POMS v1.0.1

Minor changes to fix notes/warnings when submitting to CRAN.

Now approved and hosted there: https://cran.r-project.org/web/packages/POMS/

POMS v1.0.0

Official release following POMS publication.

Includes minor changes to meet CRAN submission requirements.

POMS v0.3.1

• Fix calculation for specificity that failed under some circumstances

• Also optional POMS mode where nodes with similar underlying tips are dereplicated

POMS v0.3.0

Added code and unit tests for basic phylogenetic regression and prevalence/specificity metrics implemented using phylogenize-based code.

POMS v0.2.0

• No longer add pseudocount before computing Fisher's exact tests, which does affect the FSN results a bit, but which is fairer. This was done previously as a crude way to ensure that odds-ratios would always be finite, but that's no longer necessary.

• Now allow significance direction of manually specified BSNs as an input argument. Means that working with continuous data is now much easier.

• Cleaned up function used for prepping tree prior to plotting an output example with ggtree.

• Re-organized output of POMS_pipeline (e.g., object names are simplified and more information is provided by default without having to specify detailed_output)

• Added unit tests

• Added in documentation for exported functions

• Simplified terminology and made sure it was consistent through-out (especially in terms of BSNs and FSNs)

• Removed unused functions

• Minor clean-ups to code, mainly to make it easier to read

POMS v0.1.0 (alpha)

First alpha release used for draft manuscript results