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Changelog

Source: NEWS.md

phiper 0.4.1 (2026-04-15)

Bug fixes

Vignettes

  • New vignettes: beta diversity, delta plots, and POP plots.
  • Added calibration vignette to .Rbuildignore.

Plotting

  • Exported beta diversity plot functions.

Documentation

  • Updated README.

CI

  • Updated pkgcheck workflow to mirror phiperio behaviour.

phiper 0.4.0

New functions

  • compute_pop() replaces the old ph_prevalence_compare(). Computes per-feature prevalence comparisons (Fisher / McNemar tests) across group pairs. Unused arguments were removed, internal filtering now delegates to the shared .ph_filter_pairs() helper, and imports were trimmed.
  • scatter_static() — static ggplot2 prevalence scatter (percent1 vs percent2) with BH-corrected significance colouring and optional color_by highlighting.
  • volcano_static() — static ggplot2 volcano (log2 ratio vs −log10 p) with configurable fold-change and p-value cutoffs and raw / BH p-value modes.
  • volcano_interactive() — plotly equivalent of volcano_static().

Changes to scatter_interactive()

  • Fixed a hover-text bug that caused incorrect peptide labels to appear in some multi-rank datasets.
  • Updated peptide-library joining to follow the phiperio conventions used elsewhere in the package.
  • Removed arguments that were no longer used after the peptide-library refactor.

Plotting

  • All plots now use theme_phip() as their base theme and the phiper discrete colour / fill scales, ensuring a consistent visual style across the package.
  • phip_use_montserrat() has been removed. Font registration is handled automatically in .onLoad().

Examples and documentation

Tests

  • New test-pop_plots.R covering scatter_static(), scatter_interactive(), volcano_static(), and volcano_interactive() (return types, pair / rank filtering, BH colouring, color_by interface, background overlay, and the internal .build_color_group() helper).
  • Removed the two phip_use_montserrat() tests from test-plot_utils.R for the function that was deleted.
  • Updated vdiffr reference snapshots for deltaplot, forestplot, and ecdf_plot to reflect the new theme_phip() styling.

R CMD CHECK

Vignettes

  • Removed the pre-built .html vignette that was accidentally committed to the repository.

phiper 0.3.4

Changes to compute_delta()

  • New perm_method = "mid_p" option: computes the mid-p corrected permutation p-value, which halves the contribution of ties (), reducing the conservative bias of the standard test for discrete statistics. perm_method now defaults to "mid_p" (previously "standard").
  • New aggregate_stat = "af" option: implements an adaptive Fisher aggregation statistic. Per-peptide z-scores are converted to one-sided p-values, sorted, and the optimal truncation point is selected by maximising a harmonic-mean-weighted cumulative sum. Positive and negative tails are aggregated separately and the dominant direction is returned.

phiper 0.3.3

Tests

phiper 0.3.2

New functions

  • compute_alpha_significance(): runs global (Kruskal-Wallis or one-way ANOVA) and pairwise (Wilcoxon or Tukey HSD) hypothesis tests on every (rank, metric) combination returned by compute_alpha(). Returns a "phip_alpha_significance" list with $global (statistic, p-value, test) and $pairwise (p_raw, p_adj, Cohen’s d, significance stars) tibbles. Supports p_adjust_method (default "BH") and subsetting via metric / rank arguments. Group column is inferred automatically when not supplied.
  • plot_alpha_significance(): visualises pairwise results either as a filtered tibble (type = "table") or a symmetric Cohen’s d heatmap with significance stars (type = "heatmap"). Accepts metric, rank, and p_threshold arguments to focus on a single comparison.

Changes to plot_alpha() and plot_alpha_interactive()

  • metric now also accepts "pielou_evenness" and "berger_parker_dominance", matching all five indices added to compute_alpha() in 0.3.1.
  • New significance-bracket parameters: significance, show_significance, sig_p_threshold, sig_step_increase, sig_tip_length. Pass a "phip_alpha_significance" object and set show_significance = TRUE to overlay pairwise brackets via ggsignif (optional dependency). Non-significant pairs are automatically omitted.
  • Added ... (reserved; ignored) for forward-compatibility.

Font bundling

  • Montserrat Regular, Bold, and Italic TTF files are now shipped in inst/fonts/, so phip_use_montserrat() works offline without a Google Fonts connection.
  • phip_use_montserrat() tries the local bundle first; falls back to sysfonts::font_add_google() only when the local files are absent.
  • Package registers the font at load time via .onLoad() (showtext rendering remains opt-in; call phip_use_montserrat() explicitly to enable it).

Tests

  • New test-alpha_significance.R: 56 tests covering compute_alpha_significance() (global/pairwise tests, p-adjustment, Cohen’s d, metric/rank subsetting, group inference, single-group edge case) and plot_alpha_significance() (table and heatmap modes, error paths). Line coverage: 89.91% → 99.54%.
  • New test-alpha_plots.R: 63 tests covering all five metrics (static and interactive), faceting, group/rank filtering, custom colours, y-range, x-ordering, factor group columns, significance brackets, and plot_enrichment_counts(). Line coverage: 14.88% → 94.57%.

Documentation

Dependencies

  • Added ggsignif and rmarkdown to Suggests.
  • Added VignetteBuilder: knitr.

phiper 0.3.1

Changes to compute_alpha

  • Added pielou_evenness and berger_parker_dominance to the output (NA for samples with richness ≤ 1 and richness = 0 respectively).
  • New metrics parameter: request any subset of the five indices; defaults to all five.
  • New mode parameter ("binary", "threshold", "abundance") replaces fc_threshold. "abundance" mode uses raw values from abundance_col with optional abundance_agg ("mean", "sum", "max") at higher ranks.
  • shannon_log renamed to shannon_base; old name still works with a deprecation warning.
  • Performance: all-samples roster now collected once before the rank loop instead of re-queried per rank.
  • Hardening: all-invalid ranks now aborts with an informative error instead of silently returning empty output; n_samples attribute added to the result.
  • Validation: mode = "threshold" now requires threshold to be finite and abundance_col (when supplied) to be a character scalar.

phiper 0.3.0

Major changes

  • Extracted all data-import, class construction, and low-level utility code into the new phiperio package. phiper now declares phiperio as a hard dependency and re-exports its user-facing functions (load_example_data, get_example_path) so existing workflows require no changes.
  • Removed all functions that moved to phiperio: phip_convert, phip_convert_legacy, new_phip_data, expand_phip_data, phip_data_join, validate_phip_data, disconnect, get_comparisons, phip_example_path, phip_load_example_data, and the full logging / validation helper suite (add_quotes, word_list, .chk_*).
  • Internal logging and validation now use the unified phiperio helpers (.ph_abort, .ph_warn, .ph_log_info, .ph_with_timing, .ph_check_cond, .ph_add_quotes, .ph_word_list, .ph_check_path, .ph_check_extension, .ph_check_null_default).
  • get_peptide_meta() renamed to get_peptide_library() throughout, in line with the phiperio API.
  • compute_alpha: restored efficient same-connection peptide library handling via .ph_peplib_on_main() (DuckDB ATTACH fast path with copy_to() fallback).

Internal

  • R source files renamed to follow the new <domain>_compute / <domain>_plots convention: binary_alpha → alpha_compute, binary_alpha_plots → alpha_plots, binary_beta → beta_compute, binary_beta_plots → beta_plots, prevalence-DELTA_test → delta_compute, prevalence-DELTA_plots → delta_plots, prevalence-POP-test → pop_compute, prevalence-POP_plots → pop_plots, plot-utils → plot_utils. Test files renamed accordingly.
  • Naming conventions for source files and functions documented in CONTRIBUTING.md: exported functions use plain snake_case; all internal helpers use the .ph_ prefix.

phiper 0.2.7

  • compute_delta: added maxmean (Efron-type) as a test statistic option.
  • compute_delta: added prevalence bins for the test statistic computation.
  • compute_delta: srlr is now the default test statistic.
  • Implemented McNemar test and paired signed root likelihood ratio statistic for paired designs.
  • Welford’s online algorithm refactored into its own class; added a wrapper for post-permutation output generation.
  • Docs and R CMD CHECK fixes.

phiper 0.2.6

  • compute_delta: added stat_mode options “score” (pooled score z) and “srlr” (signed root likelihood ratio) using raw counts.
  • compute_delta: removed smoothing, prevalence filtering, BH adjustment, and fold_change/cross_prev summaries; outputs now include T_null_mean and T_null_sd and standardized T_obs uses the null mean and sample SD.
  • shift_computing: null variance uses Welford’s algorithm with sample variance in permutation loops.
  • prevalence-DELTA plots/tests updated to drop BH/categorical dependencies and use numeric-only filtering where applicable.

phiper 0.2.5

  • Removed 10 unused package dependencies (data.table, fs, htmltools, purrr, forcats, filelock, arrow from suggests)
  • Moved duckdb and dbplyr to imports; moved knitr to suggests for proper dependency management
  • Removed 360 lines of unused CAP/dispersion plotting functions and associated documentation

phiper 0.2.4

  • Updated the peptide library with the new annotations from Sasha
  • in the compute_distance –> fallback to collecting before pivoting

phiper 0.2.3

  • Added small_mixture to phip_load_example_data
  • Changed all examples and tests to use this small_mixture instead of redining it
  • Added cache to phip_load_example_data to make tests/examples faster

phiper 0.2.2

  • Separated the feature associations to PCoA vectors from compute_pcoa to a separate function.

phiper 0.2.1

Minor changes

  • Removed superassignments, changed all assignments to “<-” style
  • Stated all dependencies, removed unstated dependencies

Bug fixes

  • Fixed typos in the examples from binary_beta.R
  • fixed R CMD check (0 errors, 0 warnings, 0 notes)

Documentation

  • Documented empty params, got rid of all documentation-related wearnings,
  • removed all non-ASCII chars
  • Added CONTRIBUTING.md to .Rbuildignore (it caused a note in R CMD CHECK),

phiper 0.2.0

Minor changes

  • Removed generic and S3 methods for the expand_phip_data
  • Renamed the internal helpers involved in the data import to match the naming convention .ph_
  • documented the internal helpers involved in the data import stage

Major changes

  • Removed the backend argument entirely from the phip_convert, phip_convert_legacy, new_phip_data, .resolve_paths and other, less imporatant helpers. DuckDB is now the only supported backend
  • Changed the structure of the repo. Now all functions related to the standard/legacy import workflows live in the standard-conver.R or legacy-convert.R
  • removed the resolve-paths.R file. Moved the functions to utils.R

phiper 0.1.1

Minor changes

  • Removed old, dead and undocumented code: R/binary-analysis_peptides.R, R/vinary-analysis_stability.R, R/binary-analysis_stability_cattime.R, R/fold_change-analysis.R

  • i left other files, even if they were undocumented/untested, as they were essential for phiper to work (e.g. the data import paths)

phiper 0.1.1

Minor changes

  • Removed old, dead and undocumented code: R/binary-analysis_peptides.R, R/vinary-analysis_stability.R, R/binary-analysis_stability_cattime.R, R/fold_change-analysis.R

  • i left other files, even if they were undocumented/untested, as they were essential for phiper to work (e.g. the data import paths)

Documentation

  • Regenerated the docs, removed the old functions from NAMESPACE

phiper 0.1.0

Minor changes

  • None.

Major changes

  • None.

Features

  • None.

Bug fixes

  • None.

Documentation

  • None.

Internal

  • None.