AMOR: Abundance Matrix Operations in R

AMOR 0.2-2

1. Updated collapse_matrixto work with R version 4+ which now always defines
   matrices as type of array (Issue #32).

AMOR: Abundance Matrix Operations in R

AMOR 0.2-0

1. Added support in subset.Dataset for when only one sample remains.
2. Added travis CI build testing (Issue #6)
3. Fixed bug with plotgg_rankabun caused by update of pool_samples. Added
   option to force return of a dataset object from pool samples.
4. Fixed bug with plotgg_rankabun2 caused because some columns of the
   aggregated dataset became tables instead of vectors.
5. Moved functions out of AMOR.r into their own files and removed
   unecessary functions. Might break backwards compatibility.
6. Removed functions that identify samples for rarefaction.
   This has been deprecated since rarefaction is not recomended
   to deal with uneven sampling. Might break backwards compatibility.
7. Eliminated summarizeOTUDistribution. Never implemented.
8. Removed normalizeSample function. Might break backwards compatibility.
9. Roxygen documentation and examples for get_tax_level.
10. Removed read.pool function. Might break backwards compatibility
11. Documentation and examples for write.qiime.
12. Roxygen2 documentation for bootglm and associated methods.
13. Homgenizing method variable names for PCA and PCO. Might break
    backwards compatibility.
14. Moving documentation to roxygen2 for functions beta_diverstity,
    clean, create_dataset, find_good_samples, findGOODSamples, matrix_glm,
    matrix_glmNB, plotgg_rankabun2, plotgg_rankabun, phylogram,
    plotgg_taxon, plotgg_var, rarefaction, remove_samples,
    remove_taxons, site_diversity, compare_site_diversity and
    total_richness. (Issue #4)
15. Switched theme_blackbox to a function and added roxygen documentation.
    Might break backwards compatibility.
16. Added codecov support (Issue #7)

AMOR: Abundance Matrix Operations in R

0.1-2

1. Fixed bug introduced on previous release regarding in remove_samples.

AMOR: Abundance Matrix Operations in R

0.1-1

1. Fixed bug in remove_taxons, it now works correctly when only one
   sample or taxon remains.
2. Fixed bug in remove_samples, it now works correclty when only
   one sample or taxon remains.

AMOR: Abundance Matrix Operations in R

0.1-0

1. Fixed error in summary.PCO. It required an object called Dat.pco
2. Added fill option to plotgg. Included in documentation
3. Added option to collapse_by_taxonomy with a custom factor
4. Fixed bug in collapse_by_taxonomy.Dataset so now it can take no group
5. collapse_matrix now uses plyr instead of apply functions. This allows for
   consistent return of matrix with dimension names when the grouping factor
   contains one level (Issue #10). This breaks
   backwards compatibility. Roxygen2 documentation for collapse_matrix
6. Updated pool_samples. Changed naming conventions of parameters,
   and removed the option to return a Dataset object from default method. These
   changes break backwards compatibility. Pool samples can also now take a vector
   or grouping factor. Updated and moved documentation to
   roxygen2 and updated examples (Issue #11).

AMOR_0.0-15

Abundance Matrix Operations in R 0.0-15

0.0-14: AMOR:Abundance Matrix Operations in R

Abundance Matrix Operations in R