library(rnndescent) context("Binary data tests") # Regression test for a bug in the Jaccard distance calculation where the empty # data would not be replaced with maximally distance points # Data with identical rows and many items which are maximally dissimilar from # each other, i.e. they have 0 overlap. Because of the identical rows and many # degenerate distances we just the distance matrices are equal but not the index # matrices (but we do want to avoid 0 indices occurring) badjaccard <- matrix( c( 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0 ), nrow = 30 ) badjaccardb <- badjaccard > 0.5 badjaccards <- Matrix::drop0(badjaccard) test_that("jaccard", { metric <- "jaccard" # dense d_res <- brute_force_knn(badjaccard, k = 5, metric = metric, use_alt_metric = FALSE ) da_res <- brute_force_knn(badjaccard, k = 5, metric = metric, use_alt_metric = TRUE ) expect_false(0 %in% d_res$idx) expect_false(0 %in% da_res$idx) expect_equal(d_res$dist, da_res$dist, tol = 1e-7) # sparse s_res <- brute_force_knn(badjaccards, k = 5, metric = metric, use_alt_metric = FALSE ) sa_res <- brute_force_knn(badjaccards, k = 5, metric = metric, use_alt_metric = TRUE ) expect_false(0 %in% s_res$idx) expect_false(0 %in% sa_res$idx) expect_equal(s_res$dist, sa_res$dist, tol = 1e-7) }) test_that("hellinger", { metric <- "hellinger" # dense d_res <- brute_force_knn(badjaccard, k = 5, metric = metric, use_alt_metric = FALSE ) da_res <- brute_force_knn(badjaccard, k = 5, metric = metric, use_alt_metric = TRUE ) expect_false(0 %in% d_res$idx) expect_false(0 %in% da_res$idx) expect_equal(d_res$dist, da_res$dist, tol = 1e-7) # sparse s_res <- brute_force_knn(badjaccards, k = 5, metric = metric, use_alt_metric = FALSE ) sa_res <- brute_force_knn(badjaccards, k = 5, metric = metric, use_alt_metric = TRUE ) expect_false(0 %in% s_res$idx) expect_false(0 %in% sa_res$idx) expect_equal(s_res$dist, sa_res$dist, tol = 1e-7) }) test_that("cosine", { metric <- "cosine" # dense d_res <- brute_force_knn(badjaccard, k = 5, metric = metric, use_alt_metric = FALSE ) da_res <- brute_force_knn(badjaccard, k = 5, metric = metric, use_alt_metric = TRUE ) expect_false(0 %in% d_res$idx) expect_false(0 %in% da_res$idx) expect_equal(d_res$dist, da_res$dist, tol = 1e-7) # sparse s_res <- brute_force_knn(badjaccards, k = 5, metric = metric, use_alt_metric = FALSE ) sa_res <- brute_force_knn(badjaccards, k = 5, metric = metric, use_alt_metric = TRUE ) expect_false(0 %in% s_res$idx) expect_false(0 %in% sa_res$idx) expect_equal(s_res$dist, sa_res$dist, tol = 1e-7) }) # test non-alt distances dense vs sparse vs binary for (metric in c( "braycurtis", "canberra", "chebyshev", "correlation", "cosine", "dice", "euclidean", "hamming", "hellinger", "jaccard", "jensenshannon", "kulsinski", "manhattan", "rogerstanimoto", "russellrao", "sokalmichener", "sokalsneath", "spearmanr", "symmetrickl", "tsss", "yule" )) { test_that(metric, { # dense d_res <- brute_force_knn(badjaccard, k = 5, metric = metric) expect_false(0 %in% d_res$idx) # sparse s_res <- brute_force_knn(badjaccards, k = 5, metric = metric) expect_false(0 %in% s_res$idx) # sparse should equal dense tol = if (metric %in% c("correlation", "cosine", "jensenshannon")) 1e-5 else 1e-7 if (metric == "symmetrickl") { # KL has quite large distances (> 10) so the tolerance needs to be larger tol <- 1e-3 } expect_equal(d_res$dist, s_res$dist, tol = tol) if (metric %in% c( "dice", "hamming", "jaccard", "kulsinski", "rogerstanimoto", "russellrao", "sokalmichener", "sokalsneath", "yule" )) { # binary b_res <- brute_force_knn(badjaccardb, k = 5, metric = metric) expect_false(0 %in% b_res$idx) # binary should equal dense expect_equal(d_res$dist, b_res$dist, tol = 1e-7) } }) }