tests/testthat/test-functions_normal.R
In Sterniii3/drugdevelopR: Utility-Based Optimal Phase II/III Drug Development Planning
test_that("prior_normal returns the same results", {
expect_equal(prior_normal(x=0.5,w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.4,b=0.6),
0.81469965)
})
test_that("expanding boundaries reduces value", {
expect_gt(prior_normal(x=0.5,w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.4,b=0.6),
prior_normal(x=0.5,w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.2,b=0.8))
})
test_that("box normal returns a vector with 100000 realizations", {
expect_length(box_normal(w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.4,b=0.6), 1000000)
})
test_that("Epgo_normal returns the same results", {
expect_equal(Epgo_normal(kappa=0.2,n2=50,w=0.3,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=FALSE),0.8622991)
})
test_that("Same result for fixed effects if irrelevant input values differ",{
expect_equal(Epgo_normal(kappa=0.2,n2=50,w=0.3,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE),
Epgo_normal(kappa=0.2,n2=50,w=0.7,
Delta1=0.625, Delta2=0.5,
in1=350, in2=400,
a=0.1,b=0.6, fixed=TRUE))
})
test_that("Different Calculation of Epgo",{
expect_equal(Epgo_normal(kappa=0.2,n2=50,w=0.3,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE),
pnorm((0.625-0.2)/sqrt(4/50),0,1) )
})
test_that("Higher Treatment effect reduces n3",{
expect_gt(En3_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE),
En3_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE))
})
test_that("Higher Treatment effect increases probability of a success",{
expect_lt(EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0),
EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.5, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0))
})
test_that("Bigger success region increases probability of a success",{
expect_lt(EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0),
EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.3, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0))
})
test_that("Higher gains for each benefit category increase utility",{
expect_lt(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=TRUE),1),
getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=2000, b2=4000, b3=6000,
gamma=0, fixed=TRUE),1))
})
test_that("Sample size constraint works",{
expect_equal(getElement(utility_normal(n2=100, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=90, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=TRUE),1),-9999)
})
test_that("Cost constraint works",{
expect_equal(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=50, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=TRUE),1),-9999)
})
test_that("Lower treatment effects decrease utility",{
expect_gt(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.675, Delta2 = 0.825,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1),
getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1))
})
test_that("Higher costs decrease utility",{
expect_gt(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1),
getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.8, c3 = 0.75, c02 = 20, c03 = 25,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1))
})
test_that("n3_skipII_normal returns same results",{
expect_equal(n3_skipII_normal(alpha=0.05,beta=0.1,median_prior=0.675),
75.183296)
})
test_that("Higher treatment effect (i.e. median prior larger) leads to smaller number of n3",{
expect_gt(n3_skipII_normal(alpha=0.05,beta=0.1,median_prior=0.675),
n3_skipII_normal(alpha=0.05,beta=0.1,median_prior=0.875))
})
test_that("Higher Treatment effect increases probability of a success",{
expect_lt(EPsProg_skipII_normal(alpha = 0.05, beta = 0.1,
median_prior = 0.625, step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0),
EPsProg_skipII_normal(alpha = 0.05, beta = 0.1,
median_prior = 0.625,step1 = 0.5, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0))
})
test_that("Higher Treatment effect increases probability of a success with prior distribution",{
expect_lt(EPsProg_skipII_normal(alpha = 0.05, beta = 0.1, w=0.5,
median_prior = 0.625, step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=FALSE, gamma=0),
EPsProg_skipII_normal(alpha = 0.05, beta = 0.1, w=0.5,
median_prior = 0.625,step1 = 0.5, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=FALSE, gamma=0))
})
test_that("Utility decreases with higher costs",{
expect_gt(utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=1000, b2=2000, b3=3000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1],
utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.75, c3=25, b1=1000, b2=2000, b3=3000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1])
})
test_that("Utility increases with higher gains",{
expect_lt(utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=1000, b2=2000, b3=3000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1],
utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=2000, b2=4000, b3=6000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1])
})
test_that("Violating constraints leads to negative utility of -9999",{
expect_equal(utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=1000, b2=2000, b3=3000,
K=50, N=50, S=0.8,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1],
-9999)
})
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test_that("prior_normal returns the same results", {
expect_equal(prior_normal(x=0.5,w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.4,b=0.6),
0.81469965)
})
test_that("expanding boundaries reduces value", {
expect_gt(prior_normal(x=0.5,w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.4,b=0.6),
prior_normal(x=0.5,w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.2,b=0.8))
})
test_that("box normal returns a vector with 100000 realizations", {
expect_length(box_normal(w=0.3,Delta1=1.5,Delta2=0.95,
in1=200,in2=400,a=0.4,b=0.6), 1000000)
})
test_that("Epgo_normal returns the same results", {
expect_equal(Epgo_normal(kappa=0.2,n2=50,w=0.3,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=FALSE),0.8622991)
})
test_that("Same result for fixed effects if irrelevant input values differ",{
expect_equal(Epgo_normal(kappa=0.2,n2=50,w=0.3,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE),
Epgo_normal(kappa=0.2,n2=50,w=0.7,
Delta1=0.625, Delta2=0.5,
in1=350, in2=400,
a=0.1,b=0.6, fixed=TRUE))
})
test_that("Different Calculation of Epgo",{
expect_equal(Epgo_normal(kappa=0.2,n2=50,w=0.3,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE),
pnorm((0.625-0.2)/sqrt(4/50),0,1) )
})
test_that("Higher Treatment effect reduces n3",{
expect_gt(En3_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE),
En3_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE))
})
test_that("Higher Treatment effect increases probability of a success",{
expect_lt(EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0),
EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.5, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0))
})
test_that("Bigger success region increases probability of a success",{
expect_lt(EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0),
EPsProg_normal(kappa=0.2,n2=50,w=0.3,
alpha = 0.05, beta = 0.1,
step1 = 0.3, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0))
})
test_that("Higher gains for each benefit category increase utility",{
expect_lt(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=TRUE),1),
getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=2000, b2=4000, b3=6000,
gamma=0, fixed=TRUE),1))
})
test_that("Sample size constraint works",{
expect_equal(getElement(utility_normal(n2=100, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=90, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=TRUE),1),-9999)
})
test_that("Cost constraint works",{
expect_equal(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=50, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=TRUE),1),-9999)
})
test_that("Lower treatment effects decrease utility",{
expect_gt(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.675, Delta2 = 0.825,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1),
getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1))
})
test_that("Higher costs decrease utility",{
expect_gt(getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.675, c3 = 0.72, c02 = 15, c03 = 20,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1),
getElement(utility_normal(n2=60, kappa=0.1, w=0.3, Delta1 = 0.375, Delta2 = 0.625,
in1=300, in2=600, a = 0.25, b = 0.75,
alpha = 0.05, beta = 0.1,
c2 = 0.8, c3 = 0.75, c02 = 20, c03 = 25,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
b1=1000, b2=2000, b3=3000,
gamma=0, fixed=FALSE),1))
})
test_that("n3_skipII_normal returns same results",{
expect_equal(n3_skipII_normal(alpha=0.05,beta=0.1,median_prior=0.675),
75.183296)
})
test_that("Higher treatment effect (i.e. median prior larger) leads to smaller number of n3",{
expect_gt(n3_skipII_normal(alpha=0.05,beta=0.1,median_prior=0.675),
n3_skipII_normal(alpha=0.05,beta=0.1,median_prior=0.875))
})
test_that("Higher Treatment effect increases probability of a success",{
expect_lt(EPsProg_skipII_normal(alpha = 0.05, beta = 0.1,
median_prior = 0.625, step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0),
EPsProg_skipII_normal(alpha = 0.05, beta = 0.1,
median_prior = 0.625,step1 = 0.5, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=TRUE, gamma=0))
})
test_that("Higher Treatment effect increases probability of a success with prior distribution",{
expect_lt(EPsProg_skipII_normal(alpha = 0.05, beta = 0.1, w=0.5,
median_prior = 0.625, step1 = 0.5, step2 = 1,
Delta1=0.625, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=FALSE, gamma=0),
EPsProg_skipII_normal(alpha = 0.05, beta = 0.1, w=0.5,
median_prior = 0.625,step1 = 0.5, step2 = 1,
Delta1=0.825, Delta2=0.325,
in1=300, in2=600,
a=0.25,b=0.75, fixed=FALSE, gamma=0))
})
test_that("Utility decreases with higher costs",{
expect_gt(utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=1000, b2=2000, b3=3000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1],
utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.75, c3=25, b1=1000, b2=2000, b3=3000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1])
})
test_that("Utility increases with higher gains",{
expect_lt(utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=1000, b2=2000, b3=3000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1],
utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=2000, b2=4000, b3=6000,
K=Inf, N=Inf, S=-Inf,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1])
})
test_that("Violating constraints leads to negative utility of -9999",{
expect_equal(utility_skipII_normal(alpha = 0.05, beta = 0.1, median_prior = 0.625,
c03 = 0.72, c3=20, b1=1000, b2=2000, b3=3000,
K=50, N=50, S=0.8,
steps1=0, stepm1=0.5, stepl1=0.8,
w=0.3, Delta1=0.625, Delta2=0.325,
in1=300, in2=600,a=0.25,b=0.75,
fixed=TRUE, gamma=0)[1],
-9999)
})
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