R/incgraph-package.R

In incgraph: Incremental Graphlet Counting for Network Optimisation

#' IncGraph: incremental graphlet counting for network optimisation
#'
#' @examples
#' # Create a new (empty) network with 4 nodes
#' net <- new.incgraph.network(amnt.nodes = 4)
#'
#' # Create a new network with 4 nodes and some edges
#' net <- new.incgraph.network(links = matrix(c(1, 2, 2, 3, 1, 4), ncol=2))
#'
#' # Create a new network with 10 nodes and some edges
#' net <- new.incgraph.network(amnt.nodes = 10, links = matrix(c(1, 2, 2, 3, 1, 4), ncol=2))
#'
#' # Create a more complex network from a matrix
#' mat <- matrix(c(1, 2,
#'                 1, 3,
#'                 1, 4,
#'                 1, 5,
#'                 1, 6,
#'                 1, 7,
#'                 2, 7,
#'                 2, 8,
#'                 2, 9,
#'                 2, 10), ncol=2)
#' net <- new.incgraph.network(links=mat)
#' # Calculate the initial orbit counts using orca
#' orb.counts <- calculate.orbit.counts(net)
#' # Modify an edge and calculate the differences in orbit counts
#' flip(net, 5, 10) # add (5,10)
#' delta1 <- calculate.delta(net, 5, 10)
#' # Modify another edge
#' flip(net, 6, 10) # add (6, 10)
#' delta2 <- calculate.delta(net, 6, 10)
#' # And another
#' flip(net, 1, 5)  # remove (1, 5)
#' delta3 <- calculate.delta(net, 1, 5)
#' # Verify that the new orbit counts equals the old orbit counts plus the delta counts
#' new.orb.counts.incremental <- orb.counts +
#'   delta1$add - delta1$rem +
#'   delta2$add - delta2$rem +
#'   delta3$add - delta3$rem
#' new.orb.counts <- calculate.orbit.counts(net)
#' all(new.orb.counts.incremental == new.orb.counts) # TRUE
#'
#' ## Additional helper functions
#' # Transform the network to a matrix
#' network.as.matrix(net)
#' # Get all neighbours of a node
#' get.neighbours(net, 1)
#' # Does the network contain a specific interaction?
#' contains(net, 5, 10)
#' contains(net, 7, 10)
#' # Reinitialise to an empty network
#' reset(net)
#' network.as.matrix(net)
#'
#' @references Cannoodt, R. et al. (2017)
#' IncGraph: incremental graphlet counting for network optimisation. Under submission.
#'
#' @seealso [new.incgraph.network()], [calculate.orbit.counts()], [calculate.delta()]
#'
#' @useDynLib incgraph
#'
#' @import methods
#' @import Rcpp
#'
#' @keywords internal
"_PACKAGE"

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