Nothing
context("Test print.summary.ltmleMSM") #also print.ltmleMSM
test_that("transformOutcome NOTE is printed by print.summary.ltmleMSM", {
data(sampleDataForLtmleMSM)
Anodes <- grep("^A", names(sampleDataForLtmleMSM$data))
Lnodes <- c("CD4_1", "CD4_2")
Ynodes <- grep("^Y", names(sampleDataForLtmleMSM$data))
data <- sampleDataForLtmleMSM$data
data[,Ynodes] <- matrix(runif(length(Ynodes)*nrow(data)), nrow(data))*10
data <- as.data.frame(apply(data, 2, function(x) {
x[is.na(x)] <- max(x, na.rm=TRUE)
x
}))
expect_warning(
result <- ltmleMSM(data, Anodes=Anodes, Lnodes=Lnodes,
Ynodes=Ynodes, survivalOutcome=FALSE,
regimes=sampleDataForLtmleMSM$regimes,
summary.measures=sampleDataForLtmleMSM$summary.measures,
final.Ynodes=Ynodes,
working.msm="Y ~ time + I(pmax(time - switch.time, 0))",
estimate.time=FALSE, variance.method="ic")
, "Variance estimate is based on")
expect_that(print(result), prints_text("NOTE: The MSM is modeling the transformed outcome"))
expect_that(print(summary(result)), prints_text("NOTE: The MSM is modeling the transformed outcome"))
expect_warning(
result2 <- ltmleMSM(data, Anodes=Anodes, Lnodes=Lnodes,
Ynodes=Ynodes, survivalOutcome=FALSE,
regimes=sampleDataForLtmleMSM$regimes,
summary.measures=sampleDataForLtmleMSM$summary.measures,
final.Ynodes=Ynodes,
working.msm="Y ~ time + I(pmax(time - switch.time, 0))",
estimate.time=FALSE, variance.method="ic", gcomp=TRUE)
, "Variance estimate is based on")
expect_that(print(result2), prints_text("NOTE: The MSM is modeling the transformed outcome"))
expect_that(print(summary(result2)), prints_text("Warning: inference for gcomp is not accurate!"))
expect_warning(
result3 <- ltmle(data, Anodes=Anodes, Lnodes=Lnodes,
Ynodes=Ynodes, survivalOutcome=FALSE,
abar=list(c(1,1,1), c(0,0,0)),
estimate.time=FALSE, gcomp=TRUE, variance.method = "ic")
, "Variance estimate is based on")
expect_that(print(summary(result3)), prints_text("Warning: inference for gcomp is not accurate!"))
})
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