sample_edgelist.matrix: Low level interface to sample RPDG edgelists

In fastRG: Sample Generalized Random Dot Product Graphs in Linear Time

Low level interface to sample RPDG edgelists

Description

This is a breaks-off, no safety checks interface. We strongly recommend that you do not call sample_edgelist.matrix() unless you know what you are doing, and even then, we still do not recommend it, as you will bypass all typical input validation. extremely loud coughing All those who bypass input validation suffer foolishly at their own hand. extremely loud coughing

Usage

## S3 method for class 'matrix'
sample_edgelist(
  factor_model,
  S,
  Y,
  directed,
  poisson_edges,
  allow_self_loops,
  ...
)

## S3 method for class 'Matrix'
sample_edgelist(
  factor_model,
  S,
  Y,
  directed,
  poisson_edges,
  allow_self_loops,
  ...
)

Arguments

factor_model	An n by k1 matrix() or Matrix::Matrix() of latent node positions encoding incoming edge community membership. The X matrix in Rohe et al (2017). Naming differs only for consistency with the S3 generic.
S	A k1 by k2 mixing matrix() or Matrix::Matrix(). In the undirect case this is assumed to be symmetric but we do not check that this is the case.
Y	A d by k2 matrix() or Matrix::Matrix() of latent node positions encoding outgoing edge community membership.
directed	Logical indicating whether or not the graph should be directed. When directed = FALSE, symmetrizes S internally. Y = X together with a symmetric S implies a symmetric expectation (although not necessarily an undirected graph). When directed = FALSE, samples a directed graph with symmetric expectation, and then adds edges until symmetry is achieved.
poisson_edges	Whether or not to remove duplicate edges after sampling. See Section 2.3 of Rohe et al. (2017) for some additional details. Defaults to TRUE.
allow_self_loops	Logical indicating whether or not nodes should be allowed to form edges with themselves. Defaults to TRUE. When FALSE, sampling proceeds allowing self-loops, and these are then removed after the fact.
...	Ignored, for generic consistency only.

Details

This function implements the fastRG algorithm as described in Rohe et al (2017). Please see the paper (which is short and open access!!) for details.

Value

A single realization of a random Poisson (or Bernoulli) Dot Product Graph, represented as a tibble::tibble() with two integer columns, from and to.

NOTE: Indices for isolated nodes will not appear in the edgelist! This can lead to issues if you construct network objects from the edgelist directly.

In the undirected case, from and to do not encode information about edge direction, but we will always have from <= to for convenience of edge identification.

To avoid handling such considerations yourself, we recommend using sample_sparse(), sample_igraph(), and sample_tidygraph() over sample_edgelist().

References

Rohe, Karl, Jun Tao, Xintian Han, and Norbert Binkiewicz. 2017. "A Note on Quickly Sampling a Sparse Matrix with Low Rank Expectation." Journal of Machine Learning Research; 19(77):1-13, 2018. https://www.jmlr.org/papers/v19/17-128.html

See Also

Other samplers: sample_edgelist(), sample_igraph(), sample_sparse(), sample_tidygraph()

Examples

set.seed(46)

n <- 10000
d <- 1000

k1 <- 5
k2 <- 3

X <- matrix(rpois(n = n * k1, 1), nrow = n)
S <- matrix(runif(n = k1 * k2, 0, .1), nrow = k1)
Y <- matrix(rpois(n = d * k2, 1), nrow = d)

sample_edgelist(X, S, Y, TRUE, TRUE, TRUE)

fastRG documentation built on Aug. 22, 2023, 1:08 a.m.