NEWS

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BeviMed 5.1 (2017-07-03)

• 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 (2017-04-22)

• 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 (2017-03-01)

• 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• The BeviMed class object has been replaced by BeviMed_m, and a new BeviMed class has been introduced for inference with respect to all models: gamma 0 and gamma 1 under each mode of inheritance.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.
• printing 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 (2017-02-16)

• 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.