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Changelog

Source: NEWS.md

rbiom 3.0.1

rbiom 3.0.0

Announcements

The code for rbiom’s very fast implementations of diversity metrics, rarefaction, and tree importing has been spun off into its own dependency-free package, ecodive, to encourage adoption by other R packages. This also means rbiom will be easier to install going forward as it will no longer need to be compiled.

Breaking Changes

  • weighted and normalized arguments are no longer used by any functions.
  • Diversity metric names will now be all lowercase in returned matrices, tables, etc.

The following functions have been deprecated since rbiom v2.0 and are now removed completely. They are generally functions which have been renamed for improved organization.

alpha.div, as.percent, beta.div, comments, comments<-, counts, counts<-, depth, depths_barplot, has.phylogeny, has.sequences, id, id<-, info, is.rarefied, metadata, metadata<-, nsamples, ntaxa, phylogeny, phylogeny<-, rarefy, read.biom, read_biom, read.fasta, read.tree, repair, sample.names, sample.names<-, sample_subset, sample.sums, sequences, sequences<-, subtree, taxa.means, taxa.names, taxa.names<-, taxa.ranks, taxa.ranks<-, taxa.rollup, taxa.sums, taxonomy, taxonomy<-, tips, top.taxa, top_taxa, unifrac, write.biom, write.fasta, write.tree, write.xlsx

Additions

  • adiv_vector() returns a simple named vector of alpha diversity values.
  • Replaced rhdf5 dependency with h5lite.
  • Updated list of alpha diversity metrics: c("ace", "berger", "brillouin", "chao1", "faith", "fisher", "simpson", "inv_simpson", "margalef", "mcintosh", "menhinick", "observed", "shannon", "squares")
  • Updated list of beta diversity metrics: c("aitchison", "bhattacharyya", "bray", "canberra", "chebyshev", "chord", "clark", "sorensen", "divergence", "euclidean", "generalized_unifrac", "gower", "hamming", "hellinger", "horn", "jaccard", "jensen", "jsd", "lorentzian", "manhattan", "matusita", "minkowski", "morisita", "motyka", "normalized_unifrac", "ochiai", "psym_chisq", "soergel", "squared_chisq", "squared_chord", "squared_euclidean", "topsoe", "unweighted_unifrac", "variance_adjusted_unifrac", "wave_hedges", "weighted_unifrac")

rbiom 2.2.1

CRAN release: 2025-06-27

  • Compatibility fixes for ggplot2 4.0.0 #30

rbiom 2.2.0

CRAN release: 2025-04-04

  • Satisfy new R CMD check: no setting attributes on built-in functions. #28

rbiom 2.1.2

CRAN release: 2025-03-18

  • Fix for write_biom(format='json') where {...} should be [...].
  • Restore rline functionality in rare_corrplot().

rbiom 2.1.1

CRAN release: 2025-03-10

  • unifrac() no longer normalizes weighted values, for back-compatibility.
  • Option underscores allows keeping underscores in tree IDs.

rbiom 2.0.13

CRAN release: 2025-01-24

  • Major release with significant new features.
  • Plotting added.
  • Statistics added.
  • Caching added.
  • Clearer naming scheme for functions. Previous names still work but are deprecated.
  • Generation of human-readable ggplot2 code for modifying plots outside of rbiom.
  • Provenance tracking for BIOM objects and derivatives.

rbiom 1.0.3

CRAN release: 2021-11-05

  • Corrects for breaking changes in ‘rhdf5’ package.

rbiom 1.0.2

CRAN release: 2020-05-29

  • Improved compatibility with Debian and Solaris.
  • The ‘rhdf5’ package is now an optional dependency.
  • The select() and subset() functions now subset sequences too.

rbiom 1.0.0

CRAN release: 2020-05-26

  • Initial Release