v0.2.1 by jhollway · Pull Request #9 · stocnet/netrics

jhollway · 2026-04-04T07:50:29Z

Description

Package

Added network analysis tutorials from {manynet}

Members

Added more explanation for node_in_partition()

Checklist:

Documentation
- DESCRIPTION file version is bumped by the appropriate increment (major, minor, patch)
- Date in DESCRIPTION is correct
- Longer functions are commented inline or broken down into helper functions to help debugging
PR form
- Title indicates expected version number
- PR description above and the NEWS.md file are aligned
- Description above itemizes changes under subsection titles, e.g. "## Data"
- Closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"

Copilot

Pull request overview

This PR prepares the v0.2.1 release by expanding packaged learnr tutorials and refreshing documentation content/links, with a small re-organization of community-membership documentation.

Changes:

Added new learnr tutorials for centrality, community/cohesion, position/equivalence, and topology/resilience under inst/tutorials/.
Updated many .Rd docs to point to newer manynet documentation topics for coercion and direction-modification references.
Adjusted/expanded community-detection documentation sections (e.g., Partition/Infomap text, moving the (commented) Ensemble block).

Reviewed changes

Copilot reviewed 67 out of 71 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
R/member_community.R	Moves/extends community-membership documentation sections (incl. commented ensemble block).
man/motif_periods.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_path.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_net.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_hierarchy.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_hazard.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_exposure.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_brokerage_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/motif_brokerage_net.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/method_kselect.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/method_cluster.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_equivalence.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_diffusion.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_core.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_components.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_community.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_community_non.Rd	Adds/adjusts Partition section text + updates link targets/wrapping.
man/member_community_hier.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_cliques.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/member_brokerage.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_periods.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_hierarchy.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_fragmentation.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_features.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_diverse_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_diverse_net.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_diffusion_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_core.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_cohesion.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_closure.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_closure_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_centralities_eigen.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralities_degree.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralities_close.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralities_between.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralisation_eigen.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralisation_degree.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralisation_close.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_centralisation_between.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_central_eigen.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_central_degree.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_central_close.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_central_between.Rd	Updates `manynet::as_tidygraph()` + direction-modification link target topic.
man/measure_brokerage.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_broker_tie.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_broker_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_breadth.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_assort_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/measure_assort_net.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_triangles.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_ties.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_select_tie.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_select_node.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_nodes.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_dyads.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_diff.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_degree.Rd	Updates `manynet::as_tidygraph()` link target topic.
man/mark_core.Rd	Updates `manynet::as_tidygraph()` link target topic.
inst/tutorials/tutorial6/topology.Rmd	Adds Topology/Resilience learnr tutorial content.
inst/tutorials/tutorial5/position.Rmd	Adds Position/Equivalence learnr tutorial content.
inst/tutorials/tutorial5/position_data/data_chunks_index.txt	Adds learnr prerender index (currently points to missing artifact).
inst/tutorials/tutorial4/community.Rmd	Adds Cohesion/Community learnr tutorial content.
inst/tutorials/tutorial3/centrality.Rmd	Adds Centrality learnr tutorial content.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-04-04T07:55:09Z

+#   if(missing(.data)) {expect_nodes(); .data <- .G()}
+#   clust <- igraph::cluster_walktrap(manynet::as_igraph(.data))
+#   out <- clust$membership
+#   make_node_member(out, .data)


The commented-out node_in_ensemble block contains a redundant make_node_member(out, .data) call that discards its return value and is immediately repeated with assignment. This looks like leftover/debug code; consider removing the unused call (or the entire commented-out block) to avoid confusion about intended behavior.

Suggested change

# make_node_member(out, .data)

Copilot · 2026-04-04T07:55:09Z

@@ -0,0 +1 @@
+data.RData


data_chunks_index.txt lists data.RData, but that file is not present in inst/tutorials/tutorial5/position_data/. This will break learnr::tutorial prerender/runtime expectations; either add the missing data.RData artifact (if intended) or remove/regenerate the *_data folder and index.

Suggested change

data.RData

Copilot · 2026-04-04T07:55:10Z

+                           praise = c("C'est génial!",
+                                      "Beau travail!",
+                                      "Bravo!",
+                                      "Super!"),
+                           encouragement = c("Bon effort"))


learnr::random_phrases_add(language = "en", ...) currently registers French phrases (e.g., "C'est génial!") under the English language key. This will cause English UI feedback to be in French; either change these phrases to English or set language = "fr"/adjust language keys as intended.

Suggested change

praise = c("C'est génial!",

"Beau travail!",

"Bravo!",

"Super!"),

encouragement = c("Bon effort"))

praise = c("That's great!",

"Great job!",

"Bravo!",

"Awesome!"),

encouragement = c("Good effort"))

Copilot · 2026-04-04T07:55:10Z

+## Overview
+
+<img src="https://64.media.tumblr.com/tumblr_lvpgquhGbq1r54h4xo1_400.gif"/>
+
+In this tutorial, we'll explore:
+
+- how to create or generate different network topologies
+- the core-periphery structure of a network
+- features of a network related to its resilience
+
+This tutorial covers a range of different network topologies:
+trees, lattices, random, small-world, scale-free, and core-periphery
+networks.
+These ideal networks exaggerate centrality, clustering, and randomness features, 
+and are thus great for theory-building and investigating the relationship between rules and structure.
+
+<img src="https://media.tenor.com/images/e26e64a8cce94a6ee491f0ddeecc8b88/tenor.gif"/>


The images in this tutorial are embedded without alt text. For accessibility (screen readers) and to meet common documentation standards, add a short descriptive alt attribute (or mark as decorative with empty alt) for these images.

Copilot · 2026-04-04T07:55:10Z

+                           praise = c("C'est génial!",
+                                      "Beau travail!",
+                                      "Bravo!",
+                                      "Super!"),
+                           encouragement = c("Bon effort"))


learnr::random_phrases_add(language = "en", ...) currently registers French phrases (e.g., "C'est génial!") under the English language key. This will cause English UI feedback to be in French; either change these phrases to English or set language = "fr"/adjust language keys as intended.

Suggested change

praise = c("C'est génial!",

"Beau travail!",

"Bravo!",

"Super!"),

encouragement = c("Bon effort"))

praise = c("That's great!",

"Great job!",

"Bravo!",

"Awesome!"),

encouragement = c("Good effort"))

Copilot · 2026-04-04T07:55:10Z

+                           praise = c("C'est génial!",
+                                      "Beau travail!",
+                                      "Bravo!",
+                                      "Super!"),
+                           encouragement = c("Bon effort"))


learnr::random_phrases_add(language = "en", ...) currently registers French phrases (e.g., "C'est génial!") under the English language key. This will cause English UI feedback to be in French; either change these phrases to English or set language = "fr"/adjust language keys as intended.

Suggested change

praise = c("C'est génial!",

"Beau travail!",

"Bravo!",

"Super!"),

encouragement = c("Bon effort"))

praise = c("That's great!",

"Great job!",

"Bravo!",

"Awesome!"),

encouragement = c("Good effort!"))

Copilot · 2026-04-04T07:55:10Z

+                           praise = c("C'est génial!",
+                                      "Beau travail!",
+                                      "Bravo!",
+                                      "Super!"),
+                           encouragement = c("Bon effort"))


learnr::random_phrases_add(language = "en", ...) currently registers French phrases (e.g., "C'est génial!") under the English language key. This will cause English UI feedback to be in French; either change these phrases to English or set language = "fr"/adjust language keys as intended.

Suggested change

praise = c("C'est génial!",

"Beau travail!",

"Bravo!",

"Super!"),

encouragement = c("Bon effort"))

praise = c("That's great!",

"Good job!",

"Well done!",

"Awesome!"),

encouragement = c("Good effort"))

Copilot · 2026-04-04T07:55:11Z

+degree, betweenness, closeness, eigenvector, and other types of centrality,
+explore their distributions and calculate the corresponding centralisation.
+
+<img src="https://i.giphy.com/media/v1.Y2lkPTc5MGI3NjExbG5oYmVtYmcxMWs1d3MzOGh3Zng5dTZhc241ZHR2NTE0YThiZWp4NiZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/970Sr8vpwEbXG/giphy.gif" height="480px"/>


Several <img> tags in this tutorial omit alt text (e.g., the first hero image here). This reduces accessibility for screen-reader users; please add descriptive alt attributes (or empty alt for purely decorative images) consistently throughout the tutorial.

Suggested change

<img src="https://i.giphy.com/media/v1.Y2lkPTc5MGI3NjExbG5oYmVtYmcxMWs1d3MzOGh3Zng5dTZhc241ZHR2NTE0YThiZWp4NiZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/970Sr8vpwEbXG/giphy.gif" height="480px"/>

<img src="https://i.giphy.com/media/v1.Y2lkPTc5MGI3NjExbG5oYmVtYmcxMWs1d3MzOGh3Zng5dTZhc241ZHR2NTE0YThiZWp4NiZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/970Sr8vpwEbXG/giphy.gif" height="480px" alt=""/>

codecov · 2026-04-12T15:21:14Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.95%. Comparing base (aa15887) to head (94220e5).
⚠️ Report is 8 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main       #9      +/-   ##
==========================================
+ Coverage   81.07%   81.95%   +0.87%     
==========================================
  Files          24       24              
  Lines        2394     2394              
==========================================
+ Hits         1941     1962      +21     
+ Misses        453      432      -21

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jhollway added 3 commits March 25, 2026 13:22

Added section explaining node_in_partition()

155f852

Added tutorials from manynet

7a0cda9

Updated netrics documentation following manynet changes

b224d12

Copilot AI review requested due to automatic review settings April 4, 2026 07:50

Copilot started reviewing on behalf of jhollway April 4, 2026 07:51 View session

Updated pkg

7b7f84b

Copilot AI reviewed Apr 4, 2026

View reviewed changes

Explained why netrics should be accepted to CRAN

94220e5

jhollway merged commit 38886aa into main Apr 12, 2026
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v0.2.1#9

v0.2.1#9
jhollway merged 5 commits intomainfrom
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	<img src="https://i.giphy.com/media/v1.Y2lkPTc5MGI3NjExbG5oYmVtYmcxMWs1d3MzOGh3Zng5dTZhc241ZHR2NTE0YThiZWp4NiZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/970Sr8vpwEbXG/giphy.gif" height="480px"/>
	<img src="https://i.giphy.com/media/v1.Y2lkPTc5MGI3NjExbG5oYmVtYmcxMWs1d3MzOGh3Zng5dTZhc241ZHR2NTE0YThiZWp4NiZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/970Sr8vpwEbXG/giphy.gif" height="480px" alt=""/>

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