Fix LTO issues as reported by CRAN.

What's Changed

• LTO issues on CRAN resurfaced because of r dev autogeneration by @jdstamp in #109

Full Changelog: v2.0.2...v2.0.3

Better control over the C++ code execution.

What has changed

• 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_traits

Full Changelog: v2.0.1...v2.0.2

Package version without LTO errors due to testthat

Fixed the CRAN errors when checking with LTO enabled.

Version increment without changes for dev purposes.

v2.0.0.1

version upgrade for resubmission (#97)

First official release.

Multivariate MAPIT paper published on BiorXiv: https://www.biorxiv.org/content/10.1101/2022.11.30.518547v1

• 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.

Optimize memory consumption for the covariance matrices.

MM-58: refactoring should save a lot of memory (#54) [rinstall]

* MM-58: refactoring should save a lot of memory

* MM-58: improved davies method with C

* MM-58: not sure whether tests are working

mvMAPIT only features combinatorial approach

This is the first version that only features the combinatorial approach to mvMAPIT.

Last version with Kronecker Method

This version is the last version that features the experimental kronecker method implementation.

Hybrid mode is a test mode now. Phenotype covariance contains combinatorial.

Deprecated input argument hybrid. Now the argument test can take the value hybrid. Phenotype covariance now takes combinatorial as input parameter.

p-value computation: Saddlepoint approximation when davies does not converge

The davies-method now falls back to the saddlepoint approximation as suggested in Wu et al. (2016) [1].

1.Wu, B., Guan, W. & Pankow, J. S. On efficient and accurate calculation of significance p-values for sequence kernel association testing of variant set. Ann Hum Genet 80, 123–135 (2016).