bsocialv2 0.2.1

• Resubmission of 0.2.0 to address build artifacts flagged by CRAN pretest. No functional changes; the only difference is .Rbuildignore excluding helper scripts (_submit.R, .cran_submit.R) generated by the release tooling.

bsocialv2 0.2.0

Breaking changes

• analyze_diversity() no longer produces diversity_best_gen_plot, diversity_best_gr_plot, diversity_best_gen_table, diversity_best_gr_table. The Top-k strains ranking path has been removed; use the per-diversity-level plots instead.

New features

• New exported function plot_growth_scatter(.Object, remove_outliers, outlier_coef) renders the LogPhase-vs-NGen scatter on demand. When remove_outliers = TRUE, points above the Tukey IQR threshold in either axis are hidden and a subtitle reports the hidden count.
• plot_processed_curves() now draws the y-axis on a log10 scale with fine breaks. Non-positive OD values are dropped (consistent with the log transform).
• Per-strain cooperator/cheater/neutral badges are drawn below each facet in the plots produced by analyze_social_behavior() when summarize_social_behavior() has run.
• summarize_social_behavior() now stores stats_gen and stats_gr data frames in @resultados_analisis, containing per-strain medians, pairwise t-test p-values, and classification label.

Minor improvements

• analyze_diversity() x-axis label changed to “Species richness in consortium”.

bsocialv2 0.1.0

• Initial CRAN release.
• S4 class bsocial with six slots for organizing consortia analysis data.
• Growth parameter extraction via growthcurver (grofit available as optional backend).
• Social behavior classification: cooperators, cheaters, and neutrals.
• Diversity effect analysis relating consortium richness to fitness.
• Stability analysis via coefficient of variation across replicates.
• Biofilm assembly sequence finding using igraph shortest paths.
• Two workflow paths: raw plate reader data or pre-processed (curated) parameters.