OneSampleMR

R package of useful functions for one-sample Mendelian randomization and instrumental variable analyses

https://github.com/remlapmot/onesamplemr

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
✓
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Found codemeta.json file
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Found .zenodo.json file
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DOI references
Found 10 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (13.7%) to scientific vocabulary

Keywords

instrumental-variable instrumental-variables mendelian-randomisation mendelian-randomization mendelianrandomisation mendelianrandomization r

Last synced: 6 months ago · JSON representation ·

Repository

R package of useful functions for one-sample Mendelian randomization and instrumental variable analyses

Basic Info

Host: GitHub
Owner: remlapmot
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://remlapmot.github.io/OneSampleMR/
Size: 8.53 MB

Statistics

Stars: 23
Watchers: 3
Forks: 3
Open Issues: 2
Releases: 7

Topics

instrumental-variable instrumental-variables mendelian-randomisation mendelian-randomization mendelianrandomisation mendelianrandomization r

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.md

OneSampleMR: Useful functions for one-sample Mendelian randomization and instrumental variable analyses

Useful functions for one sample, individual level data, Mendelian randomization / instrumental variable analyses, including implementations of:

The Sanderson and Windmeijer (2016) conditional F-statistic for multiple exposure models.
Various one-sample instrumental variable estimators including the
- Multiplicative structural mean model (Robins, 1989; Hernán and Robins, 2006)
- Two-stage predictor substitution estimators (Terza, 2008)
- Two-stage residual inclusion estimators (Terza, 2008)

OneSampleMR was included in the R Views November 2021 "Top 40" New CRAN Packages here!

Installation

Released version

Install the package from CRAN using

r install.packages("OneSampleMR")

To check for updates run

r update.packages()

Issue with gmm package versions 1.6-5, 1.6-6, 1.7 on macOS

Using these old versions of the gmm package, a GNU Fortran installation was required even if the binary version of the package was installed.

The fix is to update to the current version of gmm, which is version 1.8.

If you cannot update your version of gmm then

The current version of GNU Fortran to install is documented here and available here
Note that the version of Fortran available from Homebrew will probably not work

Development version

Install the development version of the package from source from GitHub using

``` r

install.packages("remotes") # uncomment on first run

remotes::install_github("remlapmot/OneSampleMR") ```

To check for and install updates to the development version run the previous command again or run

r remotes::update_packages()

A binary of the development version of the package (for Windows, macOS, and Ubuntu Jammy Jellyfish) can be installed from r-universe using

r install.packages('OneSampleMR', repos = c('https://remlapmot.r-universe.dev', 'https://cloud.r-project.org'))

which can be updated using

r update.packages(repos = c('https://remlapmot.r-universe.dev', 'https://cloud.r-project.org'))

Owner

Name: Tom Palmer
Login: remlapmot
Kind: user

Website: https://remlapmot.github.io/
Repositories: 66
Profile: https://github.com/remlapmot

Averaging statistician ...

Citation (CITATION.cff)

cff-version: 1.2.0
message: "Please cite this software using the metadata below."
authors:
- family-names: "Palmer"
  given-names: "Tom"
  orcid: "https://orcid.org/0000-0003-4655-4511"
- family-names: "Spiller"
  given-names: "Wes"
  orcid: "https://orcid.org/0000-0002-8169-5531"
- family-names: "Sanderson"
  given-names: "Eleanor"
  orcid: "https://orcid.org/0000-0001-5188-5775"
title: "OneSampleMR - R package for one-sample Mendelian randomization and instrumental variable analyses"
type: software
version: 0.1.0
date-released: 2021-10-25
url: "https://CRAN.R-project.org/package=OneSampleMR"
repository-code: "https://github.com/remlapmot/OneSampleMR"
license: GPL-3.0

GitHub Events

Total

Create event: 4
Release event: 1
Issues event: 2
Watch event: 4
Issue comment event: 2
Push event: 34
Pull request event: 2
Fork event: 1

Last Year

Create event: 4
Release event: 1
Issues event: 2
Watch event: 4
Issue comment event: 2
Push event: 34
Pull request event: 2
Fork event: 1

Committers

Last synced: 9 months ago

All Time

Total Commits: 740
Total Committers: 2
Avg Commits per committer: 370.0
Development Distribution Score (DDS): 0.001

Past Year

Commits: 65
Committers: 2
Avg Commits per committer: 32.5
Development Distribution Score (DDS): 0.015

Top Committers

Name	Email	Commits
Tom Palmer	r**t@h**m	739
olivroy	o**1@h**m	1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 5
Total pull requests: 9
Average time to close issues: 3 days
Average time to close pull requests: 43 minutes
Total issue authors: 5
Total pull request authors: 2
Average comments per issue: 1.2
Average comments per pull request: 0.33
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 1
Average time to close issues: 3 days
Average time to close pull requests: 38 minutes
Issue authors: 3
Pull request authors: 1
Average comments per issue: 1.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

oghzzang (1)
remlapmot (1)
cherrypiecoco (1)
jielab (1)
isabelamorita (1)

Pull Request Authors

remlapmot (9)
olivroy (2)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- cran 615 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 8
Total maintainers: 1

cran.r-project.org: OneSampleMR

One Sample Mendelian Randomization and Instrumental Variable Analyses

Homepage: https://github.com/remlapmot/OneSampleMR
Documentation: http://cran.r-project.org/web/packages/OneSampleMR/OneSampleMR.pdf
License: GPL (≥ 3)
Latest release: 0.1.6
published 9 months ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 615 Last month

Rankings

Forks count: 17.0%

Stargazers count: 17.4%

Dependent repos count: 23.8%

Average: 26.6%

Dependent packages count: 28.6%

Downloads: 46.2%

Maintainers (1)

remlapmot@hotmail.com

Last synced: 7 months ago

conda-forge.org: r-onesamplemr

Homepage: https://github.com/remlapmot/OneSampleMR, https://remlapmot.github.io/OneSampleMR/
License: GPL-3.0-or-later
Latest release: 0.1.2
published over 3 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Average: 42.6%

Dependent packages count: 51.2%

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

R >= 3.6.0 depends
Formula * imports
gmm * imports
ivreg * imports
lmtest * imports
msm * imports
haven * suggests
knitr * suggests
lfe * suggests
rmarkdown * suggests
testthat >= 3.0.0 suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action v4.4.1 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite