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ecodive 2.3.1

• read_tree() now handles quoted labels per the Newick standard:

  • '' inside a quoted label is decoded as one literal apostrophe, so 'it''s' is read as it's.
  • Square brackets inside quotes are literal characters rather than comments, so labels like 'o__[Saprospirales]' are no longer truncated.
  • Newlines and whitespace inside quotes are preserved.
  • Comments ([...]) outside of quotes may contain apostrophes.

• read_tree() raises an informative error, with the position of the problem, for malformed input such as an unclosed quote, comment, or parenthesis. Previously these could return a garbled tree.

• read_tree()’s parser is now linear-time and non-recursive, making it about 4x faster on a typical 100,000-tip tree and much faster on very deep trees.

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• rescale parameter is superseded by norm parameter.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.

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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