# 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.
