ecodive JOSS citation information.robust_aitchison() beta diversity function.testthat to dependency-free tinytest for test suite.read_tree fixes for edge cases.When using CLR normalization:
pseudocount is NULL.pseudocount <- min(counts[counts>0]) / 2.norm now defaults to "none" instead of "percent".norm parameter was removed from some beta diversity functions.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integers now).n_samples parameter has been removed.warn parameter has been added.rchk issue.rescale parameter is superseded by norm parameter.alpha_div() and beta_div() will only forward applicable parameters.pairs = integer(0).pseudocount = NULL correctly selects smallest non-zero count.weighted parameter.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")