# BeviMed 5.1

- New function,
`subset_variants`

, which retains only variants with data bearing upon pathogenicity.
- Return posterior mean of
`omega`

even when not explicitly sampled in `summary.BeviMed_m`

.

# BeviMed 5.0

`bevimed_polytomous`

function added which enables application of BeviMed across multiple association models.
`BeviMed`

objects now more general, representing results of inference with respect to the baseline model `gamma = 0`

and an arbitrary number of alternative association models - typically, one for each mode of inheritance. The `$moi`

slot has been replaced with `$models`

.
`prob_pathogenic`

now returns a list when broken down by mode of inheritance/model.

# BeviMed 4.3

- Make BeviMed work smoothly when number of individuals or number of variants is 0.
- Retain names of variants from columns of original allele count matrix.
- Improvements to guide, with more detail on model selection.

# BeviMed 4.2

- Fixed bug in calculation of expected number of explaining variants by only including those with pathogenic configurations.

# BeviMed 4.0

- Previous
`bevimed`

function now replaced by `bevimed_m`

, with the `_m`

indicating that it conditions on mode of inheritance.
`bevimed`

now integrates over indicator of association (gamma) and mode of inheritance (m), allowing user to specify priors on probability of association and probability of dominance.
- The
`BeviMed`

class object has been replaced by `BeviMed_m`

, and a new `BeviMed`

class has been introduced for inference with respect to all models: gamma 0 and gamma 1 under each mode of inheritance.
- A new vignette with more detail called
`BeviMed Guide`

which relates the package to the paper.
- Names used for summary statistics in summary objects have changed, see function help pages for details on current names.
`print`

ing a `BeviMed`

object now shows conditional probabilities of pathogenicity for each mode of inheritance, and expected explained cases and expected explaining variants shown too.
- Bug fixed in adaptive tuning for omega and phi proposals.

# BeviMed 3.0

- Re-naming of parameters in
`bevimed`

function to match the names of variables in the paper (under submission).
- The allele count matrix
`G`

should now be supplied as a matrix with rows corresponding to individuals, not variants.
`expected_explained`

and `explaining_variants`

functions have been added, respectively computing the expected number of cases with their disease explained by the given variants, and expected number of pathogenic variants present amongst cases.