Nothing

```
library("testthat")
library("survival")
context("test-believedBroken.R")
#
# These tests are believed to be broken; they need confirmation and fixes
#
# test_that("Returns correct counts" ,{
# Number of rows
# Number of unique denominators
# Number of strata
# })
# test_that("Returns cross-validated variance estimate" ,{})
# test_that("Data validity when loaded with (y,dx,sx,ix)" ,{})
# test_that("Dimension checking on objects in createCyclopsModelData" ,{})
# test_that("Approximations for ties in CLR" ,{})
# test_that("getSEs() throws error when all covariates are not included", {})
# test_that("Extract Y from data object", {})
# test_that("Extract X from data object", {})
# test_that("Predict CLR model", {})
# test_that("Predict SCCS model", {})
# test_that("Predict Cox model", {})
# test_that("Throw error with more than one case in CLR" ,{})
# test_that("Check SCCS model via SQL", {})
# test_that("Check default regularization variance", {})
# test_that("Check starting regularization with cross validation", {})
# test_that("Standardize covariates", {})
# test_that("Check correct dimensions in matrices in createCyclopsData", {})
# test_that("Fail to convergence", {})
# test_that("Make intercept dense in SQL input", {})
# test_that("SCCS as conditional Poisson regression likelihoods" ,{
# expect_equal(logLik(cyclopsFit), logLik(gold.cp)) # TODO Why are these different?
#})
# test_that("SCCS as SCCS likelihoods" ,{
# expect_equal(logLik(cyclopsFit), MJS values) # TODO Why are these different?
#})
# test_that("Reuse data object", {
#
# dataPtr <- createCyclopsData(case ~ spontaneous + induced + strata(stratum),
# data = infert,
# modelType = "clr")
#
# cyclopsFit <- fitCyclopsModel(dataPtr, prior = createPrior("none"))
#
# cyclopsFitR <- fitCyclopsModel(dataPtr,
# prior = createPrior("laplace", 1, exclude = 1))
#
# # Error: both cyclopsFit and cyclopsFitR share the same interface ptr
# confint(cyclopsFit, c(1:2), includePenalty = TRUE) # Should not throw error
# })
test_that("Check asymptotic variance in Cox example with failure ties and strata", {
test <- read.table(header=T, sep = ",", text = "
start, length, event, x1, x2
0, 4, 1,0,0
0, 3, 1,2,0
0, 3, 0,0,1
0, 2, 1,0,1
0, 2, 1,1,1
0, 1, 0,1,0
0, 1, 1,1,0
")
# We get the correct answer when last entry is censored
gold <- coxph(Surv(length, event) ~ x1 + strata(x2), test, ties = "breslow")
dataPtr <- createCyclopsData(Surv(length, event) ~ x1 + strata(x2), data = test,
modelType = "cox")
cyclopsFit <- fitCyclopsModel(dataPtr)
tolerance <- 1E-4
# expect_equal(vcov(cyclopsFit), vcov(gold), tolerance = tolerance)
})
```

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