v0.2.3 by jhollway · Pull Request #11 · stocnet/netrics

jhollway · 2026-04-25T13:13:06Z

Description

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 bumps the package to v0.2.3 and updates Tutorial 5 (“Position and Equivalence”) to address an object reference issue in the structural equivalence section.

Changes:

Bumped DESCRIPTION version/date and added a NEWS.md entry for 0.2.3.
Updated Tutorial 5 source (position.Rmd) and rendered output (position.html) with revised object usage (to_named(ison_algebra) / alge).
Ignored new local/tooling files via .gitignore / .Rbuildignore.

Reviewed changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
inst/tutorials/tutorial5/position.Rmd	Updates tutorial setup and exercise chunks around `to_named()` / `alge` usage.
inst/tutorials/tutorial5/position.html	Re-rendered tutorial output reflecting the updated Rmd code and learnr metadata.
NEWS.md	Adds release notes for 0.2.3 (tutorial fix).
DESCRIPTION	Bumps package version to 0.2.3 and updates the Date field.
.gitignore	Ignores `.positai`.
.Rbuildignore	Ensures `.positai` / `.claude` aren’t included in builds; adjusts `.mailmap` entry.

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Copilot · 2026-04-25T13:16:09Z


 ```{r strict, exercise = TRUE, exercise.setup = "varyclust"}
-plot(node_in_structural(alge, k = "strict"))
+plot(node_in_structural(to_named(ison_algebra), k = "strict"))


exercise.setup = "varyclust" already defines alge <- to_named(ison_algebra) for consistent fake names. Calling to_named(ison_algebra) again here can change node labels between the dendrograms and this plot (and between runs). Use alge instead so the tutorial’s examples stay consistent.

Suggested change

plot(node_in_structural(to_named(ison_algebra), k = "strict"))

plot(node_in_structural(alge, k = "strict"))

Copilot · 2026-04-25T13:16:09Z

 data-completion="1" data-diagnostics="1" data-startover="1"
 data-lines="0" data-pipe="|&gt;">
-<pre class="text"><code>plot(node_in_structural(alge, k = 2))</code></pre>
+<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = 2))</code></pre>


This snippet switched from using the previously defined alge to calling to_named(ison_algebra) inline. Since to_named() can generate different fake names each call, this can make node labels inconsistent across the tutorial. Prefer plot(node_in_structural(alge, ...)) with alge set once in setup.

Copilot · 2026-04-25T13:16:10Z

 ^CRAN-SUBMISSION$
 ^README\.Rmd$
-^.mailmap$
+^.mailmap$


In .Rbuildignore entries are regexes; ^.mailmap$ treats . as “any character”, so it can match unintended filenames (e.g., xmailmap). Escape the dot to only ignore the .mailmap file (i.e., ^\.mailmap$).

Suggested change

^.mailmap$

^\.mailmap$

Copilot · 2026-04-25T13:16:10Z

 We can graph this of course, as above:

 ```{r strplot, exercise = TRUE, exercise.setup = "varyclust"}
+alge <- to_named(ison_algebra)


alge is already available from exercise.setup = "varyclust". Re-creating it with to_named(ison_algebra) here can change the node labels relative to the dendrograms shown earlier, making the tutorial harder to follow. Prefer using the existing alge object.

Suggested change

alge <- to_named(ison_algebra)

Copilot · 2026-04-25T13:16:10Z

+<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = &quot;elbow&quot;))
+plot(node_in_structural(to_named(ison_algebra), k = &quot;silhouette&quot;))</code></pre>


These examples now call to_named(ison_algebra) for each plot. Because to_named() may generate different fake names on each call, the elbow vs silhouette plots may not be directly comparable in the rendered tutorial. Reuse a single alge <- to_named(ison_algebra) defined once in setup and pass alge into node_in_structural().

Copilot · 2026-04-25T13:16:10Z

 data-diagnostics="1" data-startover="1" data-lines="0"
 data-pipe="|&gt;">
-<pre class="text"><code>plot(node_in_structural(alge, k = &quot;strict&quot;))</code></pre>
+<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = &quot;strict&quot;))</code></pre>


Same as the earlier chunks: this calls to_named(ison_algebra) inline, which can lead to inconsistent node labels across tutorial steps. Prefer using a single alge object created once in the tutorial setup and then calling node_in_structural(alge, k = "strict").

Copilot · 2026-04-25T13:16:10Z

+<pre class="text"><code>alge &lt;- to_named(ison_algebra)
+alge %&gt;% 


This chunk reassigns alge <- to_named(ison_algebra) locally even though the tutorial setup already creates alge. Re-running to_named() here can change fake names mid-tutorial, making it harder to relate this plot back to earlier dendrograms. Reuse the existing alge from setup instead of re-creating it.

Copilot · 2026-04-25T13:16:10Z


 ```{r k-discrete, exercise = TRUE, exercise.setup = "varyclust"}
-plot(node_in_structural(alge, k = 2))
+plot(node_in_structural(to_named(ison_algebra), k = 2))


varyclust (the exercise setup) already defines alge <- to_named(ison_algebra) for consistent fake node names across subsequent plots. Re-calling to_named(ison_algebra) here can generate a different naming each time (and undermines the comparison described above). Use the existing alge object from the setup instead of re-creating it.

Suggested change

plot(node_in_structural(to_named(ison_algebra), k = 2))

plot(node_in_structural(alge, k = 2))

Copilot · 2026-04-25T13:16:11Z

+plot(node_in_structural(to_named(ison_algebra), k = "elbow"))
+plot(node_in_structural(to_named(ison_algebra), k = "silhouette"))


Same issue as k-discrete: since exercise.setup = "varyclust" already created alge <- to_named(ison_algebra), calling to_named(ison_algebra) again here can yield different fake names between plots/runs. Reuse alge so the elbow vs silhouette outputs are directly comparable.

Suggested change

plot(node_in_structural(to_named(ison_algebra), k = "elbow"))

plot(node_in_structural(to_named(ison_algebra), k = "silhouette"))

plot(node_in_structural(alge, k = "elbow"))

plot(node_in_structural(alge, k = "silhouette"))

codecov · 2026-04-25T13:17:12Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.95%. Comparing base (d1a2aa0) to head (5f1542a).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #11   +/-   ##
=======================================
  Coverage   81.95%   81.95%           
=======================================
  Files          24       24           
  Lines        2394     2394           
=======================================
  Hits         1962     1962           
  Misses        432      432

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jhollway added 2 commits April 25, 2026 15:10

Fixed object reference in position tutorial

9e1ea74

#patch bump

5c66b70

Copilot AI review requested due to automatic review settings April 25, 2026 13:13

Copilot started reviewing on behalf of jhollway April 25, 2026 13:13 View session

Updated cran comments

5f1542a

Copilot AI reviewed Apr 25, 2026

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v0.2.3#11

v0.2.3#11
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	plot(node_in_structural(to_named(ison_algebra), k = "strict"))
	plot(node_in_structural(alge, k = "strict"))

		<pre class="text"><code>plot(node_in_structural(to_named(ison_algebra), k = "elbow"))
		plot(node_in_structural(to_named(ison_algebra), k = "silhouette"))</code></pre>

		<pre class="text"><code>alge <- to_named(ison_algebra)
		alge %>%

	plot(node_in_structural(to_named(ison_algebra), k = 2))
	plot(node_in_structural(alge, k = 2))

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jhollway commented Apr 25, 2026

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