NEWS

CBEA 0.99.3

NEW FEATURES

Created an output type object (CBEAout). This is an S3 type object that is essentially a list that incorporates the final score matrix as well as other diagnostic details.

SIGNIFICANT USER-VISIBLE CHANGES

Due to the new feature above, now instead of getting a tibble, users would have to extract the scores out either using the provided function or use a custom approach based on the list-of-list format of the CBEAout objects.
Implemented tidy and glance methods to deal with CBEAout objects

BUG FIXES

None

NEW FEATURES

Added an option (parametric) to specify whether the null is estimated parametrically or via pure permutation. To support this, an option (n_perm) was also added to specify the number of permutations. A warning will be added if parametric is FALSE but n_boot is small (< 100)
Added option (parallel_backend) to specify the parallel backend of the loop using BiocParallel
Argument control now allow for a special slot titled fix_comp that can specify which component of the two-component mixture distribution to fix during the adjustment process.

SIGNIFICANT USER-VISIBLE CHANGES

Combined raw argument with output argument for the CBEA function to specify returning raw CBEA scores (without any distribution fitting and transformation).
New and revamped vignettes
Significant reduction in dependencies, including removing native support for phyloseq

BUG FIXES

None

NEW FEATURES

None

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

NEW FEATURES

Added a NEWS.md file to track changes to the package.
Added a complete functionality to perform CBEA from scratch with bundled data set

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

None