tests/testthat/test_flash.R

In stephenslab/flashr2: Empirical Bayes Matrix Factorization

context("test_flash")

test_that("flash update improves mean squared error in simple situation", {
  set.seed(1)
  l = rnorm(5)
  f = rnorm(20)
  LF = outer(l,f)
  Y = LF + rnorm(5*20)

  data = flash_set_data(Y)
  f = flash_init_fn(data,udv_random,1)
  e1 = mean((LF - flash_get_fitted_values(f))^2) # compute mean squared error
  f = flash_update_precision(data,f,"by_column")
  Rk = flash_get_Rk(data, f, 1)
  f = flash_update_single_factor(data,f,1,"ebnm_pn",NULL,Rk)
  f = flash_update_single_loading(data,f,1,"ebnm_pn",NULL,Rk)
  e2 = mean((LF - flash_get_fitted_values(f))^2) # compute mean squared error
  expect_true(e1 > e2)
})