NEWS.md

In qpmnguyen/CBEA: Competitive Balances for Taxonomic Enrichment Analysis in R

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

CBEA 0.99.2

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

CBEA 0.99.1

NEW FEATURES

None

SIGNIFICANT USER-VISIBLE CHANGES

None

BUG FIXES

• Removed .Rproj file to conform with Bioconductor error

CBEA 0.99.0

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

qpmnguyen/CBEA documentation built on April 4, 2022, 7:25 p.m.