`lm1`

in the C++ was not being initialized. This has been fixed.

`bama`

now contains`fdr.bama`

, a`bama`

variant that controls for the false discovery rate by estimating the null PIP distribution via the permutation test. It contains options to run in parallel (ie using the`parallel`

package) as well, since the permutation test can be time consuming.`fdr.bama`

also contains a summary function,`summary.fdr.bama`

to help summarize results.

`bama`

(and`fdr.bama`

) now contain a weights parameter,`weights`

.- Change k, lm0, lm1, l from hard coded parameters in the C++ code to user set parameters (with defaults).
- Revert change that combined C1 and C2.

- Partial revamp
`bama`

documentation. - Edit DESCRIPTION, and README / vignette introduction.
- Update DOI with (online) version of record.
- Redo
`bama`

type checking.

The most notable feature in this release is the renaming of

`hdbm`

to`bama`

to prevent confusion with regards to its relationship with`hdmm`

.bama now only accepts a single extra covariate matrix C, instead of C1 and C2. ## Minor Changes

Added a summary function to

`bama`

to calculate the PIP, estimate, and credible interval of each mediator and optionally rank them.Added data quality check to ensure the matrix column norms in M, C1 and C2 are not too small. If they are too small,

`NaNs`

could be generated because of overflow problems when dividing by the norm.Improved documentation

Added checks to C, the matrix of extra covariates, and alpha.a, the initial alpha.a values.

- Initial version released on CRAN.