Changes in version 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.

                 Changes in version 2.2.6 (2026-04-14)                  

  - 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.

                        Changes in version 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.

                        Changes in version 2.2.3                        

  - Coerce counts to double before rarefaction.

                 Changes in version 2.2.2 (2026-01-16)                  

  - Drop explicit zeros from sparse matrices after rarefaction.

                 Changes in version 2.2.1 (2025-12-12)                  

  - Corrected CRAN rchk issue.

                 Changes in version 2.2.0 (2025-12-03)                  

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

                 Changes in version 2.1.0 (2025-09-26)                  

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  - rescale parameter is superseded by norm parameter.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.

                 Changes in version 2.0.0 (2025-09-21)                  

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")

                 Changes in version 1.0.0 (2025-08-22)                  

  - This is the first release of ecodive.