mvMAPIT (development version)

mvMAPIT 2.0.4 release

• 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

mvMAPIT 2.0.3 release

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

mvMAPIT 2.0.2 release

• 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

mvMAPIT 2.0.1 release

• 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.

mvMAPIT 2.0.0.1 pre-release

• CRAN issue does not show up in R CMD check. Version upgrade for resubmission.

mvMAPIT 2.0.0 release

• 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.

mvMAPIT 1.1.1-alpha prerelease

• Version that publication data was produced with. No official release.