tests/testthat/test-draw.kaplan.R

In glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

context("separate2GroupsCox")

library(survival)

test_that("Calculates kaplan-meier data", {
  result <- separate2GroupsCox(c(age = 1), ovarian$age, data.frame(time = ovarian$futime, status = ovarian$fustat))

  expect_lt(result$pvalue - 0.0518148, 1e-2)
})

test_that('Only one group in kaplan.meier gives error', {
  expect_warning(expect_error(separate2GroupsCox(c(age = 0),
                                                 ovarian$age,
                                                 data.frame(time = ovarian$futime, status = ovarian$fustat))))
})

test_that('All combinations of parameters possible for draw.kapan', {
  xdata <- ovarian[,c('age', 'resid.ds')]
  ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

  # list, data.frame, data.frame
  expect_silent(separate2GroupsCox(list(c(1,0)), xdata, ydata))
  # list, matrix, data.frame
  expect_silent(separate2GroupsCox(list(c(1,0)), as.matrix(xdata), ydata))

  # list, numeric, data.frame
  expect_silent(separate2GroupsCox(list(c(1)), xdata$age, ydata))
  # list, numeric, data.frame
  expect_silent(separate2GroupsCox(1, xdata$age, ydata))

  # numeric, data.frame, data.frame
  expect_silent(separate2GroupsCox(c(1,0), xdata, ydata))
  # numeric, matrix, data.frame
  expect_silent(separate2GroupsCox(c(1,0), as.matrix(xdata), ydata))
})

test_that('Some bad arguments for separate2GroupsCox', {
  xdata <- ovarian[,c('age', 'resid.ds')]
  ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

  # list, data.frame, data.frame
  expect_error(separate2GroupsCox(list(c(1,0), c(0,1,2)), xdata, ydata))
  # list, matrix, data.frame
  expect_error(separate2GroupsCox(list(c(1,0)), as.matrix(xdata), ydata[1:10,]))

  # list, numeric, data.frame
  expect_error(separate2GroupsCox(list(c(1,0)), xdata$age, ydata))
  # list, numeric, data.frame
  expect_error(separate2GroupsCox(c(1,2), xdata$age, ydata))

  # numeric, data.frame, data.frame
  expect_error(separate2GroupsCox(c(1,0,1), xdata, ydata))
  # numeric, matrix, data.frame
  expect_error(separate2GroupsCox(c(1,0), t(as.matrix(xdata)), ydata))
})