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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• rescale parameter is superseded by norm parameter.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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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