R Observatory: Metrics for twoPhaseGAS version 1.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

twoPhaseGAS

1.2.5Package record

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

0packages depend

1.4Kdownloads / year

30.9%test coverage

13/13flavors OK

Overview

About

Maintained by Osvaldo Espin-GarciaCRAN page ↗GitHub ↗Issues ↗

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. 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-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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-05-28

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.5

READMEYes · 106 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 1.2.5Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11
Examples that run: 71%5 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction to twoPhaseGAS HTML

How these are measured

Downloads

1.4K

CRAN downloads in the past year

Rank #16,220 · ~4/day · ~120/mo

Releases R versions

Daily download trend is not available in this view yet.

28630 days

76990 days

1.4K1 year

Compare downloads with other packages →

Also on22 r2u

How downloads are counted

Repository

egosv/twophasegas ↗Account: egosv

0Stars

1Forks

0Open issues

0Open PRs

0Releases

2Commits

1Commit identities

2 commits · Last activity 2022-11-06 · Default branch at 1.08, ahead of CRAN 1.2.5 (checked 2026-10-18)

Responsiveness

not measured

Forks over time

2026-06-28 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/egosv/twophasegas on 2026-10-18.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing twoPhaseGAS adds 10 packages (5 with compiled code, 24 MB of source tarballs). Heaviest: BH 14 MB, data.table 5.7 MB, nloptr 2.1 MB.

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.

How these are counted

Code & Tests

People & History

People (4)

Osvaldo Espin-Garcia

Author, Maintainer since 1.2.5 (2026)

Apostolos Dimitromanolakis

Author

Shelley B Bull

Thesis advisor

Radu V Craiu

Thesis advisor

Releases (1)

1.2.5Latest
record
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: 59 KB

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 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 twoPhaseGAS version 1.2.5 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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