Why does dplyr's filter drop NA values from a factor variable?

You could use this:

 filter(dat, var1 != 1 | is.na(var1))
  var1
1 <NA>
2    3
3    3
4 <NA>
5    2
6    2
7 <NA>

And it won't.

Also just for completion, dropping NAs is the intended behavior of filter as you can see from the following:

test_that("filter discards NA", {
  temp <- data.frame(
    i = 1:5,
    x = c(NA, 1L, 1L, 0L, 0L)
  )
  res <- filter(temp, x == 1)
  expect_equal(nrow(res), 2L)
})

This test above was taken from the tests for filter from github.