graph_measures: Graph measurements

In tidygraph: A Tidy API for Graph Manipulation

Graph measurements

Description

This set of functions provide wrappers to a number of ìgraphs graph statistic algorithms. As for the other wrappers provided, they are intended for use inside the tidygraph framework and it is thus not necessary to supply the graph being computed on as the context is known. All of these functions are guarantied to return scalars making it easy to compute with them.

Usage

graph_adhesion()

graph_assortativity(attr, in_attr = NULL, directed = TRUE)

graph_automorphisms(sh = "fm", colors = NULL)

graph_clique_num()

graph_clique_count(min = NULL, max = NULL, subset = NULL)

graph_component_count(type = "weak")

graph_motif_count(size = 3, cut.prob = rep(0, size))

graph_diameter(weights = NULL, directed = TRUE, unconnected = TRUE)

graph_girth()

graph_radius(mode = "out")

graph_mutual_count()

graph_asym_count()

graph_unconn_count()

graph_size()

graph_order()

graph_reciprocity(ignore_loops = TRUE, ratio = FALSE)

graph_min_cut(capacity = NULL)

graph_mean_dist(directed = TRUE, unconnected = TRUE, weights = NULL)

graph_modularity(group, weights = NULL)

graph_efficiency(weights = NULL, directed = TRUE)

Arguments

attr	The node attribute to measure on
in_attr	An alternative node attribute to use for incomming node. If NULL the attribute given by type will be used
directed	Should a directed graph be treated as directed
sh	The splitting heuristics for the BLISS algorithm. Possible values are: ‘f’: first non-singleton cell, ‘fl’: first largest non-singleton cell, ‘fs’: first smallest non-singleton cell, ‘fm’: first maximally non-trivially connected non-singleton cell, ‘flm’: first largest maximally non-trivially connected non-singleton cell, ‘fsm’: first smallest maximally non-trivially connected non-singleton cell.
colors	The colors of the individual vertices of the graph; only vertices having the same color are allowed to match each other in an automorphism. When omitted, igraph uses the color attribute of the vertices, or, if there is no such vertex attribute, it simply assumes that all vertices have the same color. Pass NULL explicitly if the graph has a color vertex attribute but you do not want to use it.
min, max	The upper and lower bounds of the cliques to be considered.
subset	The indexes of the nodes to start the search from (logical or integer). If provided only the cliques containing these nodes will be counted.
type	The type of component to count, either 'weak' or 'strong'. Ignored for undirected graphs.
size	The size of the motif.
cut.prob	Numeric vector giving the probabilities that the search graph is cut at a certain level. Its length should be the same as the size of the motif (the size argument). By default no cuts are made.
weights	Optional positive weight vector for calculating weighted distances. If the graph has a weight edge attribute, then this is used by default.
unconnected	Logical, what to do if the graph is unconnected. If FALSE, the function will return a number that is one larger the largest possible diameter, which is always the number of vertices. If TRUE, the diameters of the connected components will be calculated and the largest one will be returned.
mode	How should eccentricity be calculated. If "out" only outbound edges are followed. If "in" only inbound are followed. If "all" all edges are followed. Ignored for undirected graphs.
ignore_loops	Logical. Should loops be ignored while calculating the reciprocity
ratio	Should the old "ratio" approach from igraph < v0.6 be used
capacity	The capacity of the edges
group	The node grouping to calculate the modularity on

Value

A scalar, the type depending on the function

Functions

• graph_adhesion(): Gives the minimum edge connectivity. Wraps igraph::edge_connectivity()

• graph_assortativity(): Measures the propensity of similar nodes to be connected. Wraps igraph::assortativity()

• graph_automorphisms(): Calculate the number of automorphisms of the graph. Wraps igraph::count_automorphisms()

• graph_clique_num(): Get the size of the largest clique. Wraps igraph::clique_num()

• graph_clique_count(): Get the number of maximal cliques in the graph. Wraps igraph::count_max_cliques()

• graph_component_count(): Count the number of unconnected componenets in the graph. Wraps igraph::count_components()

• graph_motif_count(): Count the number of motifs in a graph. Wraps igraph::count_motifs()

• graph_diameter(): Measures the length of the longest geodesic. Wraps igraph::diameter()

• graph_girth(): Measrues the length of the shortest circle in the graph. Wraps igraph::girth()

• graph_radius(): Measures the smallest eccentricity in the graph. Wraps igraph::radius()

• graph_mutual_count(): Counts the number of mutually connected nodes. Wraps igraph::dyad_census()

• graph_asym_count(): Counts the number of asymmetrically connected nodes. Wraps igraph::dyad_census()

• graph_unconn_count(): Counts the number of unconnected node pairs. Wraps igraph::dyad_census()

• graph_size(): Counts the number of edges in the graph. Wraps igraph::gsize()

• graph_order(): Counts the number of nodes in the graph. Wraps igraph::gorder()

• graph_reciprocity(): Measures the proportion of mutual connections in the graph. Wraps igraph::reciprocity()

• graph_min_cut(): Calculates the minimum number of edges to remove in order to split the graph into two clusters. Wraps igraph::min_cut()

• graph_mean_dist(): Calculates the mean distance between all node pairs in the graph. Wraps igraph::mean_distance()

• graph_modularity(): Calculates the modularity of the graph contingent on a provided node grouping

• graph_efficiency(): Calculate the global efficiency of the graph

Examples

# Use e.g. to modify computations on nodes and edges
create_notable('meredith') %>%
  activate(nodes) %>%
  mutate(rel_neighbors = centrality_degree()/graph_order())

tidygraph documentation built on June 22, 2024, 11:32 a.m.