Changes in version 1.8.0                        

SIGNIFICANT USER-VISIBLE CHANGES

  - importBugphyzz() defaults to data release v1.1.0
    (10.5281/zenodo.24114812): 466,663 annotations for 93,838 taxa, 33
    attributes and 18 sources.
  - Imputed annotations are kept or dropped per attribute, by the
    lower 95% bound of a distance-matched Cohen's kappa, or R2 for
    numeric attributes (#292).
  - Discrete signature names start with bugphyzz:, not bugphyz: (#256).
  - excludeRarely and v are deprecated; use asrScoreThreshold,
    kappaThreshold and r2Threshold (#271).
  - Levi Waldron is the maintainer (#257).

NEW FEATURES

  - physiologies() also reads the scripted sources in bugphyzzExports
    sources/: the 2026 Bergey's Manual extraction, Madin et al. 2020,
    BacDive, The Microbe Directory and NCBI RefSeq assemblies (#275).
  - New attribute gc content and new shape value vibrio.
  - attribute_synonyms.tsv maps source terms to the controlled
    vocabulary (#264).
  - New arguments kappaThreshold, r2Threshold and asrScoreThreshold; a
    threshold below its default also loads the imputations the export
    left out (#292).
  - Validation scores per attribute and per state ship as
    validation_attributes.tsv and validation_states.tsv.

BUG FIXES AND MINOR IMPROVEMENTS

  - Cell length and width no longer collapse to the lower bound of their
    range (#275).
  - Downloads are cached per version.
  - Typos and missing terms in attributes.tsv are fixed (#281).
  - Tests that download data skip when offline (#266).

                       Changes in version 0.99.3                        

  - Update table with validations results in extdata to version 1.0.2

                       Changes in version 0.99.0                        

  - First version of the package for submission in Bioconductor.