test_that("[ indexing works", {
skip_if_not_installed("Matrix", minimum_version = "1.6.0")
g <- make_tree(20)
expect_equal(g[1, 2], 1)
expect_equal(
as_unnamed_dense_matrix(g[c(1, 1, 7), c(2, 3, 14)]),
vector_to_square_matrix(1, 1, 0, 1, 1, 0, 0, 0, 1)
)
expect_equal(
as_unnamed_dense_matrix(g[c(1, 1, 7), c(5, 3, 12)]),
vector_to_square_matrix(0, 0, 0, 1, 1, 0, 0, 0, 0)
)
expect_equal(
as_unnamed_dense_matrix(g[c(1, 1, 1, 1), c(2, 3, 2, 2)]),
matrix(1, 4, 4)
)
expect_equal(
as_unnamed_dense_matrix(g[c(8, 17), c(17, 8)]),
vector_to_square_matrix(1, 0, 0, 0)
)
})
test_that("[ indexing works with symbolic names", {
skip_if_not_installed("Matrix", minimum_version = "1.6.0")
g <- make_test_named_tree()
expect_equal(g["a", "b"], 1)
expect_equal(
as_unnamed_dense_matrix(g[c("a", "a", "g"), c("b", "c", "n")]),
vector_to_square_matrix(1, 1, 0, 1, 1, 0, 0, 0, 1)
)
expect_equal(
as_unnamed_dense_matrix(g[c("a", "a", "g"), c("e", "c", "l")]),
vector_to_square_matrix(0, 0, 0, 1, 1, 0, 0, 0, 0)
)
expect_equal(
as_unnamed_dense_matrix(g[c("a", "a", "a", "a"), c("b", "c", "b", "b")]),
matrix(1, 4, 4)
)
expect_equal(
as_unnamed_dense_matrix(g[c("h", "q"), c("q", "h")]),
vector_to_square_matrix(1, 0, 0, 0)
)
})
test_that("[ indexing works with logical vectors", {
skip_if_not_installed("Matrix", minimum_version = "1.6.0")
g <- make_test_named_tree()
lres <- structure(
c(
0, 0, 0, 0, 0, 0, 1, 0, 1, 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
),
.Dim = c(2L, 20L),
.Dimnames = list(
c("b", "c"),
c(
"a", "b", "c",
"d", "e", "f", "g", "h", "i", "j", "k", "l",
"m", "n", "o", "p", "q", "r", "s", "t"
)
)
)
expect_equal(g[degree(g, mode = "in") == 0, 2], 1)
expect_equal(as.matrix(g[2:3, TRUE]), lres)
})
test_that("[ indexing works with negative indices", {
g <- make_test_named_tree()
nres <- structure(
c(
0, 0, 0, 0, 1, 0, 1, 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
),
.Dim = c(2L, 19L),
.Dimnames = list(
c("b", "c"),
c(
"b", "c", "d", "e", "f", "g", "h", "i", "j",
"k", "l", "m", "n", "o", "p", "q", "r", "s",
"t"
)
)
)
expect_equal(as.matrix(g[2:3, -1]), nres)
})
test_that("[ indexing works with weighted graphs", {
skip_if_not_installed("Matrix", minimum_version = "1.6.0")
g <- make_test_weighted_tree()
expect_equal(g[1, 2], 2)
expect_equal(
as_unnamed_dense_matrix(g[c(1, 1, 7), c(2, 3, 14)]),
vector_to_square_matrix(2, 2, 0, 3, 3, 0, 0, 0, 98)
)
expect_equal(
as_unnamed_dense_matrix(g[c(1, 1, 7), c(5, 3, 12)]),
vector_to_square_matrix(0, 0, 0, 3, 3, 0, 0, 0, 0)
)
expect_equal(
as_unnamed_dense_matrix(g[c(1, 1, 1, 1), c(2, 3, 2, 2)]),
vector_to_square_matrix(2, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2)
)
expect_equal(
as_unnamed_dense_matrix(g[c(8, 17), c(17, 8)]),
vector_to_square_matrix(136, 0, 0, 0)
)
})
test_that("[ indexing works with weighted graphs and symbolic names", {
skip_if_not_installed("Matrix", minimum_version = "1.6.0")
g <- make_test_weighted_tree()
expect_equal(g["a", "b"], 2)
expect_equal(
as_unnamed_dense_matrix(g[c("a", "a", "g"), c("b", "c", "n")]),
vector_to_square_matrix(2, 2, 0, 3, 3, 0, 0, 0, 98)
)
expect_equal(
as_unnamed_dense_matrix(g[c("a", "a", "g"), c("e", "c", "l")]),
vector_to_square_matrix(0, 0, 0, 3, 3, 0, 0, 0, 0)
)
expect_equal(
as_unnamed_dense_matrix(g[c("a", "a", "a", "a"), c("b", "c", "b", "b")]),
vector_to_square_matrix(2, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2)
)
expect_equal(
as_unnamed_dense_matrix(g[c("h", "q"), c("q", "h")]),
vector_to_square_matrix(136, 0, 0, 0)
)
})
test_that("[[ indexing works with adjacent vertices", {
g <- make_test_named_tree()
expect_equal(g[[1, ]], list(a = V(g)[2:3]), ignore_attr = TRUE)
expect_equal(g[[, 2]], list(b = V(g)[1]), ignore_attr = TRUE)
expect_equal(
g[[, 2, directed = FALSE]],
list(b = V(g)[c(1, 4, 5)]),
ignore_attr = TRUE
)
expect_equal(
g[[2, directed = FALSE]],
list(b = V(g)[c(1, 4, 5)]),
ignore_attr = TRUE
)
expect_equal(
g[[1:3, ]],
list(a = V(g)[2:3], b = V(g)[4:5], c = V(g)[6:7]),
ignore_attr = TRUE
)
expect_equal(
g[[, 1:3]],
list(a = V(g)[numeric()], b = V(g)[1], c = V(g)[1]),
ignore_attr = TRUE
)
})
test_that("[[ indexing works with symbolic names", {
g <- make_test_named_tree()
expect_equal(g[["a", ]], list(a = V(g)[2:3]), ignore_attr = TRUE)
expect_equal(g[[, "b"]], list(b = V(g)[1]), ignore_attr = TRUE)
expect_equal(
g[[, "b", directed = FALSE]],
list(b = V(g)[c(1, 4, 5)]),
ignore_attr = TRUE
)
expect_equal(
g[["b", directed = FALSE]],
list(b = V(g)[c(1, 4, 5)]),
ignore_attr = TRUE
)
expect_equal(
g[[letters[1:3], ]],
list(a = V(g)[2:3], b = V(g)[4:5], c = V(g)[6:7]),
ignore_attr = TRUE
)
expect_equal(
g[[, letters[1:3]]],
list(a = V(g)[numeric()], b = V(g)[1], c = V(g)[1]),
ignore_attr = TRUE
)
})
test_that("[[ indexing works with logical vectors", {
g <- make_test_named_tree()
expect_equal(
g[[degree(g, mode = "in") == 0, ]],
list(a = V(g)[2:3]),
ignore_attr = TRUE
)
})
test_that("[[ indexing works with filtering on both ends", {
g <- make_test_named_tree()
expect_equal(
g[[1:10, 1:10]],
list(
a = V(g)[2:3],
b = V(g)[4:5],
c = V(g)[6:7],
d = V(g)[8:9],
e = V(g)[10],
f = V(g)[numeric()],
g = V(g)[numeric()],
h = V(g)[numeric()],
i = V(g)[numeric()],
j = V(g)[numeric()]
),
ignore_attr = TRUE
)
})
test_that("[[ indexing is consistent with length()", {
g <- make_test_named_tree()
expect_equal(length(g), vcount(g))
})
test_that("[[ can query incident edges", {
g <- make_test_named_tree()
expect_equal(g[[1, , edges = TRUE]], list(a = E(g)[1:2]), ignore_attr = TRUE)
expect_equal(g[[, 2, edges = TRUE]], list(b = E(g)[1]), ignore_attr = TRUE)
expect_equal(
g[[, 2, directed = FALSE, edges = TRUE]],
list(b = E(g)[c(1, 3, 4)]),
ignore_attr = TRUE
)
expect_equal(
g[[2, directed = FALSE, edges = TRUE]],
list(b = E(g)[c(1, 3, 4)]),
ignore_attr = TRUE
)
expect_equal(
g[[1:3, , edges = TRUE]],
list(a = E(g)[1:2], b = E(g)[3:4], c = E(g)[5:6]),
ignore_attr = TRUE
)
expect_equal(
g[[, 1:3, edges = TRUE]],
list(a = E(g)[numeric()], b = E(g)[1], c = E(g)[2]),
ignore_attr = TRUE
)
})
test_that("[[ queries edges with vertex names", {
g <- make_test_named_tree()
expect_equal(
g[["a", , edges = TRUE]],
list(a = E(g)[1:2]),
ignore_attr = TRUE
)
expect_equal(
g[[, "b", edges = TRUE]],
list(b = E(g)[1]),
ignore_attr = TRUE
)
expect_equal(
g[[, "b", directed = FALSE, edges = TRUE]],
list(b = E(g)[c(1, 3, 4)]),
ignore_attr = TRUE
)
expect_equal(
g[["b", directed = FALSE, edges = TRUE]],
list(b = E(g)[c(1, 3, 4)]),
ignore_attr = TRUE
)
expect_equal(
g[[letters[1:3], , edges = TRUE]],
list(a = E(g)[1:2], b = E(g)[3:4], c = E(g)[5:6]),
ignore_attr = TRUE
)
expect_equal(
g[[, letters[1:3], edges = TRUE]],
list(a = E(g)[numeric()], b = E(g)[1], c = E(g)[2]),
ignore_attr = TRUE
)
## Filtering on both ends
expect_equal(
g[[1:10, 1:10, edges = TRUE]],
list(
E(g)[1:2],
E(g)[3:4],
E(g)[5:6],
E(g)[7:8],
E(g)[9],
E(g)[numeric()],
E(g)[numeric()],
E(g)[numeric()],
E(g)[numeric()],
E(g)[numeric()]
),
ignore_attr = TRUE
)
})
test_that("[ handles from and to properly", {
g <- make_test_named_tree()
g <- make_tree(20)
expect_equal(g[from = c(1, 2, 2, 3), to = c(3, 4, 8, 7)], c(1, 1, 0, 1))
V(g)$name <- letters[1:20]
expect_equal(
g[from = c("a", "b", "b", "c"), to = c("c", "d", "h", "g")],
c(1, 1, 0, 1)
)
E(g)$weight <- (1:ecount(g))^2
expect_equal(
g[from = c("a", "b", "b", "c"), to = c("c", "d", "h", "g")],
c(4, 9, 0, 36)
)
expect_equal(
g[from = c("a", "b", "b", "c"), to = c("c", "d", "h", "g"), edges = TRUE],
c(2, 3, 0, 6)
)
})
test_that("[[ works with from and to", {
g <- make_tree(20)
expect_equal(g[[1, ]], g[[from = 1]], ignore_attr = TRUE)
expect_equal(g[[, 1]], g[[to = 1]], ignore_attr = TRUE)
expect_equal(g[[1:5, 4:10]], g[[from = 1:5, to = 4:10]], ignore_attr = TRUE)
expect_error(g[[1, from = 1]], "Cannot use both")
expect_error(g[[, 2, to = 10]], "Cannot use both")
})
test_that("[[ returns vertex and edges sequences", {
g <- make_tree(20)
expect_true(is_igraph_vs(g[[1]][[1]]))
expect_true(is_igraph_es(g[[1, edges = TRUE]][[1]]))
expect_true(is_igraph_vs(g[[1:3, 2:6]][[1]]))
expect_true(is_igraph_es(g[[1:3, 2:6, edges = TRUE]][[1]]))
})
test_that("[[ handles from and to properly even if the graph has conflicting vertex attributes", {
g <- make_tree(20)
V(g)$i <- 200:219
V(g)$j <- 200:219
expect_true(is_igraph_vs(g[[1:3, 2:6]][[1]]))
expect_true(is_igraph_vs(g[[from = 1:3, to = 2:6]][[1]]))
})
test_that("[ handles errors in input parameters well", {
g <- make_full_graph(10)
expect_error(g[from = 1, to = 1, i = 1, j = 1])
expect_error(g[from = 1])
expect_error(g[to = 1])
expect_error(g[from = NA, to = 2])
expect_error(g[from = 1, to = NA])
expect_error(g[from = 1, to = c(1, 2)])
})
test_that("[ handles all combinations of i and/or j", {
A <- matrix(
rep(
c(0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0),
c(
4L, 1L, 4L, 1L, 2L, 1L, 5L, 2L, 3L, 1L, 10L, 3L, 9L, 1L, 1L, 1L, 3L, 1L, 1L,
1L, 1L, 1L, 10L, 1L, 1L, 1L, 1L, 5L, 11L, 1L, 2L, 1L, 5L, 1L, 3L
)
),
nrow = 10L,
ncol = 10L
)
g <- graph_from_adjacency_matrix(A, "directed")
expect_equal(as_unnamed_dense_matrix(g[1:3, ]), A[1:3, ])
expect_equal(as_unnamed_dense_matrix(g[, 4:7]), A[, 4:7])
expect_equal(as_unnamed_dense_matrix(g[1:3, 4:7]), A[1:3, 4:7])
})
test_that("[ handles duplicated i/j well", {
A <- matrix(
rep(
c(0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0),
c(
4L, 1L, 4L, 1L, 2L, 1L, 5L, 2L, 3L, 1L, 10L, 3L, 9L, 1L, 1L, 1L, 3L, 1L, 1L,
1L, 1L, 1L, 10L, 1L, 1L, 1L, 1L, 5L, 11L, 1L, 2L, 1L, 5L, 1L, 3L
)
),
nrow = 10L,
ncol = 10L
)
g <- graph_from_adjacency_matrix(A, "directed")
expect_equal(as_unnamed_dense_matrix(g[c(1, 2, 2), ]), A[c(1, 2, 2), ])
expect_equal(as_unnamed_dense_matrix(g[, c(3, 3, 4, 4)]), A[, c(3, 3, 4, 4)])
expect_equal(
as_unnamed_dense_matrix(g[c(1, 2, 2), c(3, 3, 4, 4)]),
A[c(1, 2, 2), c(3, 3, 4, 4)]
)
})
test_that("[ can add and delete edges", {
g <- make_empty_graph(10)
A <- matrix(0, 10, 10)
A[1, 2] <- g[1, 2] <- TRUE
expect_equal(as_unnamed_dense_matrix(g[]), A)
A[2, 1] <- g[2, 1] <- TRUE
expect_equal(as_unnamed_dense_matrix(g[]), A)
g[2, 1] <- NULL
A[2, 1] <- 0
expect_equal(as_unnamed_dense_matrix(g[]), A)
A[1, 2] <- g[1, 2] <- FALSE
expect_equal(as_unnamed_dense_matrix(g[]), A)
g <- make_empty_graph(10)
A <- matrix(0, 10, 10)
A[-1, 1] <- g[-1, 1] <- 1
expect_equal(as_unnamed_dense_matrix(g[]), A)
})
test_that("[ can set weights and delete weighted edges", {
g <- make_empty_graph(10)
A <- matrix(0, 10, 10)
g <- set_edge_attr(g, "weight", c(), 1)
A[1, 2] <- g[1, 2] <- 1
expect_equal(as_unnamed_dense_matrix(g[]), A)
A[2, 1] <- g[2, 1] <- 2
expect_equal(as_unnamed_dense_matrix(g[]), A)
A[1, 2] <- g[1, 2] <- 3
expect_equal(as_unnamed_dense_matrix(g[]), A)
A[1:2, 2:3] <- g[1:2, 2:3, loops = TRUE] <- -1
expect_equal(as_unnamed_dense_matrix(g[]), A)
g[1, 2] <- NULL
A[1, 2] <- 0
expect_equal(as_unnamed_dense_matrix(g[]), A)
})
test_that("[ can add edges and ste weights via vertex names", {
g <- make_empty_graph(10)
A <- matrix(0, 10, 10)
V(g)$name <- letters[1:vcount(g)]
rownames(A) <- colnames(A) <- letters[1:vcount(g)]
A["a", "b"] <- g["a", "b"] <- TRUE
A["b", "c"] <- g["b", "c"] <- TRUE
expect_equal(as_unnamed_dense_matrix(g[]), as_unnamed_dense_matrix(A))
A[c("a", "f"), c("f", "a")] <- g[
c("a", "f"),
c("f", "a"),
loops = TRUE
] <- TRUE
expect_equal(as_unnamed_dense_matrix(g[]), as_unnamed_dense_matrix(A))
A[A == 1] <- NA
A[c("a", "c", "h"), c("a", "b", "c")] <-
g[c("a", "c", "h"), c("a", "b", "c"), attr = "weight", loops = TRUE] <- 3
expect_equal(as_unnamed_dense_matrix(g[]), as_unnamed_dense_matrix(A))
})
test_that("[ and the from-to notation", {
g <- make_empty_graph(10)
A <- matrix(0, 10, 10)
V(g)$name <- letters[1:vcount(g)]
rownames(A) <- colnames(A) <- letters[1:vcount(g)]
g[from = c("a", "c", "h"), to = c("a", "b", "c")] <- 1
A["a", "a"] <- A["c", "b"] <- A["h", "c"] <- 1
expect_equal(
g[from = c("a", "c", "h", "d"), to = c("a", "b", "c", "e")],
c(1, 1, 1, 0)
)
expect_equal(as_unnamed_dense_matrix(g[]), as_unnamed_dense_matrix(A))
g[
from = c("a", "c", "h", "a"),
to = c("a", "a", "a", "e"),
attr = "weight"
] <- 3
A[A != 0] <- NA
A["a", "a"] <- A["c", "a"] <- A["h", "a"] <- A["a", "e"] <- 3
expect_equal(
g[
from = c("a", "c", "h", "a", "c", "c"),
to = c("a", "a", "a", "e", "f", "b")
],
c(3, 3, 3, 3, 0, NA)
)
expect_equal(as_unnamed_dense_matrix(g[]), as_unnamed_dense_matrix(A))
})
test_that("[ and from-to with multiple values", {
g <- make_empty_graph(10)
A <- matrix(0, 10, 10)
V(g)$name <- letters[1:vcount(g)]
rownames(A) <- colnames(A) <- letters[1:vcount(g)]
g[from = c("a", "c", "h"), to = c("a", "b", "c")] <- 1
A["a", "a"] <- A["c", "b"] <- A["h", "c"] <- 1
g[
from = c("a", "c", "h", "a"),
to = c("a", "a", "a", "e"),
attr = "weight"
] <- 5:8
A[A != 0] <- NA
A["a", "a"] <- 5
A["c", "a"] <- 6
A["h", "a"] <- 7
A["a", "e"] <- 8
expect_equal(
g[
from = c("a", "c", "h", "a", "c", "c"),
to = c("a", "a", "a", "e", "f", "b")
],
c(5:8, 0, NA)
)
expect_equal(as_unnamed_dense_matrix(g[]), as_unnamed_dense_matrix(A))
})
test_that("[ manipulation works as intended for unweighted", {
# see issue https://github.com/igraph/rigraph/issues/1662
g1 <- make_empty_graph(n = 10, directed = FALSE)
A1 <- matrix(0, 10, 10)
A1[1:5, ] <- A1[, 1:5] <- g1[1:5, ] <- 1
diag(A1) <- 0
expect_equal(as_unnamed_dense_matrix(g1[]), A1)
g2 <- make_empty_graph(n = 10, directed = FALSE)
A2 <- matrix(0, 10, 10)
A2[1:5, ] <- A2[, 1:5] <- g2[, 1:5] <- 1
diag(A2) <- 0
expect_equal(as_unnamed_dense_matrix(g2[]), A2)
g3 <- make_empty_graph(n = 10, directed = TRUE)
A3 <- matrix(0, 10, 10)
A3[1:5, ] <- g3[1:5, ] <- 1
diag(A3) <- 0
expect_equal(as_unnamed_dense_matrix(g3[]), A3)
g4 <- make_empty_graph(n = 10, directed = TRUE)
A4 <- matrix(0, 10, 10)
A4[, 1:5] <- g4[, 1:5] <- 1
diag(A4) <- 0
expect_equal(as_unnamed_dense_matrix(g4[]), A4)
g5 <- make_empty_graph(n = 10, directed = TRUE)
A5 <- matrix(0, 10, 10)
g5[1, 2] <- g5[2, 1] <- A5[1, 2] <- A5[2, 1] <- 1
expect_equal(as_unnamed_dense_matrix(g5[]), A5)
g6 <- make_empty_graph(n = 10, directed = FALSE)
A6 <- matrix(0, 10, 10)
A6[6:10, 1:5] <- A6[1:5, 6:10] <- g6[6:10, 1:5] <- 1
expect_equal(as_unnamed_dense_matrix(g6[]), A6)
g7 <- make_empty_graph(n = 10, directed = TRUE)
A7 <- matrix(0, 10, 10)
g7[6:10, 1:5] <- A7[6:10, 1:5] <- 1
diag(A7) <- 0
expect_equal(as_unnamed_dense_matrix(g7[]), A7)
g8 <- make_empty_graph(n = 10, directed = TRUE)
A8 <- matrix(0, 10, 10)
g8[1:5, 6:10] <- A8[1:5, 6:10] <- 1
diag(A8) <- 0
expect_equal(as_unnamed_dense_matrix(g8[]), A8)
})
test_that("[ manipulation works as intended for weighted", {
# see issue https://github.com/igraph/rigraph/issues/1662
g1 <- make_empty_graph(n = 10, directed = FALSE)
A1 <- matrix(0, 10, 10)
A1[1:5, 1:5] <- g1[1:5, 1:5, attr = "weight"] <- 2
diag(A1) <- 0
expect_equal(as_unnamed_dense_matrix(g1[]), A1)
g2 <- make_empty_graph(n = 10, directed = FALSE)
E(g2)$weight <- 1
A2 <- matrix(0, 10, 10)
A2[1:3, 1:3] <- g2[1:3, 1:3] <- -2
diag(A2) <- 0
expect_equal(as_unnamed_dense_matrix(g2[]), A2)
})
test_that("[ manipulation handles errors properly", {
g1 <- make_empty_graph(n = 10, directed = FALSE)
expect_error(g1[1:5, ] <- 2)
})
test_that("[ deletion works as intended", {
# see issue https://github.com/igraph/rigraph/issues/1662
g1 <- make_full_graph(n = 10, directed = FALSE)
A1 <- matrix(1, 10, 10)
diag(A1) <- 0
A1[1:5, ] <- A1[, 1:5] <- g1[1:5, ] <- 0
expect_equal(as_unnamed_dense_matrix(g1[]), A1)
g2 <- make_full_graph(n = 10, directed = FALSE)
A2 <- matrix(1, 10, 10)
diag(A2) <- 0
A2[1:5, ] <- A2[, 1:5] <- g2[, 1:5] <- 0
expect_equal(as_unnamed_dense_matrix(g2[]), A2)
g3 <- make_full_graph(n = 10, directed = TRUE)
A3 <- matrix(1, 10, 10)
diag(A3) <- 0
A3[1:5, ] <- g3[1:5, ] <- 0
expect_equal(as_unnamed_dense_matrix(g3[]), A3)
g4 <- make_full_graph(n = 10, directed = TRUE)
A4 <- matrix(1, 10, 10)
diag(A4) <- 0
A4[, 1:5] <- g4[, 1:5] <- 0
expect_equal(as_unnamed_dense_matrix(g4[]), A4)
g5 <- make_full_graph(n = 10, directed = TRUE)
A5 <- matrix(1, 10, 10)
diag(A5) <- 0
g5[1, 2] <- g5[2, 1] <- A5[1, 2] <- A5[2, 1] <- 0
expect_equal(as_unnamed_dense_matrix(g5[]), A5)
g6 <- make_full_graph(n = 10, directed = FALSE)
A6 <- matrix(1, 10, 10)
diag(A6) <- 0
A6[6:10, 1:5] <- A6[1:5, 6:10] <- g6[6:10, 1:5] <- 0
expect_equal(as_unnamed_dense_matrix(g6[]), A6)
g7 <- make_full_graph(n = 10, directed = TRUE)
A7 <- matrix(1, 10, 10)
diag(A7) <- 0
g7[6:10, 1:5] <- A7[6:10, 1:5] <- 0
expect_equal(as_unnamed_dense_matrix(g7[]), A7)
g8 <- make_full_graph(n = 10, directed = TRUE)
A8 <- matrix(1, 10, 10)
diag(A8) <- 0
g8[1:5, 6:10] <- A8[1:5, 6:10] <- 0
expect_equal(as_unnamed_dense_matrix(g8[]), A8)
})
test_that("Indexing multi-graphs as adjacency list", {
g <- make_graph(~ A -+ B:C, A -+ B:C:D, simplify = FALSE)
e <- g[["A", "B", edges = TRUE]]
expect_equal(ignore_attr = TRUE, sort(e[[1]]), E(g)[1, 3])
})
test_that("Weighted indexing does not remove edges", {
# labeled as bug 1073705
g <- make_ring(10)
g[1, 2, attr = "weight"] <- 0
expect_in("weight", edge_attr_names(g))
expect_equal(E(g)$weight, c(0, rep(NA, 9)))
el <- as_edgelist(g)
g[from = el[, 1], to = el[, 2], attr = "sim"] <- rep(
0:1,
length.out = ecount(g)
)
expect_in("sim", edge_attr_names(g))
expect_equal(E(g)$sim, rep(0:1, 5))
V(g)$name <- letters[seq_len(vcount(g))]
el <- as_edgelist(g)
g[from = el[, 1], to = el[, 2], attr = "sim"] <- rep(
1:0,
length.out = ecount(g)
)
expect_equal(E(g)$sim, rep(1:0, 5))
})
test_that("indexing a vs twice works", {
edges <- data.frame(
stringsAsFactors = TRUE,
from = c("BOS", "JFK", "DEN", "BOS", "JFK", "DEN"),
to = c("JFK", "DEN", "ABQ", "JFK", "DEN", "ABQ"),
carrier = c("foo", "foo", "foo", "bar", "bar", "bar")
)
vertices <- data.frame(
stringsAsFactors = TRUE,
id = c("BOS", "JFK", "DEN", "ABQ"),
state = c("MA", "NY", "CO", "NM")
)
g <- graph_from_data_frame(edges, vertices = vertices)
x <- V(g)[3:4][state == "NM"]
expect_equal(ignore_attr = TRUE, x, V(g)["ABQ"])
})
test_that("indexing an es twice works", {
edges <- data.frame(
stringsAsFactors = TRUE,
from = c("BOS", "JFK", "DEN", "BOS", "JFK", "DEN"),
to = c("JFK", "DEN", "ABQ", "JFK", "DEN", "ABQ"),
carrier = c("foo", "foo", "foo", "bar", "bar", "bar")
)
g <- graph_from_data_frame(edges)
x <- E(g)["BOS" %->% "JFK"][carrier == "foo"]
expect_equal(
ignore_attr = TRUE,
x,
E(g)[carrier == "foo" & .from("BOS") & .to("JFK")]
)
})
test_that("deprecated indexing functions are indeed deprecated", {
g <- make_ring(10)
expect_error(V(g)[nei(1)], "was deprecated")
expect_error(V(g)[innei(1)], "was deprecated")
expect_error(V(g)[outnei(1)], "was deprecated")
expect_error(V(g)[inc(1)], "was deprecated")
expect_error(V(g)[adj(1)], "was deprecated")
expect_error(V(g)[from(1)], "was deprecated")
expect_error(V(g)[to(1)], "was deprecated")
expect_error(E(g)[adj(1)], "was deprecated")
expect_error(E(g)[inc(1)], "was deprecated")
expect_error(E(g)[from(1)], "was deprecated")
expect_error(E(g)[to(1)], "was deprecated")
})
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