TwoSampleMR 0.6.30

Some optimizations to the code, including:

• Vectorised mr_egger_regression_bootstrap()
• Vectorised weighted_median_bootstrap()
• Deleted duplicated weighted_median() function
• Replace plyr function calls with data.table function calls
  • plyr::rbind.fill(...) to data.table::rbindlist(..., fill = TRUE, use.names = TRUE)
  • plyr::ddply(dat, cols, func) to lapply() over unique combinations + data.table::rbindlist()
  • Added data.table::setDF() calls to convert back to data.frame for compatibility
  • And removed plyr from Imports list
• In flip_alleles() use chartr() instead of 4 gsub() calls
• In random_string() use single call to sample() instead of n calls
• Optimized mr_mode()
• Replaced apply(..., any(is.na())) with complete.case()
• Optimized the mr() function
• Optimized the Optimize get_r_from_lor() function
• Optimized the mr_rucker_bootstrap() and mr_rucker_jackknife_internal() functions
• Replaced sapply() with vapply() in several cases
• Optimized the simple_cap() function
• And a few other minor optimizations

TwoSampleMR 0.6.29

• Skip two tests if the MendelianRandomization package is not installed and protected the running of the perform_mr vignette.

TwoSampleMR 0.6.28

• Allowed the arguments for clump_data() to be specified from read_exposure_data() (thanks @al3xjwood).
• Fixed two function calls in mr_moe_single()

TwoSampleMR 0.6.27

• Removed the unused p2 argument from extract_instruments() and the unused clump_p2 argument from clump_data() (thanks @yikeshu0611).

TwoSampleMR 0.6.26

• Fixed the passing of the force_server argument within extract_instruments() through to ieugwasr::tophits() (thanks @yikeshu0611).
• Amended the extract_instruments() clump argument to additionally take values 1 or 0 as per the ieugwasr::tophits() clump argument (thanks @yikeshu0611).

TwoSampleMR 0.6.25

• The meta package has been moved to a soft (Suggests list) dependency due to installation problems of new versions of its hard dependencies on R 4.1.

TwoSampleMR 0.6.24

• We once again obtain mr.raps from its default branch. We issue a warning if the user has a version less than version 0.4.3 installed.

TwoSampleMR 0.6.23

• We now obtain mr.raps (version 0.4.3) from the open pull request which includes a fix. We will switch back to the default branch once that pull request is merged.

TwoSampleMR 0.6.22

• Additional reformatting of code base.
• Minor updates to GitHub Actions workflows.

TwoSampleMR 0.6.21

• Fixed typos in Steiger related documentation (thanks to @eleanorsanderson and Kaitlin Wade for providing the motivating example for this).
• Some code cleanup to make debugging easier.
• Reduced size of installed package by removing some unused files.