tests/testthat/test_predict.R

In umap: Uniform Manifold Approximation and Projection

## test for predictions

# set up training and testing datasets
iris.columns <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
i.train    <- iris[c(1:12, 61:72, 121:132), iris.columns]
i.repeat   <- iris[c(1:12), iris.columns]
i.test     <- iris[c(13:16, 73:76, 123:126), iris.columns]
# configuration for fast computation
conf.testing <- umap.defaults
conf.testing$n_neighbors <- 5
conf.testing$random_stats <- 12345
# umap once
u.train <- umap(i.train, conf.testing)

test_that("prediction method is appropriate in config", {
  utemp <- u.train
  utemp$config$method <- "bad"
  expect_error(predict(utemp, i.test), "method")
})

test_that("prediction detects when umap was trained on dist", {
  idist <- as.matrix(dist(i.train))
  u2 <- umap(idist, conf.testing, input="dist")
  expect_error(predict(u2, i.test), "dist")
})

test_that("prediction does not work with poor training data", {
  train <- matrix(1:6, ncol=3, nrow=2)
  u.train <- suppressWarnings(umap(train))
  test.data <- matrix(1:9, ncol=3, nrow=3)
  expect_error(predict(u.train, test.data), "small")
})