Changelog

mvMAPIT (development version)

Fix Bonferroni correction in the mvMAPIT.Rmd vignette.
New function binary_to_liability for LT-MAPIT support and corresponding vignette
Fix CRAN Notes - dependency compatibility.
Performance improvements in C++ implementation:
- Eliminated redundant matrix inverse computation in projection operations
- Optimized triple matrix products in Q matrix computation
- Added benchmark suite for tracking performance improvements
- Typical speedup: 3-8% depending on problem size and test method

Fix LTO issues again. The R dev automation generates RcppExport.cpp files that cause LTO issues in this package on CRAN.

Added Cauchy combination test cauchy_combined including vignette that compares combination methods
simulate_traits now returns genotype matrix with causal epistatic variants named according to the trait they affect
Added progress bar and possibility to interrupt C++ routine using RcppProgress
Fixed “incorrect number of dimensions” error in simulate_data.R

Fix LTO issues when submitting to CRAN. The testthat issue https://github.com/r-lib/testthat/issues/1230 describes the solution chosen. Created this GitHub gist to reproduce LTO errors: https://gist.github.com/jdstamp/056475683110aacdb1e6761872ab1e05.

fishers_combined and harmonic_combined now take additional arguments in form of string values. The first determines the name of the column of the tibble by which to group the p-values. The second determines the name of the column containing the p-values.
Added Dockerfile and vignette on mvMAPIT in Docker.
MvMAPIT was renamed to mvmapit.
simulate_phenotypes was renamed to simulate_traits.
Dependencies were cleaned up, e.g. R requirement 2.10 -> 3.5, old package dependencies removed.