tests/testthat/test-na_action.R

In GreenwoodLab/pcev: Principal Component of Explained Variance

context("NA actions")
set.seed(12345)
n <- 100
p <- 20
Y <- matrix(rnorm(n*p), nrow = n)
Y_row <- Y
Y_row[5,] <- NA_real_

Y_random <- Y
cells_samp <- cbind(sample(n, size = p, replace = TRUE),
                    sample(p, size = p, replace = TRUE))
for (i in seq_len(nrow(cells_samp))) {
  Y_random[cells_samp[i,1],
           cells_samp[i,2]] <- NA_real_
}
X <- rnorm(n)

test_that("NA action is fail", {
  pcev_out <- try(computePCEV(Y, X,
                              na_action = "fail"),
                  silent = TRUE)
  pcev_out2 <- try(computePCEV(Y_row, X,
                               na_action = "fail"),
                   silent = TRUE)
  pcev_out3 <- try(computePCEV(Y_random, X,
                               na_action = "fail"),
                   silent = TRUE)
  
  expect_false(inherits(pcev_out, "try-error"))
  expect_true(inherits(pcev_out2, "try-error"))
  expect_true(inherits(pcev_out3, "try-error"))
})

test_that("NA action is omit", {
  pcev_out <- try(computePCEV(Y, X,
                              na_action = "omit"),
                  silent = TRUE)
  pcev_out2 <- try(computePCEV(Y_row, X,
                               na_action = "omit"),
                   silent = TRUE)
  pcev_out3 <- try(computePCEV(Y_random, X,
                               na_action = "omit"),
                   silent = TRUE)
  
  expect_false(inherits(pcev_out, "try-error"))
  expect_false(inherits(pcev_out2, "try-error"))
  expect_false(inherits(pcev_out3, "try-error"))
})

test_that("NA action is column", {
  pcev_out <- try(computePCEV(Y, X,
                              na_action = "column"),
                  silent = TRUE)
  pcev_out2 <- try(computePCEV(Y_row, X,
                               na_action = "column"),
                   silent = TRUE)
  pcev_out3 <- try(computePCEV(Y_random, X,
                               na_action = "column"),
                   silent = TRUE)
  
  expect_false(inherits(pcev_out, "try-error"))
  expect_false(inherits(pcev_out2, "try-error"))
  expect_false(inherits(pcev_out3, "try-error"))
})

test_that("Same result when no NA", {
  pcev_out <- computePCEV(Y, X, na_action = "fail")
  pcev_out2 <- computePCEV(Y, X, na_action = "omit")
  pcev_out3 <- computePCEV(Y, X, na_action = "column")
  # This should be the only difference
  pcev_out3$pcevObj$overall <- TRUE
  
  expect_equivalent(pcev_out, pcev_out2)
  expect_equivalent(pcev_out, pcev_out3)
})

# test_that("Same result when all NA in one row", {
#   pcev_out <- computePCEV(Y_row, X, na_action = "omit")
#   pcev_out2 <- computePCEV(Y_row, X, na_action = "column")
#   # This should be the only difference
#   pcev_out2$pcevObj$overall <- TRUE
#   
#   expect_equivalent(pcev_out, pcev_out2)
#   expect_equivalent(pcev_out, pcev_out3)
# })