std <- function(x) {
x <- zapsmall(x)
apply(x, 2, function(col) {
if (any(col < 0) && col[which(col != 0)[1]] < 0) {
-col
} else {
col
}
})
}
mag_order <- function(x) {
order(abs(x), sign(x), decreasing = TRUE)
}
mag_sort <- function(x) {
x[mag_order(x)]
}
test_that("Undirected, unweighted case works", {
withr::local_seed(42)
g <- random.graph.game(10, 15, type = "gnm", directed = FALSE)
no <- 7
A <- g[]
A <- A + 1 / 2 * as(Matrix::Matrix(diag(degree(g)), doDiag = FALSE), "generalMatrix")
ss <- eigen(A)
U <- std(ss$vectors)
X <- std(ss$vectors %*% sqrt(diag(abs(ss$values))))
au_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = TRUE
)
as_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_la$D, ss$values[1:no])
expect_equal(au_la$D, ss$values[1:no])
expect_equal(std(as_la$X), std(U[, 1:no]))
expect_equal(std(au_la$X), X[, 1:no])
au_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = TRUE
)
as_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_lm$D, mag_sort(ss$values)[1:no])
expect_equal(au_lm$D, mag_sort(ss$values)[1:no])
expect_equal(std(as_lm$X), std(U[, mag_order(ss$values)][, 1:no]))
expect_equal(std(au_lm$X), X[, mag_order(ss$values)][, 1:no])
au_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = TRUE
)
as_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_sa$D, ss$values[vcount(g) - 1:no + 1])
expect_equal(au_sa$D, ss$values[vcount(g) - 1:no + 1])
expect_equal(std(as_sa$X), std(U[, vcount(g) - 1:no + 1]))
expect_equal(std(au_sa$X), X[, vcount(g) - 1:no + 1])
})
test_that("Undirected, weighted case works", {
withr::local_seed(42)
g <- random.graph.game(10, 20, type = "gnm", directed = FALSE)
E(g)$weight <- sample(1:5, ecount(g), replace = TRUE)
no <- 3
A <- g[]
A <- A + 1 / 2 * as(Matrix::Matrix(diag(degree(g)), doDiag = FALSE), "generalMatrix")
ss <- eigen(A)
U <- std(ss$vectors)
X <- std(ss$vectors %*% sqrt(diag(abs(ss$values))))
au_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = TRUE
)
as_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_la$D, ss$values[1:no])
expect_equal(std(as_la$X), std(U[, 1:no]))
expect_equal(au_la$D, ss$values[1:no])
expect_equal(std(au_la$X), X[, 1:no])
au_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = TRUE
)
as_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_lm$D, mag_sort(ss$values)[1:no])
expect_equal(au_lm$D, mag_sort(ss$values)[1:no])
expect_equal(std(as_lm$X), std(U[, mag_order(ss$values)][, 1:no]))
expect_equal(std(au_lm$X), X[, mag_order(ss$values)][, 1:no])
au_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = TRUE
)
as_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(std(as_sa$X), std(U[, vcount(g) - 1:no + 1]))
expect_equal(std(au_sa$X), X[, vcount(g) - 1:no + 1])
})
test_that("Directed, unweighted case works", {
withr::local_seed(42)
g <- random.graph.game(10, 20, type = "gnm", directed = TRUE)
no <- 3
A <- g[]
A <- A + 1 / 2 * as(Matrix::Matrix(diag(degree(g)), doDiag = FALSE), "generalMatrix")
ss <- svd(A)
U <- std(ss$u)
V <- std(ss$v)
X <- std(ss$u %*% sqrt(diag(ss$d)))
Y <- std(ss$v %*% sqrt(diag(ss$d)))
au_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = TRUE
)
as_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_la$D, ss$d[1:no])
expect_equal(au_la$D, ss$d[1:no])
expect_equal(std(as_la$X), std(U[, 1:no]))
expect_equal(std(as_la$Y), std(V[, 1:no]))
expect_equal(std(au_la$X), X[, 1:no])
expect_equal(std(au_la$Y), Y[, 1:no])
au_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = TRUE
)
as_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_lm$D, ss$d[1:no])
expect_equal(au_lm$D, ss$d[1:no])
expect_equal(std(as_lm$X), std(U[, 1:no]))
expect_equal(std(as_lm$Y), std(V[, 1:no]))
expect_equal(std(au_lm$X), X[, 1:no])
expect_equal(std(au_lm$Y), Y[, 1:no])
au_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = TRUE
)
as_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(as_sa$D, ss$d[vcount(g) - 1:no + 1])
expect_equal(au_sa$D, ss$d[vcount(g) - 1:no + 1])
expect_equal(std(as_sa$X), std(U[, vcount(g) - 1:no + 1]))
expect_equal(std(as_sa$Y), std(V[, vcount(g) - 1:no + 1]))
expect_equal(std(au_sa$X), X[, vcount(g) - 1:no + 1])
expect_equal(std(au_sa$Y), Y[, vcount(g) - 1:no + 1])
})
test_that("Directed, weighted case works", {
withr::local_seed(42)
g <- random.graph.game(10, 20, type = "gnm", directed = TRUE)
E(g)$weight <- sample(1:5, ecount(g), replace = TRUE)
no <- 3
A <- g[]
A <- A + 1 / 2 * as(Matrix::Matrix(diag(degree(g)), doDiag = FALSE), "generalMatrix")
ss <- svd(A)
U <- std(ss$u)
V <- std(ss$v)
X <- std(ss$u %*% sqrt(diag(ss$d)))
Y <- std(ss$v %*% sqrt(diag(ss$d)))
au_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = TRUE
)
as_la <- embed_adjacency_matrix(g,
no = no, which = "la",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(std(as_la$X), std(U[, 1:no]))
expect_equal(std(as_la$Y), std(V[, 1:no]))
expect_equal(std(au_la$X), X[, 1:no])
expect_equal(std(au_la$Y), Y[, 1:no])
au_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = TRUE
)
as_lm <- embed_adjacency_matrix(g,
no = no, which = "lm",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(std(as_lm$X), std(U[, 1:no]))
expect_equal(std(as_lm$Y), std(V[, 1:no]))
expect_equal(std(au_lm$X), X[, 1:no])
expect_equal(std(au_lm$Y), Y[, 1:no])
au_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = TRUE
)
as_sa <- embed_adjacency_matrix(g,
no = no, which = "sa",
cvec = degree(g) / 2, scaled = FALSE
)
expect_equal(std(as_sa$X), std(U[, vcount(g) - 1:no + 1]))
expect_equal(std(as_sa$Y), std(V[, vcount(g) - 1:no + 1]))
expect_equal(std(au_sa$X), X[, vcount(g) - 1:no + 1])
expect_equal(std(au_sa$Y), Y[, vcount(g) - 1:no + 1])
})
test_that("Issue #50 is resolved", {
withr::local_seed(12345)
g <- erdos.renyi.game(15, .4)
w <- -log(runif(ecount(g)))
X1 <- embed_adjacency_matrix(g, 2, weights = w)
E(g)$weight <- w
X2 <- embed_adjacency_matrix(g, 2)
expect_equal(X1$D, X2$D)
})
test_that("Issue #51 is resolved", {
withr::local_seed(12345)
pref.matrix <- diag(0.2, 2) + 0.2
block.sizes <- c(800, 800)
n <- sum(block.sizes)
g <- sample_sbm(n, pref.matrix, block.sizes, directed = TRUE)
for (i in 1:25) {
ase <- embed_adjacency_matrix(g, 2)
expect_equal(mean(ase$X %*% t(ase$Y)), 0.299981018354173)
}
})
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