twosamplemr - TwoSampleMR 0.6.22

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

- R
Published by remlapmot 6 months ago

twosamplemr - 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.

- R
Published by remlapmot 7 months ago

twosamplemr - TwoSampleMR 0.6.20

• TwoSampleMR now requires ieugwasr version 1.1.0 which provides improved error messages.
• Changed error handling - now if the API gives an error code it is propagated as an error with message in TwoSampleMR.
• Headers sent to API are updated.

- R
Published by remlapmot 7 months ago

twosamplemr - TwoSampleMR 0.6.19

• Further fixes for the forthcoming version 4 of ggplot2.

- R
Published by remlapmot 7 months ago

twosamplemr - TwoSampleMR 0.6.18

• Fixes to mr_forest_plot(), forest_plot_1_to_many(), mr_leaveoneout_plot(), and mr_scatter_plot() for compatibility with the forthcoming release of version 4 of ggplot2.
• Made some minor improvements in the Perform MR vignette including adding back several of the forest plots.

- R
Published by remlapmot 8 months ago

twosamplemr - TwoSampleMR 0.6.17

• Continued amends to the plot for MR-GRIP (thanks @fdudbridge)

- R
Published by remlapmot 8 months ago

twosamplemr - TwoSampleMR 0.6.16

• Added weak instrument adjustment estimate and intercept to returned output of mr_grip() (thanks @fdudbridge)
• Amended mr_scatter_plot() to issue a message about the scale the MR-GRIP estimate is plotted on (thanks @fdudbridge)

- R
Published by remlapmot 9 months ago

twosamplemr - TwoSampleMR 0.6.15

• Bumped the minimum required version of R to 4.1.0. This is due to a dependency (the scales package) of a dependency (the ggplot2 package), which now has this requirement.

- R
Published by remlapmot 10 months ago

twosamplemr - TwoSampleMR 0.6.14

• Minor amends to the mr_grip() returned object names (thanks @fdudbridge)
• Fixed some typos in the helpfiles and vignettes

- R
Published by remlapmot 11 months ago

twosamplemr - TwoSampleMR 0.6.13

• Added mr_grip() function which implements the MR-GRIP (modified MR-Egger with the Genotype Recoding Invariance Property) method of Dudbridge and Bowden et al. (2025). The new method can be accessed by mr(dat, method_list = "mr_grip") or it can be added to the default list of methods with mr(dat, method_list = c(subset(mr_method_list(), use_by_default)$obj, "mr_grip")).
• Added Pub Med IDs for more of the methods.
• The format_data() function no longer causes a stack overflow when its dat argument is not a variable (thanks to @DarwinAwardWinner)

- R
Published by remlapmot 11 months ago

twosamplemr - TwoSampleMR 0.6.12

• Fixed a bug in format_data() (thanks to @lea-urpa)
• For MVMR data extraction in mv_extract_exposures() and mv_extract_exposures_local(), SNPs that do not pass harmonisation between exposures in MVMR are now dropped (thanks @yatest)
• The comments about mr.raps in the Perform MR vignette have been updated

- R
Published by remlapmot 11 months ago

twosamplemr - TwoSampleMR v0.6.11

• The tests using mr.raps are now run conditionally.
• The rsnps package has been removed from Suggests because the configuration of mr.raps has been corrected.

- R
Published by remlapmot 12 months ago

twosamplemr - TwoSampleMR 0.6.10

• The mr.raps package was archived from CRAN on 2025-03-01. A later version (0.4.1) than was on CRAN (0.2) is available from its GitHub repo https://github.com/qingyuanzhao/mr.raps. We believe this later version still works as expected in TwoSampleMR. However, version 0.4.1 depends upon rsnps package which is itself now only available on its GitHub repo. Hence, we have added both packages to our https://mrcieu.r-universe.dev/ and added that to the Additional_repositories field in the DESCRIPTION. We have also moved mr.raps to the soft dependency list (Suggests list) and added rsnps to our Suggests list, both with remotes.
• Fix to default_parameters() helpfile

- R
Published by remlapmot 12 months ago

twosamplemr - TwoSampleMR 0.6.9

• Fixed a bug in format_data() when the log_pval argument was set to TRUE (thanks to @luddeluddis)
• Amend references to MR-Base to OpenGWAS

- R
Published by remlapmot about 1 year ago

twosamplemr - TwoSampleMR 0.6.8

• Replaced some unique() calls in power_prune() with mean() to ensure scalar iv.se values (thanks @phageghost)
• Slightly improved formatting of code base

- R
Published by remlapmot over 1 year ago

twosamplemr - TwoSampleMR 0.6.7

• Update OpenGWAS API URLs
• Minor tweak to R CMD check GitHub Actions due to the rjson hard dependency of the MendelianRandomization package now requiring R >= 4.4.0
• Add dark mode to pkgdown site

- R
Published by remlapmot over 1 year ago

twosamplemr - TwoSampleMR 0.6.6

• Improve a test
• Improve permissions in GitHub Actions workflows
• Bump minimum required version of ieugwasr to 1.0.1
• Made some amends to the code to bring it more in line with lintr recommendations
• Added omitted tidyr soft dependency

- R
Published by remlapmot over 1 year ago

twosamplemr - TwoSampleMR 0.6.5

• Bumped version of roxygen2 for creating package documentation
• Update the earliest version of R in the R CMD check GitHub Actions workflow to be 4.3.2. This is because the meta dependency depends on lme4, and the recent 1.1-35.4 release of lme4 requires Matrix 1.6-2 which was released a few days after R 4.3.2.
• Made package tests more robust to non-response from the OpenGWAS API

- R
Published by remlapmot over 1 year ago

twosamplemr - TwoSampleMR 0.6.4

• Update installation instructions in README.md

• Fixed a bug in which the wrong indels recoding function was called (thanks @ruochiz)

- R
Published by remlapmot over 1 year ago

twosamplemr - TwoSampleMR 0.6.3

• Update startup messages

- R
Published by remlapmot over 1 year ago

twosamplemr - TwoSampleMR 0.6.2

• format_data() now errors if it detects its dat object is of class 'data.table' and issues a message informing the user to make their dat object simply a 'data.frame' (thanks to Si Fang @sifang1678)

- R
Published by remlapmot almost 2 years ago

twosamplemr - TwoSampleMR 0.6.1

• The MendelianRandomization package has been moved from a hard dependency (Imports list) to a soft dependency (Suggests list). This is because its dependency package Matrix now requires R >= 4.4.0. Making MendelianRandomization a soft dependency means we don't need to make TwoSampleMR have the same requirement.

- R
Published by remlapmot almost 2 years ago

twosamplemr - TwoSampleMR 0.6.0

• TwoSampleMR now uses the CRAN version of the ieugwasr package. Importantly this includes the new authentication system for the OpenGWAS API. Please see https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication for more information about how to set this up.

- R
Published by remlapmot almost 2 years ago

twosamplemr - TwoSampleMR 0.5.11

• In mr_leaveoneout_plot() and mr_forest_plot() amended size argument to linewidth as per ggplot2 version 3.4.0.
• Add some datasets such that tests, continuous integration services, and creation of the vignettes don't rely on the availability of the OpenGWAS server.
• Various improvements to helpfiles.

- R
Published by remlapmot almost 2 years ago

twosamplemr - TwoSampleMR 0.5.10

• Added local options for clump_data
• Fixed bugs with mv_extract_exposures_local

- R
Published by explodecomputer about 2 years ago

twosamplemr - TwoSampleMR 0.5.9

• Fixed a minor issue in dat_to_RadialMR()
• Minor improvements to make_dat() default arguments and helpfile
• Minor improvements to package tests
• Amendments to GitHub Actions workflows
• Updated several URLs which had changed

- R
Published by remlapmot about 2 years ago

twosamplemr - TwoSampleMR 0.5.8

• Improved speed of harmonisation using data.table functions (thanks @nicksunderland)
• Updated URL to R-CMD-check README badge
• Updates to GitHub Actions workflows

And some other minor updates to the documentation and pkgdown site.

- R
Published by remlapmot over 2 years ago

twosamplemr - TwoSampleMR 0.5.7

• Move car package to Suggests to allow TwoSampleMR to install on R between versions 4.0.0 and 4.1.0
• In DESCRIPTION use pkgdepends syntax for MRPRESSO package due its repository name being different to the package name so that installing TwoSampleMR under pak continues to work
• Various minor code tweaks to fix 2 R CMD check notes
• Add Cairo package to Suggests list (thanks @hdraisma)
• Fix error in outcome data vignette (thanks @hdraisma)
• Some p-values that should have been ~0 were being stored as 1 in the elasticsearch database. This has now been fixed and those datasets have been clumped again to re-define the tophits. A full list of affected GWAS is available here: https://github.com/MRCIEU/opengwas-infpval-fix
• Updated steiger filtering to use effective sample size for case control studies (thanks to @niekverw)
• Fixed issue with tri-allelic SNPs in harmonisation. Credit to Clare Horscroft (@chorscroft) for spotting the error and fixing
• Fixed an issue with experimental version of local multivariable MR method. Credit to Mischa Lundberg (@MischaLundberg).
• Catching edge cases for retrieving sample size meta data
• Updating default rsq estimation function to use beta and standard error instead of p-value, should improve numerical stability
• Allow chr and pos to be read in from local summary data files
• When reading in local data without p-values, editing the inferred p-value method to be two-sided
• All images in the vignettes (and hence also in the rendered pkgdown website) now have accompanying alt text descriptions
• The accompanying website for the package now uses Bootstrap 5, which means a search facility is enabled
• The NAMESPACE has been simplified, hence the package load time is very slightly improved

- R
Published by remlapmot over 2 years ago

twosamplemr - Various minor updates

- R
Published by explodecomputer almost 5 years ago

twosamplemr - WellcomeOpen

Release to create a DOI for Wellcome Open publication

- R
Published by t0mrg over 6 years ago