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• rescale parameter is superseded by norm parameter.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.