Nothing
library("testthat")
library("survival")
#
# Small exact, conditional logistic regression
#
test_that("Small exact, conditional logistic regression with no ties", {
skip_on_cran()
gold <- clogit(case ~ spontaneous + induced + strata(stratum), data=infert)
dataPtrNoTies <- createCyclopsData(case ~ spontaneous + induced + strata(stratum),
data = infert,
modelType = "clr")
cyclopsFitNoTies <- fitCyclopsModel(dataPtrNoTies, prior = createPrior("none"))
dataPtrExact <- createCyclopsData(case ~ spontaneous + induced + strata(stratum),
data = infert,
modelType = "clr_exact")
cyclopsFitExact <- fitCyclopsModel(dataPtrExact, prior = createPrior("none"))
tolerance <- 1E-4
expect_equal(coef(cyclopsFitNoTies), coef(gold), tolerance = tolerance)
expect_equal(coef(cyclopsFitExact), coef(gold), tolerance = tolerance)
})
test_that("Small, exact conditinal logistic regression with ties" , {
skip_on_cran()
withTies <- read.table(system.file("extdata/test1-clr.txt", package="Cyclops"), sep=",")
names(withTies) <- c("stratum", "y",paste("x", 1:10, sep=""))
goldWithTies <- clogit(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 + strata(stratum),
data = withTies, method="exact")
goldWithTiesBreslow <- clogit(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 + strata(stratum),
data = withTies, method="breslow")
dataPtrWithTies <-createCyclopsData(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 + strata(stratum),
data = withTies,
modelType = "clr_exact")
cyclopsFitWithTies <- fitCyclopsModel(dataPtrWithTies, prior = createPrior("none"))
dataPtrWithTiesBreslow <-createCyclopsData(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 + strata(stratum),
data = withTies,
modelType = "clr")
cyclopsFitWithTiesBreslow <- fitCyclopsModel(dataPtrWithTiesBreslow, prior = createPrior("none"))
tolerance <- 1E-4
expect_equal(coef(cyclopsFitWithTies), coef(goldWithTies), tolerance = tolerance)
expect_equal(coef(cyclopsFitWithTiesBreslow), coef(goldWithTiesBreslow), tolerance = tolerance)
})
# test_that("Evaluate speed of exact method without ties (should be same as Breslow)", {
# gold <- clogit(case ~ spontaneous + induced + strata(stratum), data=infert)
#
# dataPtrBreslow <- createCyclopsData(case ~ spontaneous + induced + strata(stratum),
# data = infert,
# modelType = "clr")
#
# cyclopsFitBreslow <- fitCyclopsModel(dataPtrBreslow, prior = createPrior("none"), forceNewObject = TRUE)
#
# dataPtrExact <- createCyclopsData(case ~ strata(stratum), sparseFormula = ~spontaneous + induced,
# data = infert,
# modelType = "clr_exact")
#
# cyclopsFitExact <- fitCyclopsModel(dataPtrExact, prior = createPrior("none"), forceNewObject = TRUE)
#
# library(microbenchmark)
# microbenchmark(
# clogit(case ~ spontaneous + induced + strata(stratum), data=infert),
# {
# dataPtrBreslow <- createCyclopsData(case ~ spontaneous + induced + strata(stratum),
# data = infert,
# modelType = "clr")
# fitCyclopsModel(dataPtrBreslow, prior = createPrior("none"), forceNewObject = TRUE)
# },
# fitCyclopsModel(dataPtrExact, prior = createPrior("none"), forceNewObject = TRUE),
# times = 100L
# )
# })
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.