TwoSampleMR 0.7.4

• Small tweaks to the categorized forest plots to make them more similar to the original ones in the article.
• Expanded the multivariable MR section of the Perform MR vignette (thanks @mvab)

TwoSampleMR 0.7.3

• Some further code optimizations

TwoSampleMR 0.7.2

• Add outlier categorisation on mr_forest_plot() forest plot, as per https://www.nature.com/articles/s41467-024-48105-7

TwoSampleMR 0.7.1

• Added error message if unsupported method listed in the method_list argument to the mr() function (thanks @42kuroniko)
• Added warning if mr_wald_ratio() passed more than one genotype's summary statistics

TwoSampleMR 0.7.0

• Fixed a bug in the calculation in one of the code paths for the inferred p-value in format_data() (thanks @j-brody)
• Fixed the calculation of a p-value in mr_rucker_internal()
• Fixed a replacement length warning in get_population_allele_frequency()
• Reformatted code base with air

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).