context("survivalFormula")
test_that("Surv_object_takes_time_and_negated_censor_column_as_arguments",{
sF <- survivalFormula(armAsFactor=FALSE,
timeCol="my.time",
censorCol="my.cens")
expect_equal(formula("Surv(my.time, !my.cens) ~ 1"),sF)
})
test_that("armAsFactor_true_adds_arm_to_rhs_of_formula",{
sF <- survivalFormula(armAsFactor=TRUE,
timeCol="my.time",
censorCol="my.cens")
expect_equal(formula("Surv(my.time, !my.cens) ~ arm"),sF)
})
test_that("covariates__added_to_rhs_of_formula",{
sF <- survivalFormula(armAsFactor=TRUE,
timeCol="my.time",
censorCol="my.cens",
covariates="cov1")
expect_equal(formula("Surv(my.time, !my.cens) ~ arm + cov1"),sF)
sF <- survivalFormula(armAsFactor=FALSE,
timeCol="my.time",
censorCol="my.cens",
covariates=c("cov1","cov2"))
expect_equal(formula("Surv(my.time, !my.cens) ~ cov1 + cov2"),sF)
})
test_that("strata_are_added_to_rhs_of_formula",{
sF <- survivalFormula(armAsFactor=TRUE,
timeCol="my.time",
censorCol="my.cens",
strata="strata1")
expect_equal(formula("Surv(my.time, !my.cens) ~ arm + strata(strata1)"),sF)
sF <- survivalFormula(armAsFactor=FALSE,
timeCol="the.time",
censorCol="the.cens",
strata=c("strata1","strata2"),
covariates=c("cov1","cov2"))
expect_equal(formula("Surv(the.time, !the.cens) ~ cov1 + cov2 + strata(strata1)+strata(strata2)"),sF)
})
context("helpFitting")
test_that("removeNonPositiveTimes_removes_non_positive_times",{
df <- data.frame(time=c(-6,0,4),
cens=c(FALSE,FALSE,TRUE))
expect_warning(outputData <- removeNonPositiveTimes(df,"time"))
expecteddf <- data.frame(time=4,cens=TRUE)
rownames(expecteddf) <- NULL
rownames(outputData) <- NULL
expect_equal(outputData,expecteddf)
})
test_that("removeNonPositiveTimes_keeps_data_frame_unchanged_if_all_times_positive",{
df <- data.frame(time=c(-6,0,4),
time2=c(5,6,7),
cens=c(FALSE,FALSE,TRUE))
expect_equal(removeNonPositiveTimes(df,"time2"),df)
})
test_that("extract_subgroup_extracts_given_subgroup",{
df <- data.frame(subgroup=c(TRUE,TRUE,FALSE,FALSE,TRUE),
ID=c(4,7,1,3,6))
extractedDf <- extractSubgroup(df,"subgroup")
expect_equal(extractedDf$ID,c(4,7,6))
expect_equal(extractedDf$subgroup,c(TRUE,TRUE,TRUE))
})
test_that("extract_subgroup_leaves_data_unchanged_if_no_subgroup",{
df <- data.frame(subgroup=c(TRUE,TRUE,FALSE,FALSE,TRUE),
ID=c(4,7,1,3,6))
extractedDf <- extractSubgroup(df,subgroup=NA)
expect_equal(df,extractedDf)
})
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