R Observatory: Metrics for twoPhaseGAS version 1.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

twoPhaseGAS

1.2.5

Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design

0packages depend

776downloads / year

30.9%test coverage

13/13checks pass

Overview

About

Maintained by Osvaldo Espin-GarciaFirst published 2026-05-271 releasesCRAN page ↗GitHub ↗

Provides functionality for designing and analysing two-phase genetic association studies. Phase 1 data usually come from genome-wide association study (GWAS) results and we assume phase 2 data will be part of a targeted genome sequencing or fine-mapping study. At design stage, the package assists in selecting a subset of individuals that will be sequenced for phase 2 via alternative approaches, including a flexible genetic algorithm (GA) for near-optimal designs. Once phase 2 data have been collected, the package implements methods to analyse phase 1 and phase 2 data together using semi-parametric regression models via the expectation-maximization (EM) algorithm. For more details see Espin-Garcia, Craiu and Bull (2018) doi:10.1002/gepi.22099 and Espin-Garcia, Craiu and Bull (2021) doi:10.1002/sim.9211.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("egosv/twoPhaseGAS")

Development version from egosv/twoPhaseGAS. Installs pak first if it is not already available.

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-twophasegas

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-twoPhaseGAS

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-twoPhaseGAS

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.10

30.9%

Coverage · measured lines

100%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-28
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 106 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

776

CRAN downloads in the past year

Rank #13,045 · ~2/day · ~65/mo

Releases R versions

Daily download trend is not available in this view yet.

12930 days

77690 days

7761 year

Compare downloads with other packages →

Also on15 r2u

Repository

GitHub ↗ egosv/twophasegas

0Stars

1Forks

0Open issues

0Open PRs

0Releases

2Commits

1Contributors

2 commits · Last activity 2022-11-06

Forks over time

2026-06-28 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/egosv/twophasegas on 2026-08-09.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

data.table dfoptim enrichwith kofnGAMASSMatrixnloptrparallelstatsutils

LinkingTo (0)

none

Suggests (4)

gplots knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Osvaldo Espin-Garcia

Author, Maintainer

Authors (2)

Osvaldo Espin-Garcia

Author, Maintainer

Apostolos Dimitromanolakis

Author

Other (2)

Shelley B Bull

Thesis advisor

Radu V Craiu

Thesis advisor

Package Timeline

1 release. R releases are shown for context.

1.2.5Latest
2026-05-27 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-27
Total releases: 1 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("twoPhaseGAS")

Format

Espin-Garcia, O., Bull, S. B., Craiu, R. V., & Dimitromanolakis, A. (2026). twoPhaseGAS: Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design (Version 1.2.5) [Computer software]. https://doi.org/10.32614/CRAN.package.twoPhaseGAS

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 twoPhaseGAS version 1.2.5 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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