Nothing
library(exact2x2)
library(testthat)
context("Testing StatXact version 11: Difference, Invert 2 1-sided, gamma=0")
test_that("central",{
out<-uncondExact2x2(2,7,6, 13,parmtype="difference", tsmethod="central", method="score", conf.int=TRUE)
# get p-values and conf intervals from StatXact 11 and check
expect_equal(round(c(out$p.value,out$conf.int),4),c(0.5569,-0.3108,0.5787))
out<-uncondExact2x2(0,7,13, 13,parmtype="difference", tsmethod="central", method="score", conf.int=TRUE)
# The CIs below agree with SAS Ver 9.4, SAS calculates p-value as Barnard's it is p<0.0001
expect_equal(round(c(out$p.value,out$conf.int),c(9,4,4)),c(4.758e-06,0.5904,1.000))
out<-uncondExact2x2(2,7,11, 13,parmtype="ratio", tsmethod="central", method="score", conf.int=TRUE)
expect_equal(round(c(out$p.value,out$conf.int),c(5,3,1)),c(0.02064,1.078,29.1))
})
context("Testing StatXact version 11: Invert 2-sided, gamma=0")
test_that("square",{
out<-uncondExact2x2(2,7,6, 13,parmtype="difference", tsmethod="square", method="score", conf.int=TRUE)
# get p-values and conf intervals from StatXact 11 and check
expect_equal(round(c(out$p.value,out$conf.int),c(4,4,4)),c(0.5374,-0.3079,0.5542))
out<-uncondExact2x2(0,7,13, 13,parmtype="difference", tsmethod="square", method="score", conf.int=TRUE)
# Following answers are from StatXact Version 11, fails because StatXact appears to be wrong
expect_equal(round(c(out$p.value,out$conf.int),c(8,4,4)),c(2.44e-06,0.6088,0.6101))
out<-uncondExact2x2(2,7,11, 13,parmtype="ratio", tsmethod="square",
method="score", conf.int=TRUE)
## does not equal StatXact 11 CI:
expect_equal(round(c(out$p.value,out$conf.int),c(4,2,2)),c(0.0134,1.14,14.45))
})
context("Testing StatXact version 1: Invert 2 1-sided, gamma=1e-06")
test_that("central",{
out<-uncondExact2x2(2,7,6, 13,parmtype="difference", tsmethod="central", method="score", gamma=1e-06, conf.int=TRUE)
# get p-values and conf intervals from StatXact 11 (answers do not change from gamma=0) and check
expect_equal(round(c(out$p.value,out$conf.int),4),c(0.5569,-0.3108,0.5787))
out<-uncondExact2x2(0,7,13, 13,parmtype="difference", tsmethod="central", method="score", gamma=1e-06, conf.int=TRUE)
# The CIs below agree with SAS Ver 9.4, SAS calculates p-value as Barnard's it is p<0.0001
expect_equal(round(c(out$p.value,out$conf.int),c(9,4,4)),c(6.758e-06,0.5904,1.000))
out<-uncondExact2x2(2,7,11, 13,parmtype="ratio", tsmethod="central", method="score", gamma=1e-06, conf.int=TRUE)
expect_equal(round(c(out$p.value,out$conf.int),c(5,3,2)),c(0.02064,1.078,28.74))
})
context("Testing StatXact version 11: difference only with gamma=0 different from gamma=1e-06")
test_that("central example 2:",{
pgam<-uncondExact2x2(10,35, 24, 61,parmtype="difference", tsmethod="central", method="score", gamma=1e-06, conf.int=TRUE)
# get p-values and conf intervals from StatXact 11
expect_equal(round(c(pgam$p.value,pgam$conf.int),c(4,5,4)),c(0.3012,-0.09731, 0.2949))
p<-uncondExact2x2(10,35, 24, 61,parmtype="difference", tsmethod="central", method="score", gamma=0, conf.int=TRUE)$p.value
# get p-values and conf intervals from StatXact 11 and check
expect_equal(round(c(pgam$p.value,pgam$conf.int),c(4,5,4)),c(0.4284,-0.09922, 0.2949))
})
context("Testing StatXact version 11: Boschloo")
test_that("central example 2:",{
pgr<-boschloo(10,35, 24, 61, alternative="greater", conf.int=FALSE)$p.value
# get p-values from StatXact 11
expect_equal(round(c(pgr),c(4)),c(0.1513))
pml<-boschloo(10,35, 24, 61, alternative="two.sided", tsmethod="minlike", conf.int=FALSE)$p.value
# get p-value from StatXact 11 and check
expect_equal(round(c(pml),c(4)),c(0.3381))
})
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