tests/testthat/test_isomap.R

In dimRed: A Framework for Dimensionality Reduction

## no isomap specific tests, because forward method is not really
## exact.


test_that("check vs vegan isomap", {
  if (!requireNamespace(c("vegan", dimRed:::getMethodDependencies("Isomap")), quietly = TRUE)) {
    skip("Not all required packages for isomap tests installed")
  }

  eps <- 1e-8
  a <- loadDataSet("3D S Curve", n = 200)

  vegiso <- vegan::isomap(dist(getData(a)), k = 8, ndim = 2)
  vegy <- vegan::scores(vegiso)

  drdiso <- embed(a, "Isomap", knn = 8, ndim = 2)
  drdy <- drdiso@data@data

  ## Randomly fails:
  ## expect_equal(drdy, vegy, ignore_attr = TRUE)

  err1 <- max(abs(drdy - vegy))

  drdy[, 2] <- -drdy[, 2]
  err2 <- max(abs(drdy - vegy))

  drdy[, 1] <- -drdy[, 1]
  err3 <- max(abs(drdy - vegy))

  drdy[, 2] <- -drdy[, 2]
  err4 <- max(abs(drdy - vegy))

  err <- min(err1, err2, err3, err4)

  expect_true(err < eps, info = paste0("err = ", err,
                                       ", eps = ", eps,
                                       ", expected err < eps"))

})


test_that("check other.data", {
  if (!requireNamespace(dimRed:::getMethodDependencies("Isomap"), quietly = TRUE)) {
    skip("Not all required packages for isomap tests installed")
  }

  a <- loadDataSet("3D S Curve", n = 200)
  drdiso <- embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE)
  expect_true(inherits(getOtherData(drdiso)$geod, "dist"))
})