tests/testthat/test-dbscan.R

In dbscan: Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms

test_that("dbscan works", {
  data("iris")
  ## Species is a factor
  expect_error(dbscan(iris))

  iris <- as.matrix(iris[, 1:4])

  res <- dbscan(iris, eps = .4, minPts = 4)

  expect_length(res$cluster, nrow(iris))

  ## expected result of table(res$cluster) is:
  expect_identical(table(res$cluster, dnn = NULL),
      as.table(c("0" = 25L, "1" = 47L, "2" = 38L, "3" = 36L, "4" = 4L)))

  ## compare with dbscan from package fpc (only if installed)
  if (requireNamespace("fpc", quietly = TRUE)) {
      res2 <- fpc::dbscan(iris, eps = .4, MinPts = 4)

      expect_equal(res$cluster, res2$cluster)

      ## test is.corepoint
      all(res2$isseed == is.corepoint(iris, eps = .4, minPts = 4))
  }

  ## compare with precomputed frNN
  fr <- frNN(iris, eps = .4)
  res9 <- dbscan(fr, minPts = 4)
  expect_equal(res, res9)

  ## compare on example data from fpc
  set.seed(665544)
  n <- 600
  x <- cbind(
      x = runif(10, 0, 10) + rnorm(n, sd = 0.2),
      y = runif(10, 0, 10) + rnorm(n, sd = 0.2)
      )

  res <- dbscan(x, eps = .2, minPts = 4)
  expect_length(res$cluster, nrow(x))

  ## compare with dist-based versions
  res_d <- dbscan(dist(x), eps = .2, minPts = 4)
  expect_identical(res, res_d)
  res_d2 <- dbscan(x, eps = .2, minPts = 4, search = "dist")
  expect_identical(res, res_d2)

  ## compare with dbscan from package fpc (only if installed)
  if (requireNamespace("fpc", quietly = TRUE)) {
    res2 <- fpc::dbscan(x, eps = .2, MinPts = 4)
    expect_equal(res$cluster, res2$cluster)
  }

  ## missing values, but distances are fine
  x_na <- x
  x_na[c(1, 3, 5), 1] <- NA
  expect_error(dbscan(x_na, eps = .2, minPts = 4), regexp = "NA")
  res_d1 <- dbscan(x_na, eps = .2, minPts = 4, search = "dist")
  res_d2 <- dbscan(dist(x_na), eps = .2, minPts = 4)
  expect_identical(res_d1, res_d2)

  ## introduce NAs into dist
  x_na[c(1,3,5), 2] <- NA
  expect_error(dbscan(x_na, eps = .2, minPts = 4), regexp = "NA")
  expect_error(dbscan(x_na, eps = .2, minPts = 4, search = "dist"),
    regexp = "NA")
  expect_error(dbscan(dist(x_na), eps = .2, minPts = 4), regexp = "NA")
})