Nothing
n1<-35
n2<-61
x1<-10
x2<-24
xmat<- matrix(c(x2,x1,n2-x2,n1-x1),2,2)
library(Exact)
context("Exact: z-pooled, with gamma=0 and gamma>0")
test_that("pooled",{
# gamma=1e-06
expect_equal(
round(
exact.test(xmat, alternative="less", beta=1e-06, np.interval=TRUE, method="z-pooled", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
uncondExact2x2(x1,n1,x2,n2, alternative="less", parmtype="difference", method="wald-pooled",
control=ucControl(nPgrid=1000), gamma=1e-06)$p.value,4)
)
# gamma=0
expect_equal(
round(
exact.test(xmat, alternative="less", np.interval=FALSE, method="z-pooled", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
uncondExact2x2(x1,n1,x2,n2, alternative="less", parmtype="difference", method="wald-pooled",
control=ucControl(nPgrid=1000), gamma=0)$p.value,4)
)
})
context("Exact: Boschloo")
test_that("less, greater, two.sided",{
expect_equal(
round(
exact.test(xmat, alternative="less", np.interval=FALSE,
method="Boschloo", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
boschloo(x1,n1,x2,n2, alternative="less", tsmethod="minlike",
control=ucControl(nPgrid=1000))$p.value,4)
)
expect_equal(
round(
exact.test(xmat, alternative="greater", np.interval=FALSE,
method="Boschloo", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
boschloo(x1,n1,x2,n2, alternative="greater", tsmethod="minlike",
control=ucControl(nPgrid=1000))$p.value,4)
)
expect_equal(
round(
exact.test(xmat, alternative="two.sided", np.interval=FALSE,
method="Boschloo", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
boschloo(x1,n1,x2,n2, alternative="two.sided", tsmethod="minlike",
control=ucControl(nPgrid=1000))$p.value,4)
)
})
context("Exact: Beger and Boos, 1992 example")
test_that("less, greater, two.sided",{
n1<-47
n2<-283
x1<-14
x2<-48
xmat<- matrix(c(x2,x1,n2-x2,n1-x1),2,2)
# both equal to 0.061 in Berger and Boos, 1994, JASA, 1012-1016.
# first gamma=0
expect_equal(
round(
exact.test(xmat, alternative="two.sided", np.interval=FALSE,
method="z-pooled", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
uncondExact2x2(x1,n1,x2,n2, alternative="two.sided", tsmethod="square", method="wald-pooled",
control=ucControl(nPgrid=1000))$p.value,4)
)
# now gamma=0.001, Beger and Boos (1994) have p(0.001)= 0.037
# we both get 0.03781
expect_equal(
round(
exact.test(xmat, alternative="two.sided", np.interval=TRUE, beta=0.001,
method="z-pooled", npNumbers=1000, to.plot = FALSE)$p.value,4),
round(
uncondExact2x2(x1,n1,x2,n2, alternative="two.sided", tsmethod="square", method="wald-pooled",
control=ucControl(nPgrid=1000), gamma=0.001)$p.value,4)
)
})
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