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agallinat
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Oct 3, 2026
agallinat
commented
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- Fix five runtime defects and add a testthat suite
- Prepare DESCRIPTION, LICENSE and .Rbuildignore for CRAN
- Make all examples executable
- Replace deprecated ggplot2 and igraph calls
- Extract shared graph validator and collapse duplicate diffusion kernel
- Add release infrastructure and fix documentation typos
- Do not claim untested platforms in cran-comments.md
- Adopt the .9000 development-version convention
- Stop setting a future plan inside network_diffusion_with_pvalues()
- Make the plot return slot uniform across the package
- Fix silently wrong participation coefficients in calculate_roles()
- Fix NaN AUC in robustness_analysis() and audit the surrounding pattern
Swept the package for the count/total mismatch behind the calculate_roles() bug -- a quantity derived one way divided by a total derived another. Found one more real instance, in robustness_analysis(). Global efficiency divides by n(n-1), which is 0 once a single vertex remains, so it evaluated to NaN and that NaN propagated through pracma::trapz() into the AUC. This fired on the *documented default call*: steps = 50 makes step_size = 1 for any graph of about 51 nodes or fewer, so the loop does reach one vertex. On a 50-node sample_pa, auc$efficiency came back NaN while the other two metrics looked fine. Efficiency is now 0 when fewer than two vertices remain -- a collapsed network has no paths -- which is also what the robustness literature reports. A second divide-by-zero sat behind it: every metric is scaled by max(metric), once for the AUC and six times inside the plot's aes() calls. When a metric is zero throughout, which global efficiency is for a graph with no edges, that made all seven NaN. Replaced with a normalize_metric() helper (R/utils-metrics.R) that leaves the series untouched when the maximum is zero or not finite. Also dropped `fill = "Metric"` from labs(), which made ggplot2 report "Ignoring unknown labels: fill" on every robustness plot, since no fill aesthetic is mapped. Audit conclusions for the sites that are NOT bugs, recorded so they are not "fixed" later: - plot_CCDF()/compute_ccdf() divides by sum(deg_tab), i.e. the same table it tallied. This is the correct form of the pattern. - summarize_graph_metrics() divides table(deg) by length(deg); degree() cannot return NA, so the two agree by construction. - The match() calls in calculate_roles(), find_modules() and assign_attributes() index with values that are guaranteed present, or handle NA explicitly. - summarize_graph_metrics() returns NaN for Average_path_length, Clustering_coefficient, Degree_assortativity, Gini_degree and Modularity on an edgeless graph. These are undefined quantities propagated from igraph and ineq, not arithmetic errors; substituting zeros would fabricate values. A test pins the exact set so a new NaN column shows up as a regression. Corrected summarize_graph_metrics()'s @return, which promised a tibble while the function returns a data.frame, and now documents the NaN cases. Tests go from 386 to 411. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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