Nothing
## ----------------------------------------------------------------
##
## IGraph R package
## Copyright (C) 2005-2014 Gabor Csardi <csardi.gabor@gmail.com>
## 334 Harvard street, Cambridge, MA 02139 USA
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
## 02110-1301 USA
##
## -----------------------------------------------------------------
#' Takes an argument list and extracts the constructor specification and
#' constructor modifiers from it.
#'
#' This is a helper function for the common parts of `make_()` and
#' `sample_()`.
#'
#' @param ... Parameters to extract from
#' @param .operation Human-readable description of the operation that this
#' helper is a part of
#' @param .variant Constructor variant; must be one of \sQuote{make},
#' \sQuote{graph} or \sQuote{sample}. Used in cases when the same constructor
#' specification has deterministic and random variants.
#' @family constructor modifiers
#' @return A named list with three items: \sQuote{cons} for the constructor
#' function, \sQuote{mods} for the modifiers and \sQuote{args} for the
#' remaining, unparsed arguments.
#' @noRd
.extract_constructor_and_modifiers <- function(..., .operation, .variant) {
args <- list(...)
cidx <- vapply(args, inherits, TRUE, what = "igraph_constructor_spec")
if (sum(cidx) == 0) {
stop("Don't know how to ", .operation, ", nothing given")
}
if (sum(cidx) > 1) {
stop("Don't know how to ", .operation, ", multiple constructors given")
}
cons <- args[cidx][[1]]
args <- args[!cidx]
## Modifiers
wmods <- vapply(args, inherits, TRUE, what = "igraph_constructor_modifier")
mods <- args[wmods]
args <- args[!wmods]
## Resolve the actual function in the specifier if it has multiple variants
if (!is.function(cons$fun)) {
variants <- names(cons$fun)
## 'graph' can fall back to 'make' and vice versa if one is present but
## not the other
if (!(.variant %in% variants)) {
if (.variant == "graph" && "make" %in% variants) {
.variant <- "make"
} else if (.variant == "make" && "graph" %in% variants) {
.variant <- "graph"
}
}
if (.variant %in% variants) {
cons$fun <- cons$fun[[.variant]]
} else {
stop("Don't know how to ", .operation, ", unknown constructor")
}
}
list(cons = cons, mods = mods, args = args)
}
#' Applies a set of constructor modifiers to an already constructed graph.
#'
#' This is a helper function for the common parts of `make_()` and
#' `sample_()`.
#'
#' @param graph The graph to apply the modifiers to
#' @param mods The modifiers to apply
#' @family constructor modifiers
#' @return The modified graph
#' @noRd
.apply_modifiers <- function(graph, mods) {
for (m in mods) {
if (m$id == "without_attr") {
## TODO: speed this up
ga <- graph_attr_names(graph)
va <- vertex_attr_names(graph)
ea <- edge_attr_names(graph)
for (g in ga) graph <- delete_graph_attr(graph, g)
for (v in va) graph <- delete_vertex_attr(graph, v)
for (e in ea) graph <- delete_edge_attr(graph, e)
} else if (m$id == "without_loops") {
graph <- simplify(graph, remove.loops = TRUE, remove.multiple = FALSE)
} else if (m$id == "without_multiples") {
graph <- simplify(graph, remove.loops = FALSE, remove.multiple = TRUE)
} else if (m$id == "simplified") {
graph <- simplify(graph)
} else if (m$id == "with_vertex_") {
m$args <- lapply(m$args, eval)
## TODO speed this up
for (a in seq_along(m$args)) {
n <- names(m$args)[a]
v <- m$args[[a]]
stopifnot(!is.null(n))
graph <- set_vertex_attr(graph, n, value = v)
}
} else if (m$id == "with_edge_") {
m$args <- lapply(m$args, eval)
## TODO speed this up
for (a in seq_along(m$args)) {
n <- names(m$args)[a]
v <- m$args[[a]]
stopifnot(!is.null(n))
graph <- set_edge_attr(graph, n, value = v)
}
} else if (m$id == "with_graph_") {
m$args <- lapply(m$args, eval)
## TODO speed this up
for (a in seq_along(m$args)) {
n <- names(m$args)[a]
v <- m$args[[a]]
stopifnot(!is.null(n))
graph <- set_graph_attr(graph, n, value = v)
}
}
}
graph
}
#' Make a new graph
#'
#' This is a generic function for creating graphs.
#'
#' @details
#' `make_()` is a generic function for creating graphs.
#' For every graph constructor in igraph that has a `make_` prefix,
#' there is a corresponding function without the prefix: e.g.
#' for [make_ring()] there is also [ring()], etc.
#'
#' The same is true for the random graph samplers, i.e. for each
#' constructor with a `sample_` prefix, there is a corresponding
#' function without that prefix.
#'
#' These shorter forms can be used together with `make_()`.
#' The advantage of this form is that the user can specify constructor
#' modifiers which work with all constructors. E.g. the
#' [with_vertex_()] modifier adds vertex attributes
#' to the newly created graphs.
#'
#' See the examples and the various constructor modifiers below.
#'
#' @param ... Parameters, see details below.
#'
#' @seealso simplified with_edge_ with_graph_ with_vertex_
#' without_loops without_multiples
#' @export
#' @examples
#' r <- make_(ring(10))
#' l <- make_(lattice(c(3, 3, 3)))
#'
#' r2 <- make_(ring(10), with_vertex_(color = "red", name = LETTERS[1:10]))
#' l2 <- make_(lattice(c(3, 3, 3)), with_edge_(weight = 2))
#'
#' ran <- sample_(degseq(c(3, 3, 3, 3, 3, 3), method = "simple"), simplified())
#' degree(ran)
#' is_simple(ran)
make_ <- function(...) {
me <- attr(sys.function(), "name") %||% "construct"
extracted <- .extract_constructor_and_modifiers(..., .operation = me, .variant = "make")
cons <- extracted$cons
cons_args <- if (cons$lazy) lapply(cons$args, "[[", "expr") else lazy_eval(cons$args)
res <- do_call(cons$fun, cons_args, extracted$args)
.apply_modifiers(res, extracted$mods)
}
#' Sample from a random graph model
#'
#' Generic function for sampling from network models.
#'
#' @details
#' TODO
#'
#' @param ... Parameters, see details below.
#'
#' @export
#' @examples
#' pref_matrix <- cbind(c(0.8, 0.1), c(0.1, 0.7))
#' blocky <- sample_(sbm(
#' n = 20, pref.matrix = pref_matrix,
#' block.sizes = c(10, 10)
#' ))
#'
#' blocky2 <- pref_matrix %>%
#' sample_sbm(n = 20, block.sizes = c(10, 10))
#'
#' ## Arguments are passed on from sample_ to sample_sbm
#' blocky3 <- pref_matrix %>%
#' sample_(sbm(), n = 20, block.sizes = c(10, 10))
#' @family games
sample_ <- function(...) {
me <- attr(sys.function(), "name") %||% "construct"
extracted <- .extract_constructor_and_modifiers(..., .operation = me, .variant = "sample")
cons <- extracted$cons
cons_args <- if (cons$lazy) lapply(cons$args, "[[", "expr") else lazy_eval(cons$args)
res <- do_call(cons$fun, cons_args, extracted$args)
.apply_modifiers(res, extracted$mods)
}
#' Convert object to a graph
#'
#' This is a generic function to convert R objects to igraph graphs.
#'
#' @details
#' TODO
#'
#' @param ... Parameters, see details below.
#'
#' @export
#' @examples
#' ## These are equivalent
#' graph_(cbind(1:5, 2:6), from_edgelist(directed = FALSE))
#' graph_(cbind(1:5, 2:6), from_edgelist(), directed = FALSE)
graph_ <- function(...) {
me <- attr(sys.function(), "name") %||% "construct"
extracted <- .extract_constructor_and_modifiers(..., .operation = me, .variant = "graph")
cons <- extracted$cons
cons_args <- if (cons$lazy) lapply(cons$args, "[[", "expr") else lazy_eval(cons$args)
res <- do_call(cons$fun, cons_args, extracted$args)
.apply_modifiers(res, extracted$mods)
}
attr(make_, "name") <- "make_"
attr(sample_, "name") <- "sample_"
attr(graph_, "name") <- "graph_"
constructor_spec <- function(fun, ..., .lazy = FALSE) {
structure(
list(
fun = fun,
args = lazy_dots(...),
lazy = .lazy
),
class = "igraph_constructor_spec"
)
}
## -----------------------------------------------------------------
## Constructor modifiers
constructor_modifier <- function(...) {
structure(
list(...),
class = "igraph_constructor_modifier"
)
}
#' Construtor modifier to remove all attributes from a graph
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' g1 <- make_ring(10)
#' g1
#'
#' g2 <- make_(ring(10), without_attr())
#' g2
without_attr <- function() {
constructor_modifier(
id = "without_attr"
)
}
#' Constructor modifier to drop loop edges
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' # An artificial example
#' make_(full_graph(5, loops = TRUE))
#' make_(full_graph(5, loops = TRUE), without_loops())
without_loops <- function() {
constructor_modifier(
id = "without_loops"
)
}
#' Constructor modifier to drop multiple edges
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' sample_(pa(10, m = 3, algorithm = "bag"))
#' sample_(pa(10, m = 3, algorithm = "bag"), without_multiples())
without_multiples <- function() {
constructor_modifier(
id = "without_multiples"
)
}
#' Constructor modifier to drop multiple and loop edges
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' sample_(pa(10, m = 3, algorithm = "bag"))
#' sample_(pa(10, m = 3, algorithm = "bag"), simplified())
simplified <- function() {
constructor_modifier(
id = "simplified"
)
}
#' Constructor modifier to add vertex attributes
#'
#' @param ... The attributes to add. They must be named.
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' make_(
#' ring(10),
#' with_vertex_(
#' color = "#7fcdbb",
#' frame.color = "#7fcdbb",
#' name = LETTERS[1:10]
#' )
#' ) %>%
#' plot()
with_vertex_ <- function(...) {
args <- grab_args()
constructor_modifier(
id = "with_vertex_",
args = args
)
}
#' Constructor modifier to add edge attributes
#'
#' @param ... The attributes to add. They must be named.
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' make_(
#' ring(10),
#' with_edge_(
#' color = "red",
#' weight = rep(1:2, 5)
#' )
#' ) %>%
#' plot()
with_edge_ <- function(...) {
args <- grab_args()
constructor_modifier(
id = "with_edge_",
args = args
)
}
#' Constructor modifier to add graph attributes
#'
#' @param ... The attributes to add. They must be named.
#'
#' @family constructor modifiers
#'
#' @export
#' @examples
#' make_(ring(10), with_graph_(name = "10-ring"))
with_graph_ <- function(...) {
args <- grab_args()
constructor_modifier(
id = "with_graph_",
args = args
)
}
## -----------------------------------------------------------------
#' Create an igraph graph from a list of edges, or a notable graph
#'
#' @section Notable graphs:
#'
#' `make_graph()` can create some notable graphs. The name of the
#' graph (case insensitive), a character scalar must be supplied as
#' the `edges` argument, and other arguments are ignored. (A warning
#' is given is they are specified.)
#'
#' `make_graph()` knows the following graphs: \describe{
#' \item{Bull}{The bull graph, 5 vertices, 5 edges, resembles to the head
#' of a bull if drawn properly.}
#' \item{Chvatal}{This is the smallest triangle-free graph that is
#' both 4-chromatic and 4-regular. According to the Grunbaum conjecture there
#' exists an m-regular, m-chromatic graph with n vertices for every m>1 and
#' n>2. The Chvatal graph is an example for m=4 and n=12. It has 24 edges.}
#' \item{Coxeter}{A non-Hamiltonian cubic symmetric graph with 28 vertices and
#' 42 edges.}
#' \item{Cubical}{The Platonic graph of the cube. A convex regular
#' polyhedron with 8 vertices and 12 edges.}
#' \item{Diamond}{A graph with 4 vertices and 5 edges, resembles to a
#' schematic diamond if drawn properly.}
#' \item{Dodecahedral, Dodecahedron}{Another Platonic solid with 20 vertices
#' and 30 edges.}
#' \item{Folkman}{The semisymmetric graph with minimum number of
#' vertices, 20 and 40 edges. A semisymmetric graph is regular, edge transitive
#' and not vertex transitive.}
#' \item{Franklin}{This is a graph whose embedding
#' to the Klein bottle can be colored with six colors, it is a counterexample
#' to the necessity of the Heawood conjecture on a Klein bottle. It has 12
#' vertices and 18 edges.}
#' \item{Frucht}{The Frucht Graph is the smallest
#' cubical graph whose automorphism group consists only of the identity
#' element. It has 12 vertices and 18 edges.}
#' \item{Grotzsch}{The Groetzsch
#' graph is a triangle-free graph with 11 vertices, 20 edges, and chromatic
#' number 4. It is named after German mathematician Herbert Groetzsch, and its
#' existence demonstrates that the assumption of planarity is necessary in
#' Groetzsch's theorem that every triangle-free planar graph is 3-colorable.}
#' \item{Heawood}{The Heawood graph is an undirected graph with 14 vertices and
#' 21 edges. The graph is cubic, and all cycles in the graph have six or more
#' edges. Every smaller cubic graph has shorter cycles, so this graph is the
#' 6-cage, the smallest cubic graph of girth 6.}
#' \item{Herschel}{The Herschel
#' graph is the smallest nonhamiltonian polyhedral graph. It is the unique such
#' graph on 11 nodes, and has 18 edges.}
#' \item{House}{The house graph is a
#' 5-vertex, 6-edge graph, the schematic draw of a house if drawn properly,
#' basicly a triangle of the top of a square.}
#' \item{HouseX}{The same as the
#' house graph with an X in the square. 5 vertices and 8 edges.}
#' \item{Icosahedral, Icosahedron}{A Platonic solid with 12 vertices and 30
#' edges.}
#' \item{Krackhardt kite}{A social network with 10 vertices and 18
#' edges. Krackhardt, D. Assessing the Political Landscape: Structure,
#' Cognition, and Power in Organizations. Admin. Sci. Quart. 35, 342-369,
#' 1990.}
#' \item{Levi}{The graph is a 4-arc transitive cubic graph, it has 30
#' vertices and 45 edges.}
#' \item{McGee}{The McGee graph is the unique 3-regular
#' 7-cage graph, it has 24 vertices and 36 edges.}
#' \item{Meredith}{The Meredith
#' graph is a quartic graph on 70 nodes and 140 edges that is a counterexample
#' to the conjecture that every 4-regular 4-connected graph is Hamiltonian.}
#' \item{Noperfectmatching}{A connected graph with 16 vertices and 27 edges
#' containing no perfect matching. A matching in a graph is a set of pairwise
#' non-adjacent edges; that is, no two edges share a common vertex. A perfect
#' matching is a matching which covers all vertices of the graph.}
#' \item{Nonline}{A graph whose connected components are the 9 graphs whose
#' presence as a vertex-induced subgraph in a graph makes a nonline graph. It
#' has 50 vertices and 72 edges.}
#' \item{Octahedral, Octahedron}{Platonic solid
#' with 6 vertices and 12 edges.}
#' \item{Petersen}{A 3-regular graph with 10
#' vertices and 15 edges. It is the smallest hypohamiltonian graph, i.e. it is
#' non-hamiltonian but removing any single vertex from it makes it
#' Hamiltonian.}
#' \item{Robertson}{The unique (4,5)-cage graph, i.e. a 4-regular
#' graph of girth 5. It has 19 vertices and 38 edges.}
#' \item{Smallestcyclicgroup}{A smallest nontrivial graph whose automorphism
#' group is cyclic. It has 9 vertices and 15 edges.}
#' \item{Tetrahedral,
#' Tetrahedron}{Platonic solid with 4 vertices and 6 edges.}
#' \item{Thomassen}{The smallest hypotraceable graph, on 34 vertices and 52
#' edges. A hypotraceable graph does not contain a Hamiltonian path but after
#' removing any single vertex from it the remainder always contains a
#' Hamiltonian path. A graph containing a Hamiltonian path is called traceable.}
#' \item{Tutte}{Tait's Hamiltonian graph conjecture states that every
#' 3-connected 3-regular planar graph is Hamiltonian. This graph is a
#' counterexample. It has 46 vertices and 69 edges.}
#' \item{Uniquely3colorable}{Returns a 12-vertex, triangle-free graph with
#' chromatic number 3 that is uniquely 3-colorable.}
#' \item{Walther}{An identity
#' graph with 25 vertices and 31 edges. An identity graph has a single graph
#' automorphism, the trivial one.}
#' \item{Zachary}{Social network of friendships
#' between 34 members of a karate club at a US university in the 1970s. See W.
#' W. Zachary, An information flow model for conflict and fission in small
#' groups, Journal of Anthropological Research 33, 452-473 (1977). } }
#'
#' @encoding UTF-8
#' @aliases graph.famous graph
#' @param edges A vector defining the edges, the first edge points
#' from the first element to the second, the second edge from the third
#' to the fourth, etc. For a numeric vector, these are interpreted
#' as internal vertex ids. For character vectors, they are interpreted
#' as vertex names.
#'
#' Alternatively, this can be a character scalar, the name of a
#' notable graph. See Notable graphs below. The name is case
#' insensitive.
#'
#' Starting from igraph 0.8.0, you can also include literals here,
#' via igraph's formula notation (see [graph_from_literal()]).
#' In this case, the first term of the formula has to start with
#' a \sQuote{`~`} character, just like regular formulae in R.
#' See examples below.
#' @param ... For `make_graph()`: extra arguments for the case when the
#' graph is given via a literal, see [graph_from_literal()].
#' For `directed_graph()` and `undirected_graph()`:
#' Passed to `make_directed_graph()` or `make_undirected_graph()`.
#' @param n The number of vertices in the graph. This argument is
#' ignored (with a warning) if `edges` are symbolic vertex names. It
#' is also ignored if there is a bigger vertex id in `edges`. This
#' means that for this function it is safe to supply zero here if the
#' vertex with the largest id is not an isolate.
#' @param isolates Character vector, names of isolate vertices,
#' for symbolic edge lists. It is ignored for numeric edge lists.
#' @param directed Whether to create a directed graph.
#' @param dir It is the same as `directed`, for compatibility.
#' Do not give both of them.
#' @param simplify For graph literals, whether to simplify the graph.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' make_graph(c(1, 2, 2, 3, 3, 4, 5, 6), directed = FALSE)
#' make_graph(c("A", "B", "B", "C", "C", "D"), directed = FALSE)
#'
#' solids <- list(
#' make_graph("Tetrahedron"),
#' make_graph("Cubical"),
#' make_graph("Octahedron"),
#' make_graph("Dodecahedron"),
#' make_graph("Icosahedron")
#' )
#'
#' graph <- make_graph(
#' ~ A - B - C - D - A, E - A:B:C:D,
#' F - G - H - I - F, J - F:G:H:I,
#' K - L - M - N - K, O - K:L:M:N,
#' P - Q - R - S - P, T - P:Q:R:S,
#' B - F, E - J, C - I, L - T, O - T, M - S,
#' C - P, C - L, I - L, I - P
#' )
make_graph <- function(edges, ..., n = max(edges), isolates = NULL,
directed = TRUE, dir = directed, simplify = TRUE) {
if (inherits(edges, "formula")) {
if (!missing(n)) stop("'n' should not be given for graph literals")
if (!missing(isolates)) {
stop("'isolates' should not be given for graph literals")
}
if (!missing(directed)) {
stop("'directed' should not be given for graph literals")
}
mf <- as.list(match.call())[-1]
mf[[1]] <- mf[[1]][[2]]
graph_from_literal_i(mf)
} else {
if (!missing(simplify)) {
stop("'simplify' should only be used for graph literals")
}
if (!missing(dir) && !missing(directed)) {
stop("Only give one of 'dir' and 'directed'")
}
if (!missing(dir) && missing(directed)) directed <- dir
if (is.character(edges) && length(edges) == 1) {
if (!missing(n)) warning("'n' is ignored for the '", edges, "' graph")
if (!missing(isolates)) {
warning("'isolates' is ignored for the '", edges, "' graph")
}
if (!missing(directed)) {
warning("'directed' is ignored for the '", edges, "' graph")
}
if (!missing(dir)) {
warning("'dir' is ignored for the '", edges, "' graph")
}
if (length(list(...))) stop("Extra arguments in make_graph")
make_famous_graph(edges)
## NULL and empty logical vector is allowed for compatibility
} else if (is.numeric(edges) || is.null(edges) ||
(is.logical(edges) && length(edges) == 0)) {
if (is.null(edges) || is.logical(edges)) edges <- as.numeric(edges)
if (!is.null(isolates)) {
warning("'isolates' ignored for numeric edge list")
}
old_graph <- function(edges, n = max(edges), directed = TRUE) {
on.exit(.Call(R_igraph_finalizer))
if (missing(n) && (is.null(edges) || length(edges) == 0)) {
n <- 0
}
.Call(
R_igraph_create, as.numeric(edges) - 1, as.numeric(n),
as.logical(directed)
)
}
args <- list(edges, ...)
if (!missing(n)) args <- c(args, list(n = n))
if (!missing(directed)) args <- c(args, list(directed = directed))
do.call(old_graph, args)
} else if (is.character(edges)) {
if (!missing(n)) {
warning("'n' is ignored for edge list with vertex names")
}
if (length(list(...))) stop("Extra arguments in make_graph")
el <- matrix(edges, ncol = 2, byrow = TRUE)
res <- graph_from_edgelist(el, directed = directed)
if (!is.null(isolates)) {
isolates <- as.character(isolates)
res <- res + vertices(isolates)
}
res
} else {
stop("'edges' must be numeric or character")
}
}
}
make_famous_graph <- function(name) {
name <- gsub("\\s", "_", name)
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_famous, as.character(name))
if (igraph_opt("add.params")) {
res$name <- capitalize(name)
}
res
}
#' @rdname make_graph
#' @export
make_directed_graph <- function(edges, n = max(edges)) {
if (missing(n)) {
make_graph(edges, directed = TRUE)
} else {
make_graph(edges, n = n, directed = TRUE)
}
}
#' @rdname make_graph
#' @export
make_undirected_graph <- function(edges, n = max(edges)) {
if (missing(n)) {
make_graph(edges, directed = FALSE)
} else {
make_graph(edges, n = n, directed = FALSE)
}
}
#' @rdname make_graph
#' @export
directed_graph <- function(...) constructor_spec(make_directed_graph, ...)
#' @rdname make_graph
#' @export
undirected_graph <- function(...) constructor_spec(make_undirected_graph, ...)
## -----------------------------------------------------------------
#' A graph with no edges
#'
#' @aliases graph.empty
#' @concept Empty graph.
#' @param n Number of vertices.
#' @param directed Whether to create a directed graph.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' make_empty_graph(n = 10)
#' make_empty_graph(n = 5, directed = FALSE)
make_empty_graph <- function(n = 0, directed = TRUE) {
# Argument checks
if (is.null(n)) {
stop("number of vertices must be an integer")
}
n <- suppressWarnings(as.integer(n))
if (is.na(n)) {
stop("number of vertices must be an integer")
}
directed <- as.logical(directed)
on.exit(.Call(R_igraph_finalizer))
# Function call
res <- .Call(R_igraph_empty, n, directed)
res
}
#' @rdname make_empty_graph
#' @param ... Passed to `make_graph_empty`.
#' @export
empty_graph <- function(...) constructor_spec(make_empty_graph, ...)
## -----------------------------------------------------------------
#' Creating (small) graphs via a simple interface
#'
#' This function is useful if you want to create a small (named) graph
#' quickly, it works for both directed and undirected graphs.
#'
#' @details
#' `graph_from_literal()` is very handy for creating small graphs quickly.
#' You need to supply one or more R expressions giving the structure of
#' the graph. The expressions consist of vertex names and edge
#' operators. An edge operator is a sequence of \sQuote{`-`} and
#' \sQuote{`+`} characters, the former is for the edges and the
#' latter is used for arrow heads. The edges can be arbitrarily long,
#' i.e. you may use as many \sQuote{`-`} characters to \dQuote{draw}
#' them as you like.
#'
#' If all edge operators consist of only \sQuote{`-`} characters
#' then the graph will be undirected, whereas a single \sQuote{`+`}
#' character implies a directed graph.
#'
#' Let us see some simple examples. Without arguments the function
#' creates an empty graph:
#' \preformatted{ graph_from_literal()
#' }
#'
#' A simple undirected graph with two vertices called \sQuote{A} and
#' \sQuote{B} and one edge only:
#' \preformatted{ graph_from_literal(A-B)
#' }
#'
#' Remember that the length of the edges does not matter, so we could
#' have written the following, this creates the same graph:
#' \preformatted{ graph_from_literal( A-----B )
#' }
#'
#' If you have many disconnected components in the graph, separate them
#' with commas. You can also give isolate vertices.
#' \preformatted{ graph_from_literal( A--B, C--D, E--F, G--H, I, J, K )
#' }
#'
#' The \sQuote{`:`} operator can be used to define vertex sets. If
#' an edge operator connects two vertex sets then every vertex from the
#' first set will be connected to every vertex in the second set. The
#' following form creates a full graph, including loop edges:
#' \preformatted{ graph_from_literal( A:B:C:D -- A:B:C:D )
#' }
#'
#' In directed graphs, edges will be created only if the edge operator
#' includes a arrow head (\sQuote{+}) *at the end* of the edge:
#' \preformatted{ graph_from_literal( A -+ B -+ C )
#' graph_from_literal( A +- B -+ C )
#' graph_from_literal( A +- B -- C )
#' }
#' Thus in the third example no edge is created between vertices `B`
#' and `C`.
#'
#' Mutual edges can be also created with a simple edge operator:
#' \preformatted{ graph_from_literal( A +-+ B +---+ C ++ D + E)
#' }
#' Note again that the length of the edge operators is arbitrary,
#' \sQuote{`+`}, \sQuote{`++`} and \sQuote{`+-----+`} have
#' exactly the same meaning.
#'
#' If the vertex names include spaces or other special characters then
#' you need to quote them:
#' \preformatted{ graph_from_literal( "this is" +- "a silly" -+ "graph here" )
#' }
#' You can include any character in the vertex names this way, even
#' \sQuote{+} and \sQuote{-} characters.
#'
#' See more examples below.
#'
#' @aliases graph.formula
#' @param ... For `graph_from_literal()` the formulae giving the
#' structure of the graph, see details below. For `from_literal()`
#' all arguments are passed to `graph_from_literal()`.
#' @param simplify Logical scalar, whether to call [simplify()]
#' on the created graph. By default the graph is simplified, loop and
#' multiple edges are removed.
#' @return An igraph graph
#'
#' @family deterministic constructors
#' @export
#' @examples
#' # A simple undirected graph
#' g <- graph_from_literal(
#' Alice - Bob - Cecil - Alice,
#' Daniel - Cecil - Eugene,
#' Cecil - Gordon
#' )
#' g
#'
#' # Another undirected graph, ":" notation
#' g2 <- graph_from_literal(Alice - Bob:Cecil:Daniel, Cecil:Daniel - Eugene:Gordon)
#' g2
#'
#' # A directed graph
#' g3 <- graph_from_literal(
#' Alice +-+ Bob --+ Cecil +-- Daniel,
#' Eugene --+ Gordon:Helen
#' )
#' g3
#'
#' # A graph with isolate vertices
#' g4 <- graph_from_literal(Alice -- Bob -- Daniel, Cecil:Gordon, Helen)
#' g4
#' V(g4)$name
#'
#' # "Arrows" can be arbitrarily long
#' g5 <- graph_from_literal(Alice +---------+ Bob)
#' g5
#'
#' # Special vertex names
#' g6 <- graph_from_literal("+" -- "-", "*" -- "/", "%%" -- "%/%")
#' g6
#'
graph_from_literal <- function(..., simplify = TRUE) {
mf <- as.list(match.call())[-1]
graph_from_literal_i(mf)
}
graph_from_literal_i <- function(mf) {
## In case 'simplify' is given
simplify <- TRUE
if ("simplify" %in% names(mf)) {
w <- which(names(mf) == "simplify")
if (length(w) > 1) {
stop("'simplify' specified multiple times")
}
simplify <- eval(mf[[w]])
mf <- mf[-w]
}
## Operators first
f <- function(x) {
if (is.call(x)) {
return(list(as.character(x[[1]]), lapply(x[-1], f)))
} else {
return(NULL)
}
}
ops <- unlist(lapply(mf, f))
if (all(ops %in% c("-", ":"))) {
directed <- FALSE
} else if (all(ops %in% c("-", "+", ":"))) {
directed <- TRUE
} else {
stop("Invalid operator in formula")
}
f <- function(x) {
if (is.call(x)) {
if (length(x) == 3) {
return(list(f(x[[2]]), op = as.character(x[[1]]), f(x[[3]])))
} else {
return(list(op = as.character(x[[1]]), f(x[[2]])))
}
} else {
return(c(sym = as.character(x)))
}
}
ret <- lapply(mf, function(x) unlist(f(x)))
v <- unique(unlist(lapply(ret, function(x) {
x[names(x) == "sym"]
})))
## Merge symbols for ":"
ret <- lapply(ret, function(x) {
res <- list()
for (i in seq(along.with = x)) {
if (x[i] == ":" && names(x)[i] == "op") {
## SKIP
} else if (i > 1 && x[i - 1] == ":" && names(x)[i - 1] == "op") {
res[[length(res)]] <- c(res[[length(res)]], unname(x[i]))
} else {
res <- c(res, x[i])
}
}
res
})
## Ok, create the edges
edges <- numeric()
for (i in seq(along.with = ret)) {
prev.sym <- character()
lhead <- rhead <- character()
for (j in seq(along.with = ret[[i]])) {
act <- ret[[i]][[j]]
if (names(ret[[i]])[j] == "op") {
if (length(lhead) == 0) {
lhead <- rhead <- act
} else {
rhead <- act
}
} else if (names(ret[[i]])[j] == "sym") {
for (ps in prev.sym) {
for (ps2 in act) {
if (lhead == "+") {
edges <- c(edges, unname(c(ps2, ps)))
}
if (!directed || rhead == "+") {
edges <- c(edges, unname(c(ps, ps2)))
}
}
}
lhead <- rhead <- character()
prev.sym <- act
}
}
}
ids <- seq(along.with = v)
names(ids) <- v
res <- make_graph(unname(ids[edges]), n = length(v), directed = directed)
if (simplify) res <- simplify(res)
res <- set_vertex_attr(res, "name", value = v)
res
}
#' @rdname graph_from_literal
#' @export
from_literal <- function(...) {
constructor_spec(graph_from_literal, ..., .lazy = TRUE)
}
## -----------------------------------------------------------------
#' Create a star graph, a tree with n vertices and n - 1 leaves
#'
#' `star()` creates a star graph, in this every single vertex is
#' connected to the center vertex and nobody else.
#'
#' @aliases graph.star
#' @concept Star graph
#' @param n Number of vertices.
#' @param mode It defines the direction of the
#' edges, `in`: the edges point *to* the center, `out`:
#' the edges point *from* the center, `mutual`: a directed
#' star is created with mutual edges, `undirected`: the edges
#' are undirected.
#' @param center ID of the center vertex.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' make_star(10, mode = "out")
#' make_star(5, mode = "undirected")
make_star <- function(n, mode = c("in", "out", "mutual", "undirected"),
center = 1) {
mode <- igraph.match.arg(mode)
mode1 <- switch(mode,
"out" = 0,
"in" = 1,
"undirected" = 2,
"mutual" = 3
)
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_star, as.numeric(n), as.numeric(mode1),
as.numeric(center) - 1
)
if (igraph_opt("add.params")) {
res$name <- switch(mode,
"in" = "In-star",
"out" = "Out-star",
"Star"
)
res$mode <- mode
res$center <- center
}
res
}
#' @rdname make_star
#' @param ... Passed to `make_star()`.
#' @export
star <- function(...) constructor_spec(make_star, ...)
## -----------------------------------------------------------------
#' Create a full graph
#'
#' @aliases graph.full
#' @concept Full graph
#' @param n Number of vertices.
#' @param directed Whether to create a directed graph.
#' @param loops Whether to add self-loops to the graph.
#' @return An igraph graph
#'
#' @family deterministic constructors
#' @export
#' @examples
#' make_full_graph(5)
#' print_all(make_full_graph(4, directed = TRUE))
make_full_graph <- function(n, directed = FALSE, loops = FALSE) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_full, as.numeric(n), as.logical(directed),
as.logical(loops)
)
if (igraph_opt("add.params")) {
res$name <- "Full graph"
res$loops <- loops
}
res
}
#' @rdname make_full_graph
#' @param ... Passed to `make_full_graph()`.
#' @export
full_graph <- function(...) constructor_spec(make_full_graph, ...)
## -----------------------------------------------------------------
#' Create a lattice graph
#'
#' `make_lattice()` is a flexible function, it can create lattices of
#' arbitrary dimensions, periodic or aperiodic ones. It has two
#' forms. In the first form you only supply `dimvector`, but not
#' `length` and `dim`. In the second form you omit
#' `dimvector` and supply `length` and `dim`.
#'
#' @aliases graph.lattice
#' @concept Lattice
#' @param dimvector A vector giving the size of the lattice in each
#' dimension.
#' @param length Integer constant, for regular lattices, the size of the
#' lattice in each dimension.
#' @param dim Integer constant, the dimension of the lattice.
#' @param nei The distance within which (inclusive) the neighbors on the
#' lattice will be connected. This parameter is not used right now.
#' @param directed Whether to create a directed lattice.
#' @param mutual Logical, if `TRUE` directed lattices will be
#' mutually connected.
#' @param circular Logical, if `TRUE` the lattice or ring will be
#' circular.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' make_lattice(c(5, 5, 5))
#' make_lattice(length = 5, dim = 3)
make_lattice <- function(dimvector = NULL, length = NULL, dim = NULL,
nei = 1, directed = FALSE, mutual = FALSE,
circular = FALSE) {
if (is.numeric(length) && length != floor(length)) {
warning("length was rounded to the nearest integer")
length <- round(length)
}
if (is.null(dimvector)) {
dimvector <- rep(length, dim)
}
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_lattice, as.numeric(dimvector), as.numeric(nei),
as.logical(directed), as.logical(mutual),
as.logical(circular)
)
if (igraph_opt("add.params")) {
res$name <- "Lattice graph"
res$dimvector <- dimvector
res$nei <- nei
res$mutual <- mutual
res$circular <- circular
}
res
}
#' @rdname make_lattice
#' @param ... Passed to `make_lattice()`.
#' @export
lattice <- function(...) constructor_spec(make_lattice, ...)
## -----------------------------------------------------------------
#' Create a ring graph
#'
#' A ring is a one-dimensional lattice and this function is a special case
#' of [make_lattice()].
#'
#' @aliases make_ring graph.ring
#' @param n Number of vertices.
#' @param directed Whether the graph is directed.
#' @param mutual Whether directed edges are mutual. It is ignored in
#' undirected graphs.
#' @param circular Whether to create a circular ring. A non-circular
#' ring is essentially a \dQuote{line}: a tree where every non-leaf
#' vertex has one child.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' print_all(make_ring(10))
#' print_all(make_ring(10, directed = TRUE, mutual = TRUE))
make_ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_ring, as.numeric(n), as.logical(directed),
as.logical(mutual), as.logical(circular)
)
if (igraph_opt("add.params")) {
res$name <- "Ring graph"
res$mutual <- mutual
res$circular <- circular
}
res
}
#' @rdname make_ring
#' @param ... Passed to `make_ring()`.
#' @export
ring <- function(...) constructor_spec(make_ring, ...)
## -----------------------------------------------------------------
#' Create tree graphs
#'
#' Create a k-ary tree graph, where almost all vertices other than the leaves
#' have the same number of children.
#'
#' @aliases graph.tree
#' @concept Trees.
#' @param n Number of vertices.
#' @param children Integer scalar, the number of children of a vertex
#' (except for leafs)
#' @param mode Defines the direction of the
#' edges. `out` indicates that the edges point from the parent to
#' the children, `in` indicates that they point from the children
#' to their parents, while `undirected` creates an undirected
#' graph.
#' @return An igraph graph
#'
#' @family deterministic constructors
#' @export
#' @examples
#' make_tree(10, 2)
#' make_tree(10, 3, mode = "undirected")
make_tree <- function(n, children = 2, mode = c("out", "in", "undirected")) {
mode <- igraph.match.arg(mode)
mode1 <- switch(mode,
"out" = 0,
"in" = 1,
"undirected" = 2
)
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_tree, as.numeric(n), as.numeric(children),
as.numeric(mode1)
)
if (igraph_opt("add.params")) {
res$name <- "Tree"
res$children <- children
res$mode <- mode
}
res
}
#' Sample trees randomly and uniformly
#'
#' `sample_tree()` generates a random with a given number of nodes uniform
#' at random from the set of labelled trees.
#'
#' In other words, the function generates each possible labelled tree with the
#' given number of nodes with the same probability.
#'
#' @param n The number of nodes in the tree
#' @param directed Whether to create a directed tree. The edges of the tree are
#' oriented away from the root.
#' @param method The algorithm to use to generate the tree. \sQuote{prufer}
#' samples Prüfer sequences uniformly and then converts the sampled sequence to
#' a tree. \sQuote{lerw} performs a loop-erased random walk on the complete
#' graph to uniformly sampleits spanning trees. (This is also known as Wilson's
#' algorithm). The default is \sQuote{lerw}. Note that the method based on
#' Prüfer sequences does not support directed trees at the moment.
#' @return A graph object.
#'
#' @family games
#' @keywords graphs
#' @examples
#'
#' g <- sample_tree(100, method = "lerw")
#'
#' @export
sample_tree <- tree_game_impl
#' @rdname make_tree
#' @param ... Passed to `make_tree()` or `sample_tree()`.
#' @export
tree <- function(...) constructor_spec(list(make = make_tree, sample = sample_tree), ...)
## -----------------------------------------------------------------
#' Create an undirected tree graph from its Prüfer sequence
#'
#' `make_from_prufer()` creates an undirected tree graph from its Prüfer
#' sequence.
#'
#' The Prüfer sequence of a tree graph with n labeled vertices is a sequence of
#' n-2 numbers, constructed as follows. If the graph has more than two vertices,
#' find a vertex with degree one, remove it from the tree and add the label of
#' the vertex that it was connected to to the sequence. Repeat until there are
#' only two vertices in the remaining graph.
#'
#' @param prufer The Prüfer sequence to convert into a graph
#' @return A graph object.
#'
#' @seealso [to_prufer()] to convert a graph into its Prüfer sequence
#' @keywords graphs
#' @examples
#'
#' g <- make_tree(13, 3)
#' to_prufer(g)
#' @family trees
#' @export
make_from_prufer <- from_prufer_impl
#' @rdname make_from_prufer
#' @param ... Passed to `make_from_prufer()`
#' @export
from_prufer <- function(...) constructor_spec(make_from_prufer, ...)
## -----------------------------------------------------------------
#' Create a graph from the Graph Atlas
#'
#' `graph_from_atlas()` creates graphs from the book
#' \sQuote{An Atlas of Graphs} by
#' Roland C. Read and Robin J. Wilson. The atlas contains all undirected
#' graphs with up to seven vertices, numbered from 0 up to 1252. The
#' graphs are listed:
#' \enumerate{
#' \item in increasing order of number of nodes;
#' \item for a fixed number of nodes, in increasing order of the number
#' of edges;
#' \item for fixed numbers of nodes and edges, in increasing order of
#' the degree sequence, for example 111223 < 112222;
#' \item for fixed degree sequence, in increasing number of
#' automorphisms.
#' }
#'
#' @aliases graph.atlas
#' @concept Graph Atlas.
#' @param n The id of the graph to create.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' ## Some randomly picked graphs from the atlas
#' graph_from_atlas(sample(0:1252, 1))
#' graph_from_atlas(sample(0:1252, 1))
graph_from_atlas <- function(n) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_atlas, as.numeric(n))
if (igraph_opt("add.params")) {
res$name <- sprintf("Graph from the Atlas #%i", n)
res$n <- n
}
res
}
#' @rdname graph_from_atlas
#' @param ... Passed to `graph_from_atlas()`.
#' @export
atlas <- function(...) constructor_spec(graph_from_atlas, ...)
## -----------------------------------------------------------------
#' Create an extended chordal ring graph
#'
#' `make_chordal_ring()` creates an extended chordal ring.
#' An extended chordal ring is regular graph, each node has the same
#' degree. It can be obtained from a simple ring by adding some extra
#' edges specified by a matrix. Let p denote the number of columns in
#' the \sQuote{`W`} matrix. The extra edges of vertex `i`
#' are added according to column `i mod p` in
#' \sQuote{`W`}. The number of extra edges is the number
#' of rows in \sQuote{`W`}: for each row `j` an edge
#' `i->i+w[ij]` is added if `i+w[ij]` is less than the number
#' of total nodes. See also Kotsis, G: Interconnection Topologies for
#' Parallel Processing Systems, PARS Mitteilungen 11, 1-6, 1993.
#'
#' @aliases graph.extended.chordal.ring
#' @param n The number of vertices.
#' @param w A matrix which specifies the extended chordal ring. See
#' details below.
#' @param directed Logical scalar, whether or not to create a directed graph.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' chord <- make_chordal_ring(
#' 15,
#' matrix(c(3, 12, 4, 7, 8, 11), nr = 2)
#' )
make_chordal_ring <- function(n, w, directed = FALSE) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
R_igraph_extended_chordal_ring, as.integer(n),
as.matrix(w), as.logical(directed)
)
if (igraph_opt("add.params")) {
res$name <- "Extended chordal ring"
res$w <- w
}
res
}
#' @rdname make_chordal_ring
#' @param ... Passed to `make_chordal_ring()`.
#' @export
chordal_ring <- function(...) constructor_spec(make_chordal_ring, ...)
## -----------------------------------------------------------------
#' Line graph of a graph
#'
#' This function calculates the line graph of another graph.
#'
#' The line graph `L(G)` of a `G` undirected graph is defined as
#' follows. `L(G)` has one vertex for each edge in `G` and two
#' vertices in `L(G)` are connected by an edge if their corresponding
#' edges share an end point.
#'
#' The line graph `L(G)` of a `G` directed graph is slightly
#' different, `L(G)` has one vertex for each edge in `G` and two
#' vertices in `L(G)` are connected by a directed edge if the target of
#' the first vertex's corresponding edge is the same as the source of the
#' second vertex's corresponding edge.
#'
#' @aliases line.graph
#' @param graph The input graph, it can be directed or undirected.
#' @return A new graph object.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}, the first version of
#' the C code was written by Vincent Matossian.
#' @keywords graphs
#' @examples
#'
#' # generate the first De-Bruijn graphs
#' g <- make_full_graph(2, directed = TRUE, loops = TRUE)
#' make_line_graph(g)
#' make_line_graph(make_line_graph(g))
#' make_line_graph(make_line_graph(make_line_graph(g)))
#'
#' @export
make_line_graph <- function(graph) {
ensure_igraph(graph)
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_linegraph, graph)
if (igraph_opt("add.params")) {
res$name <- "Line graph"
}
res
}
#' @rdname make_line_graph
#' @param ... Passed to `make_line_graph()`.
#' @export
line_graph <- function(...) constructor_spec(make_line_graph, ...)
## -----------------------------------------------------------------
#' De Bruijn graphs
#'
#' De Bruijn graphs are labeled graphs representing the overlap of strings.
#'
#' A de Bruijn graph represents relationships between strings. An alphabet of
#' `m` letters are used and strings of length `n` are considered. A
#' vertex corresponds to every possible string and there is a directed edge
#' from vertex `v` to vertex `w` if the string of `v` can be
#' transformed into the string of `w` by removing its first letter and
#' appending a letter to it.
#'
#' Please note that the graph will have `m` to the power `n` vertices
#' and even more edges, so probably you don't want to supply too big numbers
#' for `m` and `n`.
#'
#' De Bruijn graphs have some interesting properties, please see another
#' source, e.g. Wikipedia for details.
#'
#' @aliases graph.de.bruijn
#' @param m Integer scalar, the size of the alphabet. See details below.
#' @param n Integer scalar, the length of the labels. See details below.
#' @return A graph object.
#' @author Gabor Csardi <csardi.gabor@@gmail.com>
#' @seealso [make_kautz_graph()], [make_line_graph()]
#' @keywords graphs
#' @export
#' @examples
#'
#' # de Bruijn graphs can be created recursively by line graphs as well
#' g <- make_de_bruijn_graph(2, 1)
#' make_de_bruijn_graph(2, 2)
#' make_line_graph(g)
make_de_bruijn_graph <- function(m, n) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_de_bruijn, as.numeric(m), as.numeric(n))
if (igraph_opt("add.params")) {
res$name <- sprintf("De-Bruijn graph %i-%i", m, n)
res$m <- m
res$n <- n
}
res
}
#' @rdname make_de_bruijn_graph
#' @param ... Passed to `make_de_bruijn_graph()`.
#' @export
de_bruijn_graph <- function(...) constructor_spec(make_de_bruijn_graph, ...)
## -----------------------------------------------------------------
#' Kautz graphs
#'
#' Kautz graphs are labeled graphs representing the overlap of strings.
#'
#' A Kautz graph is a labeled graph, vertices are labeled by strings of length
#' `n+1` above an alphabet with `m+1` letters, with the restriction
#' that every two consecutive letters in the string must be different. There is
#' a directed edge from a vertex `v` to another vertex `w` if it is
#' possible to transform the string of `v` into the string of `w` by
#' removing the first letter and appending a letter to it.
#'
#' Kautz graphs have some interesting properties, see e.g. Wikipedia for
#' details.
#'
#' @aliases graph.kautz
#' @param m Integer scalar, the size of the alphabet. See details below.
#' @param n Integer scalar, the length of the labels. See details below.
#' @return A graph object.
#' @author Gabor Csardi <csardi.gabor@@gmail.com>, the first version in R was
#' written by Vincent Matossian.
#' @seealso [make_de_bruijn_graph()], [make_line_graph()]
#' @keywords graphs
#' @export
#' @examples
#'
#' make_line_graph(make_kautz_graph(2, 1))
#' make_kautz_graph(2, 2)
#'
make_kautz_graph <- function(m, n) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_kautz, as.numeric(m), as.numeric(n))
if (igraph_opt("add.params")) {
res$name <- sprintf("Kautz graph %i-%i", m, n)
res$m <- m
res$n <- n
}
res
}
#' @rdname make_kautz_graph
#' @param ... Passed to `make_kautz_graph()`.
#' @export
kautz_graph <- function(...) constructor_spec(make_kautz_graph, ...)
## -----------------------------------------------------------------
#' Create a full bipartite graph
#'
#' Bipartite graphs are also called two-mode by some. This function creates a
#' bipartite graph in which every possible edge is present.
#'
#' Bipartite graphs have a \sQuote{`type`} vertex attribute in igraph,
#' this is boolean and `FALSE` for the vertices of the first kind and
#' `TRUE` for vertices of the second kind.
#'
#' @aliases graph.full.bipartite
#' @param n1 The number of vertices of the first kind.
#' @param n2 The number of vertices of the second kind.
#' @param directed Logical scalar, whether the graphs is directed.
#' @param mode Scalar giving the kind of edges to create for directed graphs.
#' If this is \sQuote{`out`} then all vertices of the first kind are
#' connected to the others; \sQuote{`in`} specifies the opposite
#' direction; \sQuote{`all`} creates mutual edges. This argument is
#' ignored for undirected graphs.x
#' @return An igraph graph, with the \sQuote{`type`} vertex attribute set.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @seealso [make_full_graph()] for creating one-mode full graphs
#' @keywords graphs
#' @examples
#'
#' g <- make_full_bipartite_graph(2, 3)
#' g2 <- make_full_bipartite_graph(2, 3, directed = TRUE)
#' g3 <- make_full_bipartite_graph(2, 3, directed = TRUE, mode = "in")
#' g4 <- make_full_bipartite_graph(2, 3, directed = TRUE, mode = "all")
#'
#' @export
make_full_bipartite_graph <- function(n1, n2, directed = FALSE,
mode = c("all", "out", "in")) {
n1 <- as.integer(n1)
n2 <- as.integer(n2)
directed <- as.logical(directed)
mode1 <- switch(igraph.match.arg(mode),
"out" = 1,
"in" = 2,
"all" = 3,
"total" = 3
)
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_full_bipartite, n1, n2, as.logical(directed), mode1)
if (igraph_opt("add.params")) {
res$graph$name <- "Full bipartite graph"
res$n1 <- n1
res$n2 <- n2
res$mode <- mode
}
set_vertex_attr(res$graph, "type", value = res$types)
}
#' @rdname make_full_bipartite_graph
#' @param ... Passed to `make_full_bipartite_graph()`.
#' @export
full_bipartite_graph <- function(...) constructor_spec(make_full_bipartite_graph, ...)
## -----------------------------------------------------------------
#' Create a bipartite graph
#'
#' A bipartite graph has two kinds of vertices and connections are only allowed
#' between different kinds.
#'
#' Bipartite graphs have a `type` vertex attribute in igraph, this is
#' boolean and `FALSE` for the vertices of the first kind and `TRUE`
#' for vertices of the second kind.
#'
#' `make_bipartite_graph()` basically does three things. First it checks the
#' `edges` vector against the vertex `types`. Then it creates a graph
#' using the `edges` vector and finally it adds the `types` vector as
#' a vertex attribute called `type`. `edges` may contain strings as
#' vertex names; in this case, `types` must be a named vector that specifies
#' the type for each vertex name that occurs in `edges`.
#'
#' `is_bipartite()` checks whether the graph is bipartite or not. It just
#' checks whether the graph has a vertex attribute called `type`.
#'
#' @aliases make_bipartite_graph graph.bipartite is.bipartite is_bipartite
#' @param types A vector giving the vertex types. It will be coerced into
#' boolean. The length of the vector gives the number of vertices in the graph.
#' When the vector is a named vector, the names will be attached to the graph
#' as the `name` vertex attribute.
#' @param edges A vector giving the edges of the graph, the same way as for the
#' regular [graph()] function. It is checked that the edges indeed
#' connect vertices of different kind, according to the supplied `types`
#' vector. The vector may be a string vector if `types` is a named vector.
#' @param directed Whether to create a directed graph, boolean constant. Note
#' that by default undirected graphs are created, as this is more common for
#' bipartite graphs.
#' @param graph The input graph.
#' @return `make_bipartite_graph()` returns a bipartite igraph graph. In other
#' words, an igraph graph that has a vertex attribute named `type`.
#'
#' `is_bipartite()` returns a logical scalar.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @seealso [graph()] to create one-mode networks
#' @keywords graphs
#' @examples
#'
#' g <- make_bipartite_graph(rep(0:1, length.out = 10), c(1:10))
#' print(g, v = TRUE)
#'
#' @export
make_bipartite_graph <- function(types, edges, directed = FALSE) {
vertex.names <- names(types)
if (is.character(edges)) {
if (is.null(vertex.names)) {
stop("`types` vector must be named when the edge vector contains strings")
}
edges <- match(edges, vertex.names)
if (any(is.na(edges))) {
stop("edge vector contains a vertex name that is not found in `types`")
}
}
types <- as.logical(types)
edges <- as.numeric(edges) - 1
directed <- as.logical(directed)
on.exit(.Call(R_igraph_finalizer))
res <- .Call(R_igraph_create_bipartite, types, edges, directed)
res <- set_vertex_attr(res, "type", value = types)
if (!is.null(vertex.names)) {
res <- set_vertex_attr(res, "name", value = vertex.names)
}
res
}
#' @rdname make_bipartite_graph
#' @param ... Passed to `make_bipartite_graph()`.
#' @export
bipartite_graph <- function(...) constructor_spec(make_bipartite_graph, ...)
## -----------------------------------------------------------------
#' Create a complete (full) citation graph
#'
#' `make_full_citation_graph()` creates a full citation graph. This is a
#' directed graph, where every `i->j` edge is present if and only if
#' \eqn{j<i}. If `directed=FALSE` then the graph is just a full graph.
#'
#' @aliases graph.full.citation
#' @param n The number of vertices.
#' @param directed Whether to create a directed graph.
#' @return An igraph graph.
#'
#' @family deterministic constructors
#' @export
#' @examples
#' print_all(make_full_citation_graph(10))
make_full_citation_graph <- function(n, directed = TRUE) {
# Argument checks
n <- as.integer(n)
directed <- as.logical(directed)
on.exit(.Call(R_igraph_finalizer))
# Function call
res <- .Call(R_igraph_full_citation, n, directed)
res <- set_graph_attr(res, "name", "Full citation graph")
res
}
#' @rdname make_full_citation_graph
#' @param ... Passed to `make_full_citation_graph()`.
#' @export
full_citation_graph <- function(...) constructor_spec(make_full_citation_graph, ...)
## -----------------------------------------------------------------
#' Creating a graph from LCF notation
#'
#' LCF is short for Lederberg-Coxeter-Frucht, it is a concise notation for
#' 3-regular Hamiltonian graphs. It constists of three parameters, the number
#' of vertices in the graph, a list of shifts giving additional edges to a
#' cycle backbone and another integer giving how many times the shifts should
#' be performed. See <http://mathworld.wolfram.com/LCFNotation.html> for
#' details.
#'
#'
#' @aliases graph.lcf graph_from_lcf
#' @param n Integer, the number of vertices in the graph.
#' @param shifts Integer vector, the shifts.
#' @param repeats Integer constant, how many times to repeat the shifts.
#' @return A graph object.
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @seealso [graph()] can create arbitrary graphs, see also the other
#' functions on the its manual page for creating special graphs.
#' @keywords graphs
#' @examples
#'
#' # This is the Franklin graph:
#' g1 <- graph_from_lcf(12, c(5, -5), 6)
#' g2 <- make_graph("Franklin")
#' isomorphic(g1, g2)
#' @export
graph_from_lcf <- lcf_vector_impl
## -----------------------------------------------------------------
#' Creating a graph from a given degree sequence, deterministically
#'
#' It is often useful to create a graph with given vertex degrees. This function
#' creates such a graph in a deterministic manner.
#'
#' Simple undirected graphs are constructed using the Havel-Hakimi algorithm
#' (undirected case), or the analogous Kleitman-Wang algorithm (directed case).
#' These algorithms work by choosing an arbitrary vertex and connecting all its
#' stubs to other vertices. This step is repeated until all degrees have been
#' connected up.
#'
#' The \sQuote{method} argument controls in which order the vertices are
#' selected during the course of the algorithm.
#'
#' The \dQuote{smallest} method selects the vertex with the smallest remaining
#' degree. The result is usually a graph with high negative degree assortativity.
#' In the undirected case, this method is guaranteed to generate a connected
#' graph, regardless of whether multi-edges are allowed, provided that a
#' connected realization exists. See Horvát and Modes (2021) for details.
#' In the directed case it tends to generate weakly connected graphs, but this
#' is not guaranteed. This is the default method.
#'
#' The \dQuote{largest} method selects the vertex with the largest remaining
#' degree. The result is usually a graph with high positive degree assortativity,
#' and is often disconnected.
#'
#' The \dQuote{index} method selects the vertices in order of their index.
#'
#' @param out.deg Numeric vector, the sequence of degrees (for undirected
#' graphs) or out-degrees (for directed graphs). For undirected graphs its sum
#' should be even. For directed graphs its sum should be the same as the sum of
#' `in.deg`.
#' @param in.deg For directed graph, the in-degree sequence. By default this is
#' `NULL` and an undirected graph is created.
#' @param method Character, the method for generating the graph; see above.
#' @param allowed.edge.types Character, specifies the types of allowed edges.
#' \dQuote{simple} allows simple graphs only (no loops, no multiple edges).
#' \dQuote{multiple} allows multiple edges but disallows loop.
#' \dQuote{loops} allows loop edges but disallows multiple edges (currently
#' unimplemented). \dQuote{all} allows all types of edges. The default is
#' \dQuote{simple}.
#' @return The new graph object.
#' @seealso [sample_degseq()] for a randomized variant that samples
#' from graphs with the given degree sequence.
#' @references V. Havel,
#' Poznámka o existenci konečných grafů (A remark on the existence of finite graphs),
#' Časopis pro pěstování matematiky 80, 477-480 (1955).
#' https://eudml.org/doc/19050
#'
#' S. L. Hakimi,
#' On Realizability of a Set of Integers as Degrees of the Vertices of a Linear Graph,
#' Journal of the SIAM 10, 3 (1962).
#' \doi{https://doi.org/10.1137/0111010}
#'
#' D. J. Kleitman and D. L. Wang,
#' Algorithms for Constructing Graphs and Digraphs with Given Valences and Factors,
#' Discrete Mathematics 6, 1 (1973).
#' \doi{10.1016/0012-365X(73)90037-X}
#'
#' Sz. Horvát and C. D. Modes,
#' Connectedness matters: construction and exact random sampling of connected networks (2021).
#' \doi{10.1088/2632-072X/abced5}
#' @export
#' @keywords graphs
#' @examples
#'
#' g <- realize_degseq(rep(2, 100))
#' degree(g)
#' is_simple(g)
#'
#' ## Exponential degree distribution, with high positive assortativity.
#' ## Loop and multiple edges are explicitly allowed.
#' ## Note that we correct the degree sequence if its sum is odd.
#' degs <- sample(1:100, 100, replace = TRUE, prob = exp(-0.5 * (1:100)))
#' if (sum(degs) %% 2 != 0) {
#' degs[1] <- degs[1] + 1
#' }
#' g4 <- realize_degseq(degs, method = "largest", allowed.edge.types = "all")
#' all(degree(g4) == degs)
#'
#' ## Power-law degree distribution, no loops allowed but multiple edges
#' ## are okay.
#' ## Note that we correct the degree sequence if its sum is odd.
#' degs <- sample(1:100, 100, replace = TRUE, prob = (1:100)^-2)
#' if (sum(degs) %% 2 != 0) {
#' degs[1] <- degs[1] + 1
#' }
#' g5 <- realize_degseq(degs, allowed.edge.types = "multi")
#' all(degree(g5) == degs)
realize_degseq <- realize_degree_sequence_impl
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.