# 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* `rescale` parameter is superseded by `norm` parameter.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.
