tests/testthat/test-unit-regression.R

In gemtc: Network Meta-Analysis Using Bayesian Methods

context("regression")

test_that("regressionParams is correct", {
  expect_equal(regressionParams(list('coefficient'='shared', 'control'=1), 4), c('B'))
  expect_equal(regressionParams(list('coefficient'='shared', 'control'=3), 5), c('B'))

  expect_equal(regressionParams(list('coefficient'='unrelated', 'control'=1), 4), c('beta[2]', 'beta[3]', 'beta[4]'))
  expect_equal(regressionParams(list('coefficient'='unrelated', 'control'=3), 5), c('beta[1]', 'beta[2]', 'beta[4]', 'beta[5]'))
  expect_equal(regressionParams(list('coefficient'='unrelated', 'control'=4), 4), c('beta[1]', 'beta[2]', 'beta[3]'))

  expect_equal(regressionParams(list('coefficient'='exchangeable', 'control'=3), 4), c('beta[1]', 'beta[2]', 'beta[4]', 'B'))

  expect_equal(regressionParams(list('coefficient'='unrelated'), 8, nc=3), c('B[2]', 'B[3]'))
})

test_that("regressionAdjustMatrix is correct", {
  trt <- function(tx) factor(tx, levels=1:4)
  expect_equal(regressionAdjustMatrix(trt(c(1,1,2)), trt(c(1,2,3)), list('coefficient'='shared', 'control'=1), 4),
               cbind(0,1,0))
  expect_equal(regressionAdjustMatrix(trt(c(1,1,2)), trt(c(1,2,3)), list('coefficient'='shared', 'control'=2), 4),
               cbind(0,-1,1))

  expect_equal(regressionAdjustMatrix(trt(c(1,1,2)), trt(c(1,2,3)), list('coefficient'='unrelated', 'control'=1), 4),
               cbind(c(0,0,0), c(1,0,0), c(-1,1,0)))
  expect_equal(regressionAdjustMatrix(trt(c(1,1,2)), trt(c(1,2,3)), list('coefficient'='unrelated', 'control'=2), 4),
               cbind(c(0,0,0), c(-1,0,0), c(0,1,0)))
  expect_equal(regressionAdjustMatrix(trt(1), trt(3), list('coefficient'='unrelated', 'control'=3), 4),
               cbind(c(-1,0,0)))

  expect_equal(regressionAdjustMatrix(trt(c(1,1,2)), trt(c(1,2,3)), list('coefficient'='exchangeable', 'control'=1), 4),
               cbind(c(0,0,0,0), c(1,0,0,0), c(-1,1,0,0)))

  expect_equal(regressionAdjustMatrix(trt(c(1,1,2,2)), trt(c(1,2,3,4)), list('coefficient'='shared', 'classes'=list('C'=1, 'X'=c(2,3), 'Y'=4)), 4),
               cbind(c(0, 0), c(1,0), c(0, 0), c(-1, 1)))
})

test_that("Degenerate covariate is detected", {
  network <- mtc.network(
    data=data.frame(
      study=c('A', 'A', 'B', 'B'),
      treatment=c('X', 'Y', 'X', 'Y'),
      responders=3,
      sampleSize=10),
    studies=data.frame(
      study=c('A', 'B'),
      covariate=0
    )
  )
  expect_error(mtc.model(network, type='regression', regressor=list(variable='covariate', 'coefficient'='shared', 'control'='X')),
    "covariate is degenerate");
})