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## -----------------------------------------------------------------------
##
## IGraph R package
## Copyright (C) 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
##
## -----------------------------------------------------------------------
#' Rewiring edges of a graph
#'
#' See the links below for the implemented rewiring methods.
#'
#' @param graph The graph to rewire
#' @param with A function call to one of the rewiring methods,
#' see details below.
#' @return The rewired graph.
#'
#' @family rewiring functions
#' @export rewire
#' @examples
#' g <- make_ring(10)
#' g %>%
#' rewire(each_edge(p = .1, loops = FALSE)) %>%
#' plot(layout=layout_in_circle)
#' str(rewire(g, with = keeping_degseq(niter = vcount(g) * 10)))
rewire <- function(graph, with) {
if (! is(with, "igraph_rewiring_method")) {
stop("'with' is not an igraph rewiring method")
}
do_call(with$fun, list(graph), .args = with$args)
}
#' Graph rewiring while preserving the degree distribution
#'
#' This function can be used together with \code{\link{rewire}} to
#' randomly rewire the edges while preserving the original graph's degree
#' distribution.
#'
#' The rewiring algorithm chooses two arbitrary edges in each step ((a,b)
#' and (c,d)) and substitutes them with (a,d) and (c,b), if they not
#' already exists in the graph. The algorithm does not create multiple
#' edges.
#'
#' @param loops Whether to allow destroying and creating loop edges.
#' @param niter Number of rewiring trials to perform.
#'
#' @author Tamas Nepusz \email{ntamas@@gmail.com} and Gabor Csardi
#' \email{csardi.gabor@@gmail.com}
#' @family rewiring functions
#' @seealso \code{\link{sample_degseq}}
#' @export
#' @keywords graphs
#' @examples
#' g <- make_ring(10)
#' g %>%
#' rewire(keeping_degseq(niter = 20)) %>%
#' degree()
#' str(rewire(g, with = keeping_degseq(niter = vcount(g) * 10)))
keeping_degseq <- function(loops = FALSE, niter = 100) {
method <- list(
fun = rewire_keeping_degseq,
args = list(loops = loops, niter = niter)
)
add_class(method, "igraph_rewiring_method")
}
rewire_keeping_degseq <- function(graph, loops, niter) {
if (!is_igraph(graph)) {
stop("Not a graph object")
}
loops <- as.logical(loops)
mode <- if (loops) 1 else 0
on.exit( .Call("R_igraph_finalizer", PACKAGE="igraph") )
.Call("R_igraph_rewire", graph, as.numeric(niter), as.numeric(mode),
PACKAGE="igraph")
}
#' Rewires the endpoints of the edges of a graph to a random vertex
#'
#' This function can be used together with \code{\link{rewire}}.
#' This method rewires the endpoints of the edges with a constant probability
#' uniformly randomly to a new vertex in a graph.
#'
#' Note that this method might create graphs with multiple and/or loop edges.
#'
#' @param prob The rewiring probability, a real number between zero and one.
#' @param loops Logical scalar, whether loop edges are allowed in the rewired
#' graph.
#' @param multiple Logical scalar, whether multiple edges are allowed int the
#' generated graph.
#'
#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
#' @family rewiring functions
#' @export
#' @keywords graphs
#' @examples
#'
#' # Some random shortcuts shorten the distances on a lattice
#' g <- make_lattice(length = 100, dim = 1, nei = 5)
#' mean_distance(g)
#' g <- rewire(g, each_edge(prob = 0.05))
#' mean_distance(g)
each_edge <- function(prob, loops = FALSE, multiple = FALSE) {
method <- list(
fun = rewire_each_edge,
args = list(prob = prob, loops = loops, multiple = multiple)
)
add_class(method, "igraph_rewiring_method")
}
rewire_each_edge <- function(graph, prob, loops=FALSE, multiple=FALSE) {
if (!is_igraph(graph)) {
stop("Not a graph object")
}
on.exit( .Call("R_igraph_finalizer", PACKAGE="igraph") )
.Call("R_igraph_rewire_edges", graph, as.numeric(prob), as.logical(loops),
as.logical(multiple),
PACKAGE="igraph")
}
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