incgraph incrementally calculates the differences in orbit counts when performing single edge modifications in a network. For evolving networks, calculating the differences in orbit counts is much more performant than recalculating all orbit counts from scratch for each time point.

Installation

Install incgraph from CRAN with:

install.packages("incgraph")

Examples

Create a new (empty) network with 4 nodes

library(incgraph)
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

[1] TRUE

Examples of additional helper functions

Transform the network to a matrix

network.as.matrix(net)

     [,1] [,2]
[1,]    1    2
[2,]    1    5
[3,]    2    7
[4,]    3    7
[5,]    4    8
[6,]    5    9
[7,]    5   10

Get all neighbours of a node

get.neighbours(net, 1)

[1] 1 2 5

Does the network contain a specific interaction?

contains(net, 5, 10)

[1] TRUE

contains(net, 7, 10)

[1] FALSE

Reinitialise to an empty network

reset(net)
network.as.matrix(net)

     [,1] [,2]