (cor)
omega <- Omega(index=1, index2=2, value=0.25, type="cor")
expect_error(omega %>% standardise(), regexp="Argument 'parameters' is needed to convert a covariance into a correlation")
})
test_that("Malformed omega is not valid and can't be standardised", {
omega1 <- Omega(index=1, index2=2, value=0, type="covar")
# Force type to be unknown
omega1@type <- "unknown"
# Check omega is not valid
expect_error(validObject(omega1), regexp="Parameter type must be 'covar' or 'cor'")
# Check omega can't be standardised
expect_error(omega1 %>% standardise(), regexp="Type of parameter OMEGA_1_2 must be 'covar' or 'cor'")
omega2 <- Omega(index=2, index2=2, value=0, type="var")
# Force type to be unknown
omega2@type <- "unknown"
# Check omega is not valid
expect_error(validObject(omega2), regexp="Type should be one of: 'var', 'sd', 'covar', 'cor', 'cv' or 'cv%'")
# Check omega can't be standardised
expect_error(omega2 %>% standardise(), regexp="Type should be one of: 'var', 'sd', 'cv' or 'cv%'")
# Force type to be covar
omega2@type <- "covar"
# Check omega can't be standardised
expect_error(omega2 %>% standardise(), regexp="Type of parameter OMEGA_2_2 can't be 'covar'")
})
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