v1.0.0 by jhollway · Pull Request #18 · stocnet/netrics

jhollway · 2026-08-09T14:02:11Z

Description

Package

Removed the CRAN version check from .onAttach() making library(netrics) faster to attach
- It now runs once, for the whole stack, in {migraph}, where it is cached and checks GitHub as well as CRAN
Updated GitHub Actions workflows to latest major action versions
Fixed release workflow referring to actions/actions/checkout, a doubled path segment that would have failed every step using it
Added param_cutoff roxygen template, correctly documenting geodesic cutoff for six functions

Measures

Added net_by_cyclicality() for detecting generalised exchange
Added net_by_compactness() for the average closeness of all pairs of nodes
Added node_by_decay() and net_by_decay() for decay centrality, which
weights alters by distance instead of truncating at a cutoff
Added node_by_integration() and net_by_integration() for Valente and
Foreman's integration and radiality
- Note these two centralizations normalize over node scores rather
  than reusing net_by_reach()'s denominator, which assumes scores bounded
  by N-1 and would return negative values here
Added net_by_inconsistency(), which scores how far a partition's blocks depart
from ideal types (nul, com, reg, rdo, cdo, dnc), generalising
net_by_factions() beyond structural equivalence

Memberships

Added node_in_labels() for label propagation community detection
Fixed node_in_regular() to compute regular equivalence using recursive
similarity (regularity = "rolesim" (default) or "rege") between nodes
rather than a triad census
- Note existing scripts calling node_in_regular() will now return more correct results
- Moved former behaviour of node_in_regular() to node_in_motif(),
  documented as capturing similarity of local embedding not role equivalence
Added node_in_block() for direct blockmodelling, searching partitions
for the one that minimises net_by_inconsistency()

Motifs

Added node_x_clique(), returning which maximal cliques each node belongs to,
and branching on two-mode networks to find bicliques (closes Clique census functions #8, thanks @noortjemay)
- Note that node_x_clique() considers only positive ties,
  since a clique is a cohesive subgroup
Added node_x_ties(), describing the distribution of each node's tie values,
or its spread across layers in a multiplex network
Added node_x_alters() and node_x_similarity(), describing the composition
of each node's alters and their similarity to it, each branching on whether
the attribute given is categorical or continuous
- For two-mode networks, node_x_similarity() compares each node with those
  at distance two, that is, those it shares a node of the other mode with,
  following the tertius effect of {migraph} and {goldfish}
  (Haunss and Hollway 2023)
Added net_x_homophily(), returning the table behind the EI index together
with an expected-EI baseline and Yule's Q
- Note that on weighted networks this counts ties where
  net_by_heterophily() sums weights, so the two agree only when unweighted

Methods

Added regularity_rolesim() and regularity_rege(), recursive role similarity methods
- Note regularity_rege() degenerate on unweighted connected ones, where it warns

Tutorials

Updated position tutorial to use node_in_regular() for regular equivalence rather than the triad census

Checklist:

Documentation
- Longer functions are commented inline or broken down into helper functions to help debugging
PR form
- PR description above and the NEWS.md file are aligned

…rics)` faster to attach

… cutoff for six functions

…ongs to

…homophily()

…hods

…f nodes

…cks depart from ideal types

…valence rather than the triad census

codecov · 2026-08-09T14:06:03Z

Codecov Report

❌ Patch coverage is 94.23920% with 92 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.62%. Comparing base (6dfd5a9) to head (f9f5176).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
R/class_metrics.R	74.64%	18 Missing ⚠️
R/member_community.R	93.68%	18 Missing ⚠️
R/measure_features.R	89.61%	16 Missing ⚠️
R/method_k.R	65.38%	9 Missing ⚠️
R/method_coreness.R	94.28%	8 Missing ⚠️
R/motif_composition.R	96.62%	5 Missing ⚠️
R/member_core.R	92.15%	4 Missing ⚠️
R/measure_diffusion.R	91.42%	3 Missing ⚠️
R/member_cliques.R	62.50%	3 Missing ⚠️
R/netrics-utils.R	78.57%	3 Missing ⚠️
... and 4 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #18      +/-   ##
==========================================
+ Coverage   82.05%   88.62%   +6.56%     
==========================================
  Files          24       30       +6     
  Lines        2441     3533    +1092     
==========================================
+ Hits         2003     3131    +1128     
+ Misses        438      402      -36

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Copilot

Pull request overview

Releases {netrics} v0.5.0 with substantial new analytic functionality (new measures, motifs, memberships, and regularity methods), plus documentation/tutorial updates and CI/workflow maintenance.

Changes:

Added new measures/methods/memberships (cyclicality, compactness, decay/integration centralities, blockmodel inconsistency + direct blockmodelling search, label propagation, clique/biclique participation, ego-composition motifs, RoleSim/REGE regularity).
Refactored regular equivalence: node_in_regular() now uses recursive similarity (regularity_*) and the prior census-based behavior is moved to node_in_motif().
Updated docs/tutorials/reference index, NEWS/versioning, and modernized GitHub Actions workflow action versions.

Reviewed changes

Copilot reviewed 93 out of 107 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
vignettes/articles/position.Rmd	Updates tutorial narrative and examples for `net_by_inconsistency()`/`node_in_block()` and the new regularity/motif split.
inst/tutorials/netrics3/position.Rmd	Mirrors the position tutorial updates for the bundled tutorial version.
tests/testthat/test-motif_nodes.R	Expands motif test exclusions to cover new node motifs requiring attributes.
tests/testthat/test-motif_net.R	Adds homophily-specific skips and attribute-only handling in motif-net tests.
tests/testthat/test-motif_composition.R	Adds tests for new ego-composition motifs (`node_x_ties`, `node_x_alters`, `node_x_similarity`, `net_x_homophily`).
tests/testthat/test-motif_cliques.R	Adds tests for `node_x_clique()` on one-mode and two-mode networks and empty networks.
tests/testthat/test-member_equivalence.R	Adds coverage for `node_in_motif()`, regularity methods, updated `node_in_regular()`, and `node_in_block()`.
tests/testthat/test-member_community.R	Adds tests for new `node_in_labels()` label propagation membership.
tests/testthat/test-measure_fit.R	Adds tests for `net_by_inconsistency()` and relocates fit-related tests from features.
tests/testthat/test-measure_features.R	Removes fit-related tests now housed under `test-measure_fit.R`.
tests/testthat/test-measure_cohesion.R	Adds tests for `net_by_compactness()` and direction-respecting behavior.
tests/testthat/test-measure_closure.R	Adds tests for `net_by_cyclicality()`.
tests/testthat/test-measure_centrality.R	Adds tests for `node_by_decay()`, `node_by_integration()`, and their centralizations.
R/zzz.R	Removes CRAN version-check/update prompt from `.onAttach()` while keeping interactive-only startup behavior.
R/netrics-utils.R	Introduces shared local-search perturbation helpers used by membership search algorithms.
R/motif_composition.R	Adds ego-composition motifs (`node_x_ties`, `node_x_alters`, `node_x_similarity`) and `net_x_homophily()`.
R/motif_cliques.R	Adds `node_x_clique()` including biclique support for two-mode networks and signed-tie handling.
R/method_regularity.R	Adds recursive regularity similarity methods (`regularity_rolesim`, `regularity_rege`).
R/member_equivalence.R	Updates `node_in_regular()` to use recursive regularity; adds `node_in_motif()` and `node_in_block()`.
R/member_community.R	Adds `node_in_labels()` based on igraph label propagation and documents it.
R/member_cliques.R	Removes duplicated perturbation helpers now centralized in `R/netrics-utils.R`.
R/measure_cohesion.R	Adds `net_by_compactness()` and documentation for compactness/global efficiency.
R/measure_closure.R	Adds `net_by_cyclicality()` and documentation contrasting it with transitivity.
R/measure_centrality_closeness.R	Adds decay and integration centralities plus decay/integration centralization functions and shared cutoff roxygen.
pkgdown/_pkgdown.yml	Reorganizes reference index sections to surface new measure families and pages.
NEWS.md	Adds v0.5.0 release notes aligned with the PR description.
NAMESPACE	Exports newly added functions across measures, motifs, memberships, and methods.
man/motif_periods.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_path.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_node.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_net.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_homophily.Rd	New Rd for `net_x_homophily()`.
man/motif_hierarchy.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_hazard.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_exposure.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_composition.Rd	New Rd for ego-composition motifs.
man/motif_clique.Rd	New Rd for `node_x_clique()`.
man/motif_brokerage_node.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/motif_brokerage_net.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/method_regularity.Rd	New Rd for `regularity_rolesim()` / `regularity_rege()`.
man/method_kselect.Rd	Updates `.data` parameter docs.
man/method_cluster.Rd	Updates `.data` parameter docs.
man/member_equivalence.Rd	Documents new `node_in_motif()` / `node_in_block()` and updated `node_in_regular()` signature/behavior.
man/member_diffusion.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/member_core.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/member_components.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/member_community.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/member_community_non.Rd	Adds `node_in_labels()` documentation section and references; updates `.data` parameter docs.
man/member_community_hier.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/member_cliques.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/member_brokerage.Rd	Updates `.data` parameter docs and adds new motif pages to “See also”.
man/measure_periods.Rd	Updates `.data` parameter docs and links to new `measure_fit`.
man/measure_hierarchy.Rd	Updates `.data` parameter docs and links to new `measure_fit`.
man/measure_fragmentation.Rd	Updates `.data` parameter docs and links to new `measure_fit`.
man/measure_fit.Rd	New Rd page separating “fit” measures from intrinsic “features” and documenting `net_by_inconsistency()`.
man/measure_features.Rd	Removes core/factions/modularity from “features” page and links to `measure_fit`.
man/measure_diverse_node.Rd	Updates `.data` parameter docs and links to new motif pages and `measure_fit`.
man/measure_diverse_net.Rd	Updates `.data` parameter docs and links to new motif pages and `measure_fit`.
man/measure_diffusion_node.Rd	Updates `.data` parameter docs and links to new motif pages and `measure_fit`.
man/measure_diffusion_net.Rd	Links to new `measure_fit`.
man/measure_diffusion_infection.Rd	Links to new `measure_fit`.
man/measure_core.Rd	Updates `.data` parameter docs and links to new motif pages and `measure_fit`.
man/measure_cohesion.Rd	Adds `net_by_compactness()` docs and updates `.data` parameter docs; links to `measure_fit`.
man/measure_closure.Rd	Adds `net_by_cyclicality()` docs and updates `.data` parameter docs; links to `measure_fit`.
man/measure_closure_node.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_centralities_eigen.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_centralities_degree.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_centralities_close.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_centralities_between.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_centralisation_eigen.Rd	Updates `.data` parameter docs.
man/measure_centralisation_degree.Rd	Updates `.data` parameter docs.
man/measure_centralisation_close.Rd	Adds `net_by_decay()`/`net_by_integration()` docs and shared cutoff/decay args; updates `.data` parameter docs.
man/measure_centralisation_between.Rd	Updates `.data` parameter docs.
man/measure_central_eigen.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/measure_central_degree.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/measure_central_close.Rd	Adds `node_by_decay()`/`node_by_integration()` docs and shared cutoff/decay args; updates `.data` parameter docs.
man/measure_central_between.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/measure_brokerage.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/measure_broker_tie.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_broker_node.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/measure_breadth.Rd	Updates `.data` parameter docs; links to `measure_fit`.
man/measure_assort_node.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/measure_assort_net.Rd	Updates `.data` parameter docs; links to new motif pages and `measure_fit`.
man/mark_triangles.Rd	Updates `.data` parameter docs.
man/mark_ties.Rd	Updates `.data` parameter docs.
man/mark_select_tie.Rd	Updates `.data` parameter docs.
man/mark_select_node.Rd	Updates `.data` parameter docs; links to new motif pages.
man/mark_nodes.Rd	Updates `.data` parameter docs; links to new motif pages.
man/mark_dyads.Rd	Updates `.data` parameter docs.
man/mark_diff.Rd	Updates `.data` parameter docs; links to new motif pages.
man/mark_degree.Rd	Updates `.data` parameter docs; links to new motif pages.
man/mark_core.Rd	Updates `.data` parameter docs; links to new motif pages.
man-roxygen/param_data.R	Updates shared `.data` parameter roxygen template to reference `stocnet` and `as_stocnet()`.
man-roxygen/param_cutoff.R	New shared cutoff parameter template used across multiple docs.
DESCRIPTION	Bumps package version to 0.5.0.
.Rbuildignore	Ignores `Rplots.pdf` artifacts in package builds.
.gitignore	Adds `Rplots.pdf` to git ignores.
.github/workflows/pushrelease.yml	Updates actions to newer majors and fixes checkout path usage.
.github/workflows/prchecks.yml	Updates actions to newer majors.
.github/CONTRIBUTING.md	Adds explicit naming conventions for method-helper families and membership naming guidance.

Files not reviewed (7)

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man/mark_degree.Rd: Generated file
man/mark_diff.Rd: Generated file
man/mark_dyads.Rd: Generated file
man/mark_nodes.Rd: Generated file
man/mark_select_node.Rd: Generated file
man/mark_select_tie.Rd: Generated file

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+  dists <- igraph::distances(manynet::as_igraph(.data),
+                             mode = match.arg(direction))
+  diag(dists) <- Inf # exclude self from own score
+  out <- rowSums(decay^(dists-1), na.rm = TRUE) # unreachable contribute 0
+  if(normalized) out <- out/(manynet::net_nodes(.data)-1)


…erpreted

…rection = "out")`

…cay()` as a shortcut for decay centrality

… could exceed 1

…tion

… silently returning unweighted scores for weighted networks

…e-periphery

…of all applicable algorithms

…()` erroring on networks holding signs as negative weights

Kaladani · 2026-08-28T00:42:09Z

I could only briefly check the position tutorial and the nodes_in_motif and nodes_in_regular implementation. They both seem to work as intended, but the question is if nodes_in_motif really is what users could believe it to be: a local approximation of regular equivalence based on the local role ego has in a triad ("role equivalence" after Burt).

And i don't think renaming as nodes_in_local would really change this. The same MAN triad can have multiple roles for ego, e.g.

i -> k -> j

has i as the sender, k as the intermediary and j as the endpoint.

For the flattened networker data set the three approaches result in different partitions:

Regular is relatively coarse here.

Motifs seem to reflect structurally similar communities.

Orbits seem to recover local role similarity quite well but is probably too fine grained here.

The last is based on my rcpp version of the orbit counting algorithm I implemented in my local clone of develop. I will make an undirected and tetrad/quad version that also allow taking covariate labels into account for my use. Maybe it would be interesting to add that in a later version of the package, but i don't think it can be fast enough without c++.

Maybe for now it would be a good idea to clarify that nodes_in_motif() just takes triad profiles without taking into account the node's role, which is not the same as in Burt and also different to the orbit-aware tetrard census in Ortman and Brandes.

…uring whole

Kaladani · 2026-08-28T16:06:46Z

Two things I ran into in R/method_cluster.R while working on #28. The first looks like a
straightforward bug; the second is maybe just clarifying documentation. Neither
is new here but both concern the cluster = argument on the node_in_*() functions, which is.

cluster_cosine() clusters the features, not the nodes

cluster_hierarchical() transposes before correlating; cluster_cosine() doesn't:

cluster_hierarchical <- ... manynet::to_correlation(t(motif))   # n x n  (nodes)
cluster_cosine       <- ... manynet::to_cosine(motif)           # F x F  (features)

So cluster = "cosine" clusters the census columns and returns them as a node membership,
without erroring:

node_in_structural(ison_algebra, cluster = "cosine")
#> 4 groups
#> V1 V2 V3 V4 ...
#> length 96, for a 16-node network

96 is node_x_tie(ison_algebra)'s column count (16 nodes × 2 directions × 3 tie types).
to_cosine(t(motif)) fixes it.

The bug is invisible whenever the census happens to be square.

The @section for cluster_hierarchical() describes a different pipeline

The @section says "a distance matrix is created by subtracting these correlations from 1,
and this is given to stats::hclust()", which describes as.dist(1 - C) —> one profile
comparison. The code inserts stats::dist(), so the clustering runs on distances between the
rows of 1 - C, i.e. a second comparison, on the dissimilarity profiles.

The one-step version is I think more established: sna::sedist() offers correlation, euclidean,
hamming and gamma as alternative ways to make that single comparison: "SE similarity/difference
scores are computed by comparing vertex rows and columns using the measure indicated by
method". And then says "once these similarities/differences are calculated, the results can
be used with a clustering routine (such as equiv.clust)", which duly does
hclust(as.dist(equiv.dist)). On that reading, correlation is a choice of first comparison
rather than something a distance is subsequently taken over.

It might be intentional: clustering the rows of a similarity matrix is not unusual, and
Hoffman's positional-analysis chapter runs kmeans() on exactly such a matrix. But there it
looks like a consequence of kmeans() needing a data matrix rather than a dissimilarity,
and hclust() has no equivalent constraint, since it takes a dist object directly.

It also isn't purely cosmetic: k_silhouette() is the default k and reads hc$distances,
so which pipeline is meant reaches the returned membership, not just the dendrogram.

jhollway added 15 commits August 8, 2026 10:31

Added net_by_cyclicality

7fe186f

Updated GitHub Actions workflows to latest major action versions

df6f489

Removed the CRAN version check from .onAttach() making `library(net…

57f8249

…rics)` faster to attach

Added node_in_labels() for label propagation community detection

e01ce85

Added param_cutoff roxygen template, correctly documenting geodesic…

244fd4c

… cutoff for six functions

Added node_x_clique() returning which maximal cliques each node bel…

ba48feb

…ongs to

Added node_x_ties(), node_x_alters(), node_x_similarity(), and net_x_…

be50e87

…homophily()

Restructured website

05b08cb

Added sim_rolesim() and sim_rege(), recursive role similarity met…

7887403

…hods

Added net_by_compactness() for the average closeness of all pairs o…

53e154e

…f nodes

Fixed node_in_regular() to compute regular equivalence

f65286c

Added net_by_inconsistency() which scores how far a partition's blo…

986c266

…cks depart from ideal types

Added node_in_block() for direct blockmodelling

36afdf9

Updated position tutorial to use node_in_regular() for regular equi…

4ee40e6

…valence rather than the triad census

Added net/node_by_decay() and net/node_by_integration()

691c674

jhollway self-assigned this Aug 9, 2026

Copilot AI lite review requested due to automatic review settings August 9, 2026 14:02

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jhollway added 10 commits August 9, 2026 19:35

Improved measures to record what they computed, so results can be int…

94419e5

…erpreted

Added family-wide contract test sweeping every node-level centrality

96da6f1

Added node_by_radiality() as a shortcut for `node_by_integration(di…

6ce3703

…rection = "out")`

Added decay argument to node_by_harmonic(), and added `node_by_de…

051f67f

…cay()` as a shortcut for decay centrality

Improved node_by_closeness() to validate direction via match.arg()

7c72b38

Fixed node_by_reach() counting the node itself so normalised scores…

067d145

… could exceed 1

Fixed how node_by_vitality() treats cut nodes

7c8fc7b

Moved node_by_posneg() (PN centrality) to eigenvector doc group

d7dbc17

Fixed node_by_degree() to default to alpha = 0 to match documenta…

c1de2ed

…tion

Fixed node_by_eigenvector() discarding tie weights it had computed,…

438855d

… silently returning unweighted scores for weighted networks

jhollway added 9 commits August 27, 2026 18:29

Renamed node_by_coreness() to node_by_core()

5155130

Improved node_in_core()

21f69b3

Updated topology tutorial with weighted, directed, and continuous cor…

21c2813

…e-periphery

Stop README advertising old functions

6e20bd7

Added consensus= to node_in_community() for combining partitions …

2fd966e

…of all applicable algorithms

Added Louvain and consensus examples to community tutorial

3b1541f

Renamed coreness_richcore to coreness_rich

2126ac5

Fixed net_by_diameter(), net_by_length(), and `net_by_compactness…

023414a

…()` erroring on networks holding signs as negative weights

Get around manynet version requirement

792bfa6

jhollway added 13 commits August 28, 2026 08:37

Fixed signless call in test

dcb31f5

Fixed node_in_fluid() and node_in_spinglass()

3b1873b

Fixed net_by_independence() erroring on multilevel networks by meas…

7242154

…uring whole

Improved net_x_triad() by adding a mixed census

8e59fde

Improved node_x_tie() erroring on multiplex networks

d8e01a9

Updated CONTRIBUTING from current practice

e189d15

Fixed various test errors for Github CI

88efcd4

Avoided polluting test output with console output

773ddff

Skip tutorial testing on CRAN

97aebe3

Cleaned up some easy documentation

46249ae

Added roxygen templates to standardise argument vocabulary

1cd843e

Added split_bins(), split_quantiles() and split_kmeans()

15782e9

Fixed net_by_waves() reporting one wave where waves are held as time

4f733a5

jhollway mentioned this pull request Aug 28, 2026

Add an orbit-aware triad and quad census #28

Open

jhollway added 3 commits August 28, 2026 15:00

Avoid using new datasets for testing

bcd9946

Using faster irps_books example in the tutorial instead of irps_blogs

40c7a5e

Added connectivity= for whether strong or weak connectedness matters

f9f5176

jhollway merged commit da4503d into main Aug 28, 2026
7 checks passed

jhollway mentioned this pull request Aug 29, 2026

Expose the proximity stage and use a one-step profile comparison #29

Open

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jhollway commented Aug 9, 2026

Description

Package

Measures

Memberships

Motifs

Methods

Tutorials

Checklist:

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