test_that(
  "amr_mdr correctly identifies MDR isolates",
  {

    dat <- data.frame(
      isolate = 1:5,
      AMP = c("R", "R", "S", "R", "S"),
      TET = c("R", "S", "S", "R", "S"),
      CIP = c("R", "S", "S", "R", "R"),
      GEN = c("S", "S", "R", "R", "S")
    )

    result <- amr_mdr(
      data = dat,
      antibiotic_columns = c(
        "AMP",
        "TET",
        "CIP",
        "GEN"
      ),
      isolate_id = "isolate",
      min_classes = 3
    )

    expect_equal(
      nrow(result),
      5
    )

    expect_true(
      "MDR" %in% names(result)
    )

    expect_true(
      "resistant_antibiotics" %in% names(result)
    )
  }
)


test_that(
  "amr_mdr counts resistant antibiotics correctly",
  {

    dat <- data.frame(
      isolate = 1,
      AMP = "R",
      TET = "R",
      CIP = "R",
      GEN = "S"
    )

    result <- amr_mdr(
      data = dat,
      antibiotic_columns = c(
        "AMP",
        "TET",
        "CIP",
        "GEN"
      ),
      min_classes = 3
    )

    expect_equal(
      result$resistant_antibiotics,
      3
    )

    expect_true(
      result$MDR
    )
  }
)


test_that(
  "amr_mdr correctly identifies non-MDR isolates",
  {

    dat <- data.frame(
      AMP = "R",
      TET = "S",
      CIP = "S",
      GEN = "S"
    )

    result <- amr_mdr(
      data = dat,
      antibiotic_columns = c(
        "AMP",
        "TET",
        "CIP",
        "GEN"
      ),
      min_classes = 3
    )

    expect_equal(
      result$resistant_antibiotics,
      1
    )

    expect_false(
      result$MDR
    )
  }
)


test_that(
  "amr_mdr rejects missing antibiotic columns",
  {

    dat <- data.frame(
      AMP = c("R", "S"),
      TET = c("S", "R")
    )

    expect_error(
      amr_mdr(
        data = dat,
        antibiotic_columns = c(
          "AMP",
          "TET",
          "CIP"
        )
      ),
      "Missing columns"
    )
  }
)