build_dynamic_networks2: Creating One or Multiple Networks Using Structured or...

In agoutsmedt/networkflow: Functions For A Workflow To Manipulate Networks

Creating One or Multiple Networks Using Structured or Statistical Backbone Extraction

Description

build_dynamic_networks2() builds one or several networks (as tidygraph objects) from a table of nodes and directed edges, with support for both structured cooccurrence methods and statistical backbone extraction using the backbone package. The function is useful for constructing bibliometric or affiliation networks across static or dynamic time windows.

Usage

build_dynamic_networks2(
  nodes,
  directed_edges,
  source_id,
  target_id,
  time_variable = NULL,
  time_window = NULL,
  backbone_method = c("statistical", "structured"),
  statistical_method = c("sdsm", "fdsm", "fixedfill", "fixedfrow", "fixedcol"),
  alpha = alpha,
  coupling_measure = c("coupling_angle", "coupling_strength", "coupling_similarity"),
  edges_threshold = 1,
  overlapping_window = FALSE,
  compute_size = FALSE,
  keep_singleton = FALSE,
  filter_components = FALSE,
  ...,
  verbose = TRUE
)

Arguments

nodes	Table of nodes and their metadata. One row per node. For example, a table of articles with identifiers, authors, publication year, etc.
directed_edges	Table of edges representing the links between nodes and associated entities (e.g., references, authors, affiliations).
source_id	Quoted name of the column giving the unique identifier of each node.
target_id	Quoted name of the column giving the identifier of the element linked to each node.
time_variable	Optional name of the column with a temporal variable (e.g., publication year).
time_window	Optional size of the time window (in units of time_variable) to construct temporal networks.
backbone_method	Method used to extract the network backbone. Choose between: "structured": uses cooccurrence measures from the biblionetwork package; "statistical": uses statistical models from the backbone package.
statistical_method	For backbone_method = "statistical", select the null model: one of "sdsm", "fdsm", "fixedfill", "fixedfrow", "fixedcol".
alpha	Significance threshold for statistical backbone extraction. Required if backbone_method = "statistical".
coupling_measure	For backbone_method = "structured", choose the cooccurrence method: "coupling_angle" (biblio_coupling); "coupling_strength"; "coupling_similarity".
edges_threshold	Threshold for edge weight filtering in structured methods.
overlapping_window	Logical. If TRUE, builds networks using rolling time windows.
compute_size	Logical. If TRUE, computes the number of incoming edges per node (e.g., citation count).
keep_singleton	Logical. If FALSE, removes nodes with no edges in the final network.
filter_components	Logical. If TRUE, keeps only the main component(s) using networkflow::filter_components().
...	Additional arguments passed to filter_components().
verbose	Logical. If TRUE, displays progress messages.

Details

build_dynamic_networks2() generalizes build_dynamic_networks() by adding support for statistical backbone extraction using null models from the backbone package. The cooccurence methods used in build_dynamic_networks() can be viewed as deterministic methods to extract the network backbone. The backbone is defined as the significant edges in the network.

As with build_dynamic_networks(), the function constructs networks for each time window. If time_variable and time_window are defined, the function constructs networks for each time window (sliding or non-overlapping). Otherwise, it builds a single static network.

If backbone_method = "structured", cooccurrence edges are computed using bibliometric coupling techniques. The term structured refers to deterministic methods based on thresholding cooccurrence measures. If backbone_method = "statistical", the function constructs a bipartite incidence matrix and extracts statistically significant edges using one of the null models from the backbone package.

Value

• A single tidygraph object if time_window is NULL;

• A list of tidygraph objects (one per time window) otherwise.

See Also

biblionetwork::biblio_coupling(), backbone::sdsm()

agoutsmedt/networkflow documentation built on July 3, 2025, 8:54 p.m.