test_that(
  "amr_xdr identifies XDR isolates",
  {

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

    result <- amr_xdr(
      data = dat,
      antibiotic_columns = c(
        "AMP",
        "TET",
        "CIP",
        "GEN",
        "CTX"
      ),
      min_resistant = 5
    )

    expect_s3_class(
      result,
      "data.frame"
    )

    expect_equal(
      result$resistant_antibiotics,
      c(5, 2, 0)
    )

    expect_equal(
      result$XDR,
      c(TRUE, FALSE, FALSE)
    )
  }
)


test_that(
  "amr_xdr identifies XDR using a lower threshold",
  {

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

    result <- amr_xdr(
      data = dat,
      antibiotic_columns = c(
        "AMP",
        "TET",
        "CIP",
        "GEN",
        "CTX"
      ),
      min_resistant = 3
    )

    expect_equal(
      result$resistant_antibiotics,
      c(3, 1)
    )

    expect_equal(
      result$XDR,
      c(TRUE, FALSE)
    )
  }
)


test_that(
  "amr_xdr supports custom resistance values",
  {

    dat <- data.frame(
      AMP = c(
        "Resistant",
        "Resistant"
      ),
      TET = c(
        "Resistant",
        "Susceptible"
      ),
      CIP = c(
        "Resistant",
        "Susceptible"
      )
    )

    result <- amr_xdr(
      data = dat,
      antibiotic_columns = c(
        "AMP",
        "TET",
        "CIP"
      ),
      resistant_value = "Resistant",
      min_resistant = 3
    )

    expect_equal(
      result$resistant_antibiotics,
      c(3, 1)
    )

    expect_equal(
      result$XDR,
      c(TRUE, FALSE)
    )
  }
)