R Observatory: Metrics for GEint version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GEint

1.1Package record

Misspecified Models for Gene-Environment Interaction

0packages depend

2.2Kdownloads / year

60.0%test coverage

13/13flavors OK

Overview

About

Maintained by Ryan SunCRAN page ↗

The first major functionality is to compute the bias in regression coefficients of misspecified linear gene-environment interaction models. The most generalized function for this objective is GE_bias(). However GE_bias() requires specification of many higher order moments of covariates in the model. If users are unsure about how to calculate/estimate these higher order moments, it may be easier to use GE_bias_normal_squaredmis(). This function places many more assumptions on the covariates (most notably that they are all jointly generated from a multivariate normal distribution) and is thus able to automatically calculate many of the higher order moments automatically, necessitating only that the user specify some covariances. There are also functions to solve for the bias through simulation and non-linear equation solvers; these can be used to check your work. Second major functionality is to implement the Bootstrap Inference with Correct Sandwich (BICS) testing procedure, which we have found to provide better finite-sample performance than other inference procedures for testing GxE interaction. More details on these functions are available in Sun, Carroll, Christiani, and Lin (2018) doi:10.1111/biom.12813.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("GEint", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-geint

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-GEint

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7 (2 internal)
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

GEint Tutorial HTML

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #19,961 · ~6/day · ~182/mo

Releases R versions

Daily download trend is not available in this view yet.

29530 days

65890 days

2.2K1 year

Compare downloads with other packages →

Also on82 r2u

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing GEint adds 33 packages (20 with compiled code, 21 MB of source tarballs). Heaviest: stringi 11 MB, mvtnorm 1.0 MB, vctrs 1.0 MB.

Depends (0)

none

Imports (8)

mvtnorm bindata nleqslv pracma speedglm rje geepackstats

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Ryan Sun

Author, Maintainer since 0.1.1 (2016)

Richard Barfield

Contributor · added in 0.1.4

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-10-01
1.1Latest
record
2025-10-01 · current release · diff ↗ ·
removed 9 exports
GE_BICS_old, GE_bias_normal_squaredmis_old, GE_bias_old, GE_enumerate_inputs, GE_enumerate_inputs_old, GE_nleqslv_old, GE_scoreeq_sim_old, GE_test_moment_calcs_old, GE_translate_inputs_old
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2023-03-31
requires archived package 'speedglm'
unarchivedReturned to CRAN
2022-05-18
1.0
record
2022-05-18 · diff ↗
archivedRemoved from CRAN
2022-05-09
check problems were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.5
record
2019-01-15 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 5 earlier eventsHide 5 earlier events

0.1.4
record
2017-08-09 · diff ↗ ·
added 8 exports
GE_BICS_old, GE_bias_normal_squaredmis_old, GE_bias_old, GE_enumerate_inputs_old, GE_nleqslv_old, GE_scoreeq_sim_old, GE_test_moment_calcs_old, GE_translate_inputs_old
R
R 3.4.0 released · 2017-04-21
0.1.2
record
2017-01-06 · diff ↗
0.1.1
record
2016-10-01
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-10-01
Total releases: 6 / 10 yrs
License: GPL-3 OSI
Download size: 60 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GEint")

Format

Sun, R., & Barfield, R. (2025). GEint: Misspecified Models for Gene-Environment Interaction (Version 1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.GEint

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for GEint version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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