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ecodive 2.3.0

  • Added ecodive JOSS citation information.
  • New robust_aitchison() beta diversity function.
  • Switch from testthat to dependency-free tinytest for test suite.
  • read_tree fixes for edge cases.

ecodive 2.2.6

  • When using CLR normalization:

    • Warns when zeros are detected and pseudocount is NULL.
    • Then continues with pseudocount <- min(counts[counts>0]) / 2.

Breaking Changes

  • norm now defaults to "none" instead of "percent".
  • norm parameter was removed from some beta diversity functions.

ecodive 2.2.4

Breaking Changes

  • The rarefy() function has been simplified:

    • drop = FALSE now returns samples with original counts when sum < depth.
    • drop = TRUE no longer drops zero-sum features - only zero-sum samples.
    • depth can no longer be a fraction (only positive integers now).
    • n_samples parameter has been removed.
    • warn parameter has been added.

ecodive 2.2.3

  • Coerce counts to double before rarefaction.

ecodive 2.2.2

  • Drop explicit zeros from sparse matrices after rarefaction.

ecodive 2.2.1

  • Corrected CRAN rchk issue.

ecodive 2.2.0

  • Dedicated rarefaction backends for dense and sparse matrices.
  • Auto-conversion to col-major sparse matrix for distance/diversity calculations.

ecodive 2.1.0

Breaking Changes

  • rescale parameter is superseded by norm parameter.

Fixes

  • alpha_div() and beta_div() will only forward applicable parameters.
  • No longer crashes when pairs = integer(0).
  • pseudocount = NULL correctly selects smallest non-zero count.

ecodive 2.0.0

Breaking Changes

  • Input matrix is now samples as rows.
  • Removed weighted parameter.

Added New Diversity Methods

  • Updated Alpha Options: c("ace", "berger", "brillouin", "chao1", "faith", "fisher", "simpson", "inv_simpson", "margalef", "mcintosh", "menhinick", "observed", "shannon", "squares")

  • Updated Beta Options: 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")

ecodive 1.0.0

  • This is the first release of ecodive.