test_that("numeric matrix", { m <- matrix(1:12 / 12, ncol = 2) res <- dig(m, function() 1) expect_equal(length(res), 4) expect_equal(res, rep(list(1), 4)) }) test_that("logical matrix", { m <- matrix(rep(c(T, F), 6), ncol = 2) res <- dig(m, function() 1) expect_equal(length(res), 4) expect_equal(res, rep(list(1), 4)) }) test_that("data frame", { d <- data.frame(a = 1:6 / 10, b = c(T, T, T, F, F, F)) res <- dig(d, function() 1) expect_equal(length(res), 4) expect_equal(res, rep(list(1), 4)) }) test_that("select condition columns", { m <- matrix(rep(c(T, F), 12), ncol = 3) res <- dig(m, f = function(condition) list(cond = condition), condition = c("1", "3")) expect_equal(length(res), 4) expect_equal(res, list(list(cond = integer(0)), list(cond = c("1"=1L)), list(cond = c("3"=3L)), list(cond = c("1"=1L, "3"=3L)))) }) test_that("select condition columns with names", { m <- matrix(rep(c(T, F), 12), ncol = 3) colnames(m) <- c("aaah", "blee", "ciis") res <- dig(m, f = function(condition) list(cond = condition), condition = c("aaah", "ciis")) expect_equal(length(res), 4) expect_equal(res, list(list(cond = integer(0)), list(cond = c("aaah"=1L)), list(cond = c("ciis"=3L)), list(cond = c("aaah"=1L, "ciis"=3L)))) }) test_that("condition arg", { m <- matrix(1:12 / 12, ncol = 2) res <- dig(m, function(condition) list(cond = condition)) expect_equal(length(res), 4) expect_equal(res, list(list(cond = integer(0)), list(cond = c("2"=2L)), list(cond = c("1"=1L)), list(cond = c("2"=2L, "1"=1L)))) }) test_that("condition arg with names", { m <- matrix(1:12 / 12, ncol = 2) colnames(m) <- c("aaah", "blee") res <- dig(m, function(condition) list(cond = condition)) expect_equal(length(res), 4) expect_equal(res, list(list(cond = integer(0)), list(cond = c("blee"=2L)), list(cond = c("aaah"=1L)), list(cond = c("blee"=2L, "aaah"=1L)))) }) test_that("support arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, function(support) list(sup = support)) expect_equal(length(res), 4) expect_equal(res, list(list(sup = 1), list(sup = 4/6), list(sup = 3/6), list(sup = 2/6)), tolerance = 1e-6) }) test_that("sum arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, function(sum) list(sum = sum)) expect_equal(length(res), 4) expect_equal(res, list(list(sum = 6), list(sum = 4), list(sum = 3), list(sum = 2))) }) test_that("indices arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, function(indices) list(i = indices)) expect_equal(length(res), 4) expect_equal(res, list(list(i = c(T,T,T,T,T,T)), list(i = c(T,T,T,T,F,F)), list(i = c(T,F,T,F,T,F)), list(i = c(T,F,T,F,F,F)))) }) test_that("weights arg", { c1 <- c(0.0, 0.2, 0.4, 0.6, 0.8, 1.0) c2 <- c(0.5, 0.6, 0.7, 0.8, 0.9, 1.0) m <- matrix(c(c1, c2), ncol = 2) res <- dig(m, function(weights) list(w = weights)) expect_equal(length(res), 4) expect_equal(res, list(list(w = c(1,1,1,1,1,1)), list(w = c2), list(w = c1), list(w = c1 * c2)), tolerance = 1e-6) }) test_that("foci_supports arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, f = function(foci_supports) list(fs = foci_supports), condition = "1", focus = "2") expect_equal(length(res), 2) expect_equal(res, list(list(fs = c("2" = 3/6)), list(fs = c("2" = 2/6))), tolerance = 1e-6) }) test_that("pp arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, f = function(pp) list(fs = pp), condition = "1", focus = "2") expect_equal(length(res), 2) expect_equal(res, list(list(fs = c("2" = 3)), list(fs = c("2" = 2))), tolerance = 1e-6) }) test_that("np arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, f = function(np) list(fs = np), condition = "1", focus = "2") expect_equal(length(res), 2) expect_equal(res, list(list(fs = c("2" = 3)), list(fs = c("2" = 1))), tolerance = 1e-6) }) test_that("pn arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,F,F), ncol = 2) res <- dig(m, f = function(pn) list(fs = pn), condition = "1", focus = "2") expect_equal(length(res), 2) expect_equal(res, list(list(fs = c("2" = 4)), list(fs = c("2" = 2))), tolerance = 1e-6) }) test_that("nn arg", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,F,T), ncol = 2) res <- dig(m, f = function(nn) list(fs = nn), condition = "1", focus = "2") expect_equal(length(res), 2) expect_equal(res, list(list(fs = c("2" = 3)), list(fs = c("2" = 1))), tolerance = 1e-6) }) test_that("complex contingency table test (logical)", { set.seed(234) cols <- 5 rows <- 65 m <- matrix(sample(c(T, F), cols * rows, TRUE), nrow = rows) colnames(m) <- letters[seq_len(cols)] a <- m[, "a"] b <- m[, "b"] c <- m[, "c"] d <- m[, "d"] e <- m[, "e"] res <- dig(m, f = function(condition, pp, pn, np, nn) { list(cond = format_condition(sort(colnames(m)[condition])), a_pp = pp[1], a_pn = pn[1], a_np = np[1], a_nn = nn[1], b_pp = pp[2], b_pn = pn[2], b_np = np[2], b_nn = nn[2]) }, condition = c:e, focus = a:b) res <- lapply(res, as.data.frame) res <- do.call(rbind, res) rownames(res) <- res$cond res$cond <- NULL expect_true(is.data.frame(res)) expect_equal(nrow(res), 8) expect_equal(ncol(res), 8) expect_equal(res["{}", "a_pp"], sum(a), tolerance = 1e-6) expect_equal(res["{}", "a_pn"], sum(!a), tolerance = 1e-6) expect_equal(res["{}", "a_np"], sum(a), tolerance = 1e-6) expect_equal(res["{}", "a_nn"], sum(!a), tolerance = 1e-6) expect_equal(res["{}", "b_pp"], sum(b), tolerance = 1e-6) expect_equal(res["{}", "b_pn"], sum(!b), tolerance = 1e-6) expect_equal(res["{}", "b_np"], sum(b), tolerance = 1e-6) expect_equal(res["{}", "b_nn"], sum(!b), tolerance = 1e-6) expect_equal(res["{d}", "a_pp"], sum(d & a), tolerance = 1e-6) expect_equal(res["{d}", "a_pn"], sum(d & !a), tolerance = 1e-6) expect_equal(res["{d}", "a_np"], sum(!d & a), tolerance = 1e-6) expect_equal(res["{d}", "a_nn"], sum(!d & !a), tolerance = 1e-6) expect_equal(res["{d}", "b_pp"], sum(d & b), tolerance = 1e-6) expect_equal(res["{d}", "b_pn"], sum(d & !b), tolerance = 1e-6) expect_equal(res["{d}", "b_np"], sum(!d & b), tolerance = 1e-6) expect_equal(res["{d}", "b_nn"], sum(!d & !b), tolerance = 1e-6) expect_equal(res["{d,e}", "a_pp"], sum(e & d & a), tolerance = 1e-6) expect_equal(res["{d,e}", "a_pn"], sum(e & d & !a), tolerance = 1e-6) expect_equal(res["{d,e}", "a_np"], sum(!(e & d) & a), tolerance = 1e-6) expect_equal(res["{d,e}", "a_nn"], sum(!(e & d) & !a), tolerance = 1e-6) expect_equal(res["{d,e}", "b_pp"], sum(e & d & b), tolerance = 1e-6) expect_equal(res["{d,e}", "b_pn"], sum(e & d & !b), tolerance = 1e-6) expect_equal(res["{d,e}", "b_np"], sum(!(e & d) & b), tolerance = 1e-6) expect_equal(res["{d,e}", "b_nn"], sum(!(e & d) & !b), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_pp"], sum(e & c & d & a), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_pn"], sum(e & c & d & !a), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_np"], sum(!(e & c & d) & a), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_nn"], sum(!(e & c & d) & !a), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_pp"], sum(e & c & d & b), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_pn"], sum(e & c & d & !b), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_np"], sum(!(e & c & d) & b), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_nn"], sum(!(e & c & d) & !b), tolerance = 1e-6) }) test_that("complex contingency table test (numeric)", { set.seed(234) cols <- 5 rows <- 65 m <- matrix(sample(c(0:10) / 10, cols * rows, TRUE), nrow = rows) colnames(m) <- letters[seq_len(cols)] a <- m[, "a"] b <- m[, "b"] c <- m[, "c"] d <- m[, "d"] e <- m[, "e"] res <- dig(m, f = function(condition, pp, pn, np, nn) { list(cond = format_condition(sort(colnames(m)[condition])), a_pp = pp[1], a_pn = pn[1], a_np = np[1], a_nn = nn[1], b_pp = pp[2], b_pn = pn[2], b_np = np[2], b_nn = nn[2]) }, condition = c:e, focus = a:b, t_norm = "goedel") res <- lapply(res, as.data.frame) res <- do.call(rbind, res) rownames(res) <- res$cond res$cond <- NULL expect_true(is.data.frame(res)) expect_equal(nrow(res), 8) expect_equal(ncol(res), 8) expect_equal(res["{}", "a_pp"], sum(a), tolerance = 1e-6) expect_equal(res["{}", "a_pn"], sum(1 - a), tolerance = 1e-6) expect_equal(res["{}", "a_np"], sum(a), tolerance = 1e-6) expect_equal(res["{}", "a_nn"], sum(1 - a), tolerance = 1e-6) expect_equal(res["{}", "b_pp"], sum(b), tolerance = 1e-6) expect_equal(res["{}", "b_pn"], sum(1 - b), tolerance = 1e-6) expect_equal(res["{}", "b_np"], sum(b), tolerance = 1e-6) expect_equal(res["{}", "b_nn"], sum(1 - b), tolerance = 1e-6) expect_equal(res["{d}", "a_pp"], sum(pmin(d, a)), tolerance = 1e-6) expect_equal(res["{d}", "a_pn"], sum(pmin(d, 1 - a)), tolerance = 1e-6) expect_equal(res["{d}", "a_np"], sum(pmin(1 - d, a)), tolerance = 1e-6) expect_equal(res["{d}", "a_nn"], sum(pmin(1 - d, 1 - a)), tolerance = 1e-6) expect_equal(res["{d}", "b_pp"], sum(pmin(d, b)), tolerance = 1e-6) expect_equal(res["{d}", "b_pn"], sum(pmin(d, 1 - b)), tolerance = 1e-6) expect_equal(res["{d}", "b_np"], sum(pmin(1 - d, b)), tolerance = 1e-6) expect_equal(res["{d}", "b_nn"], sum(pmin(1 - d, 1 - b)), tolerance = 1e-6) expect_equal(res["{d,e}", "a_pp"], sum(pmin(e, d, a)), tolerance = 1e-6) expect_equal(res["{d,e}", "a_pn"], sum(pmin(e, d, 1 - a)), tolerance = 1e-6) expect_equal(res["{d,e}", "a_np"], sum(pmin(1 - pmin(e, d), a)), tolerance = 1e-6) expect_equal(res["{d,e}", "a_nn"], sum(pmin(1 - pmin(e, d), 1 - a)), tolerance = 1e-6) expect_equal(res["{d,e}", "b_pp"], sum(pmin(e, d, b)), tolerance = 1e-6) expect_equal(res["{d,e}", "b_pn"], sum(pmin(e, d, 1 - b)), tolerance = 1e-6) expect_equal(res["{d,e}", "b_np"], sum(pmin(1 - pmin(e, d), b)), tolerance = 1e-6) expect_equal(res["{d,e}", "b_nn"], sum(pmin(1 - pmin(e, d), 1 - b)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_pp"], sum(pmin(e, c, d, a)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_pn"], sum(pmin(e, c, d, 1 - a)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_np"], sum(pmin(1 - pmin(e, c, d), a)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "a_nn"], sum(pmin(1 - pmin(e, c, d), 1 - a)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_pp"], sum(pmin(e, c, d, b)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_pn"], sum(pmin(e, c, d, 1 - b)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_np"], sum(pmin(1 - pmin(e, c, d), b)), tolerance = 1e-6) expect_equal(res["{c,d,e}", "b_nn"], sum(pmin(1 - pmin(e, c, d), 1 - b)), tolerance = 1e-6) }) test_that("min_length filter", { m <- matrix(1:12 / 12, ncol = 2) res <- dig(m, function() 1, min_length = 0L) expect_equal(length(res), 4) res <- dig(m, function() 1, min_length = 1L) expect_equal(length(res), 3) res <- dig(m, function() 1, min_length = 2L) expect_equal(length(res), 1) res <- dig(m, function() 1, min_length = 3L) expect_equal(length(res), 0) }) test_that("max_length filter", { m <- matrix(1:12 / 12, ncol = 2) res <- dig(m, function() 1, max_length = 0L) expect_equal(length(res), 1) res <- dig(m, function() 1, max_length = 1L) expect_equal(length(res), 3) res <- dig(m, function() 1, max_length = 2L) expect_equal(length(res), 4) res <- dig(m, function() 1, max_length = Inf) expect_equal(length(res), 4) }) test_that("min_support filter", { m <- matrix(c(T,T,T,T,F,F, T,F,T,F,T,F), ncol = 2) res <- dig(m, function() 1, min_support = 0) expect_equal(length(res), 4) res <- dig(m, function() 1, min_support = 0.001) expect_equal(length(res), 4) res <- dig(m, function() 1, min_support = 0.5) expect_equal(length(res), 3) res <- dig(m, function() 1, min_support = 0.6) expect_equal(length(res), 2) res <- dig(m, function() 1, min_support = 1) expect_equal(length(res), 1) }) test_that("disjoint filter", { m <- matrix(T, ncol = 3) res <- dig(m, function() 1) expect_equal(length(res), 8) # disjoint 1, 2, 3 res <- dig(m, function(condition) list(cond = condition), disjoint = c(1, 2, 3)) expect_equal(length(res), 8) expect_equal(res, list(list(cond = integer(0)), list(cond = c("1"=1L)), list(cond = c("2"=2L)), list(cond = c("3"=3L)), list(cond = c("1"=1L, "3"=3L)), list(cond = c("2"=2L, "3"=3L)), list(cond = c("1"=1L, "2"=2L)), list(cond = c("1"=1L, "2"=2L, "3"=3L)))) # disjoint 1, 1, 2 res <- dig(m, function(condition) list(cond = condition), disjoint = c(1, 1, 2)) expect_equal(length(res), 6) expect_equal(res, list(list(cond = integer(0)), list(cond = c("1"=1L)), list(cond = c("2"=2L)), list(cond = c("3"=3L)), list(cond = c("1"=1L, "3"=3L)), list(cond = c("2"=2L, "3"=3L)))) # disjoint 1, 1, 1 res <- dig(m, function(condition) list(cond = condition), disjoint = c(1, 1, 1)) expect_equal(length(res), 4) expect_equal(res, list(list(cond = integer(0)), list(cond = c("1"=1L)), list(cond = c("2"=2L)), list(cond = c("3"=3L)))) # disjoint 1, 1, 2 with condition and focus m <- m[, c(1:3, 1:3), drop = FALSE] res <- dig(m, function(condition) list(cond = condition), disjoint = c(1, 1, 2, 3, 4, 5), condition = 1:3, focus = 4:6) expect_equal(length(res), 6) expect_equal(res, list(list(cond = integer(0)), list(cond = c("1"=1L)), list(cond = c("2"=2L)), list(cond = c("3"=3L)), list(cond = c("1"=1L, "3"=3L)), list(cond = c("2"=2L, "3"=3L)))) }) test_that("conditions and foci are disjoint", { d <- data.frame(a = c(T, T, T, F, F), b = c(T, F, T, T, T), c = c(T, T, F, F, F), d = c(T, F, F, F, F)) f <- function(condition, foci_supports) { paste(paste(sort(names(condition)), collapse = "&"), "~", paste(names(foci_supports), collapse = "|")) } expected <- c(" ~ a|b|c|d", "a ~ c|d", "b ~ c|d", "c ~ a|b|d", "d ~ a|b|c", "a&c ~ d", "a&d ~ c", "b&c ~ d", "b&d ~ c", "c&d ~ a|b", "a&c&d ~ ", "b&c&d ~ ") res <- dig(d, f, condition = everything(), focus = everything(), disjoint = c(1, 1, 2, 3)) res <- unlist(res) expect_equal(sort(res), sort(expected)) }) test_that("conditions and foci are disjoint even if disjoints are not defined", { d <- data.frame(a = c(T, T, T, F, F), b = c(T, F, T, T, T), c = c(T, T, F, F, F)) f <- function(condition, foci_supports) { paste(paste(sort(names(condition)), collapse = "&"), "~", paste(names(foci_supports), collapse = "|")) } expected <- c(" ~ a|b|c", "a ~ b|c", "b ~ a|c", "c ~ a|b", "a&b ~ c", "a&c ~ b", "b&c ~ a", "a&b&c ~ ") res <- dig(d, f, condition = everything(), focus = everything(), disjoint = NULL) res <- unlist(res) expect_equal(sort(res), sort(expected)) }) test_that("data frame select & disjoint", { set.seed(32344) d <- data.frame(a = c(T, T, T, F, F), b = c(T, F, T, T, T), c = c(T, T, F, F, F), d = c(T, F, F, F, F), x = c(1.0, 0.1, 0.2, 0.3, 0.4), y = c(1.0, 0.9, 0.8, 0.7, 0.6), z = c(1.0, 0.8, 0.6, 0.4, 0.2), w = c(1.0, 0, 0, 0, 0)) f <- function(condition, support) { paste(paste(sort(names(condition)), collapse = " & "), "=", round(support, 2)) } disjoint <- c(1, 1, 2, 3, 5, 5, 6, 7) expected <- c("a = 0.6", "b = 0.8", "c = 0.4", "x = 0.4", "y = 0.8", "z = 0.6", "a & c = 0.4", "a & x = 0.26", "a & y = 0.54", "a & z = 0.48", "b & c = 0.2", "b & x = 0.38", "b & y = 0.62", "b & z = 0.44", "c & x = 0.22", "c & y = 0.38", "c & z = 0.36", "x & z = 0.28", "y & z = 0.52") # permutation 1 perm <- seq_along(d) res <- dig(d[, perm], f, condition = c(a, b, c, x, y, z), disjoint = disjoint[perm], min_length = 1, max_length = 2) expect_equal(sort(unlist(res)), sort(expected)) # permutation 2 perm <- sample(perm) res <- dig(d[, perm], f, condition = c(a, b, c, x, y, z), disjoint = disjoint[perm], min_length = 1, max_length = 2) expect_equal(sort(unlist(res)), sort(expected)) # permutation 3 perm <- sample(perm) res <- dig(d[, perm], f, condition = c(a, b, c, x, y, z), disjoint = disjoint[perm], min_length = 1, max_length = 2) expect_equal(sort(unlist(res)), sort(expected)) # permuted condition 1 res <- dig(d[, perm], f, condition = c(x, y, z, a, b, c), disjoint = disjoint[perm], min_length = 1, max_length = 2) expect_equal(sort(unlist(res)), sort(expected)) # permuted condition 2 res <- dig(d[, perm], f, condition = c(x, a, y, b, z, c), disjoint = disjoint[perm], min_length = 1, max_length = 2) expect_equal(sort(unlist(res)), sort(expected)) }) test_that("t-norm goedel", { c1 <- c(0.0, 0.2, 0.4, 0.6, 0.8, 1.0) c2 <- c(0.5, 0.6, 0.7, 0.8, 0.9, 1.0) m <- matrix(c(c1, c2), ncol = 2) res <- dig(m, function(weights) list(w = weights), min_length = 2, t_norm = "goedel") expect_equal(length(res), 1) expect_equal(res, list(list(w = pmin(c1, c2))), tolerance = 1e-6) }) test_that("t-norm goguen", { c1 <- c(0.0, 0.2, 0.4, 0.6, 0.8, 1.0) c2 <- c(0.5, 0.6, 0.7, 0.8, 0.9, 1.0) m <- matrix(c(c1, c2), ncol = 2) res <- dig(m, function(weights) list(w = weights), min_length = 2, t_norm = "goguen") expect_equal(length(res), 1) expect_equal(res, list(list(w = c1 * c2)), tolerance = 1e-6) }) test_that("t-norm lukas", { c1 <- c(0.0, 0.2, 0.4, 0.6, 0.8, 1.0) c2 <- c(0.5, 0.6, 0.7, 0.8, 0.9, 1.0) m <- matrix(c(c1, c2), ncol = 2) res <- dig(m, function(weights) list(w = weights), min_length = 2, t_norm = "lukas") expect_equal(length(res), 1) expect_equal(res, list(list(w = pmax(0, c1 + c2 - 1))), tolerance = 1e-6) }) test_that("multithread", { m <- matrix(T, ncol = 10, nrow=100) res <- dig(m, function() 1, threads = 24) expect_equal(length(res), 1024) }) test_that("min_focus_support & filter_empty_foci", { m <- matrix(c(c(1,1,1,1,1,1,1,1,0,0), c(1,1,1,1,1,1,0,0,1,1), c(0,0,0,1,1,1,1,1,1,1), c(0,0,0,0,1,1,1,1,1,1)), ncol = 4) f <- function(condition, foci_supports) { paste(paste(condition, collapse = " & "), "=", paste(round(foci_supports, 1), collapse = ", ")) } res <- dig(m, f, condition = 1:2, focus = 3:4, min_support = 0.1, min_focus_support = 0.5, filter_empty_foci = FALSE) expect_equal(unlist(res), c(" = 0.7, 0.6", "1 = 0.5", "2 = 0.5", "1 & 2 = ")) res <- dig(m, f, condition = 1:2, focus = 3:4, min_support = 0.1, min_focus_support = 0.5, filter_empty_foci = TRUE) expect_equal(unlist(res), c(" = 0.7, 0.6", "1 = 0.5", "2 = 0.5")) })