R Observatory: Metrics for PONG2 version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PONG2

1.0.1

KIR Genotype Imputation and Model Training from SNP Array Data

0packages depend

536downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Suraju A. SadeeqFirst published 2026-06-241 releasesCRAN page ↗GitHub ↗

A scalable and accurate tool for Killer-cell Immunoglobulin-like Receptor (KIR) genotype imputation directly from SNP array data using supervised machine learning models trained across five continental ancestry groups. Uses attribute bagging and an ensemble classifier method with haplotype inference for SNPs and KIR types. Models are built from global populations in the 1000 Genomes Project and validated across diverse biobank cohorts. Methods are based on Zheng et al. (2014) doi:10.1016/j.ajhg.2013.12.015 and Sadeeq et al. (2026) https://github.com/NormanLabUCD/PONG2.

Install

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

install.packages("PONG2", 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("NormanLabUCD/PONG2")

Development version from NormanLabUCD/PONG2. 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-pong2

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-PONG2

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-PONG2

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

Health

CRAN checks

13OK

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

75%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-25
8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,391 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

536

CRAN downloads in the past year

Rank #20,613 · ~1/day · ~45/mo

Releases R versions

Daily download trend is not available in this view yet.

16230 days

53690 days

5361 year

Compare downloads with other packages →

Also on33 r2u

Repository

GitHub ↗ normanlabucd/pong2

3Stars

1Forks

0Open issues

0Open PRs

1Releases

122Commits

2Contributors

122 commits · Last activity 2026-08-01 · 0% stars, 30d

Stars over time

2025-09-18 · 12026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/normanlabucd/pong2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (5)

parallelgraphicsstatsutilstools

LinkingTo (2)

Rcpp RcppParallel

Suggests (5)

HIBAG knitr rmarkdown pkgdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Suraju A. Sadeeq

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Contributors (1)

Xiuwen Zheng

Contributor, Copyright holder

Copyright holders (1)

Xiuwen Zheng

Contributor, Copyright holder

Package Timeline

1 release. R releases are shown for context.

1.0.1Latest
2026-06-24 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-24
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 7.9 KB / 1 file
Download size: 130 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PONG2")

Format

Sadeeq, S. A., Kichula, K. M., Leaton, L. A., Norman, P. J., & Zheng, X. (2026). PONG2: KIR Genotype Imputation and Model Training from SNP Array Data (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.PONG2

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 PONG2 version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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