context("communities")
test_that("community detection functions work", {
library(igraph)
set.seed(42)
F <- list("cluster_edge_betweenness", "cluster_fast_greedy",
"cluster_label_prop", "cluster_leading_eigen",
"cluster_louvain", "cluster_spinglass", "cluster_walktrap")
if (has_glpk()) F <- c(F, list("cluster_optimal"))
karate <- make_graph("Zachary")
for (f in F) {
f <- get(f)
comm <- f(karate)
expect_that(modularity(comm),
equals(modularity(karate, membership(comm))))
cc <- communities(comm)
expect_true(all(!duplicated(unlist(cc))))
expect_true(all(unlist(cc) <= vcount(karate) & unlist(cc) >= 1))
expect_that(length(comm), equals(max(membership(comm))))
}
fc <- cluster_fast_greedy(karate)
m1 <- modularity(karate, cut_at(fc, no=1))
m2 <- modularity(karate, cut_at(fc, no=2))
m3 <- modularity(karate, cut_at(fc, no=3))
m4 <- modularity(karate, cut_at(fc, no=4))
expect_that(m1, equals(0))
expect_that(m2, equals(0.3717948718))
expect_that(m3, equals(0.3806706114))
expect_that(m4, equals(0.3759861933))
cr <- crossing(fc, karate)
expect_that(cr, equals(c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE,
TRUE, FALSE, FALSE, TRUE, TRUE, TRUE,
FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE,
FALSE, TRUE, FALSE, TRUE, FALSE, FALSE,
TRUE, TRUE, TRUE, FALSE, TRUE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
TRUE, TRUE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, TRUE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
FALSE, FALSE, FALSE, FALSE) ))
})
test_that("creating communities objects works", {
library(igraph)
set.seed(42)
karate <- make_graph("Zachary")
membership <- sample(1:2, vcount(karate), replace=TRUE)
mod <- modularity(karate, membership)
comm <- make_clusters(algorithm="random", membership=membership,
modularity = mod)
expect_that(as.vector(membership(comm)), equals(membership))
expect_that(modularity(comm), equals(mod))
expect_that(algorithm(comm), equals("random"))
})
test_that("communities function works", {
skip_if_no_glpk()
library(igraph)
g <- make_graph("Zachary")
oc <- cluster_optimal(g)
gr <- communities(oc)
expect_that(gr, equals
(structure(list(`1` = c(1L, 2L, 3L, 4L, 8L, 12L, 13L, 14L, 18L,
20L, 22L), `2` = c(5L, 6L, 7L, 11L, 17L), `3` = c(9L, 10L, 15L,
16L, 19L, 21L, 23L, 27L, 30L, 31L, 33L, 34L), `4` = c(24L, 25L,
26L, 28L, 29L, 32L)), .Dim = 4L, .Dimnames = list(c("1", "2",
"3", "4")))))
g <- make_ring(5) + make_ring(5)
V(g)$name <- letters[1:10]
oc <- cluster_optimal(g)
gr <- communities(oc)
expect_that(gr, equals(structure(list(`1` = letters[1:5],
`2` = letters[6:10]),
.Dim = 2L,
.Dimnames = list(c("1", "2")))))
})
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