R Observatory: Metrics for snpAIMeR version 2.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

snpAIMeR

2.1.1

Assess the Diagnostic Power of Genomic Marker Combinations

0packages depend

2.1Kdownloads / year

7.8%test coverage

13/13checks pass

Overview

About

Maintained by Kim VertacnikFirst published 2023-12-172 releasesCRAN page ↗GitHub ↗

Population genetics package for designing diagnostic panels. Candidate markers, marker combinations, and different panel sizes are assessed for how well they can predict the source population of known samples. Requires a genotype file of candidate markers in STRUCTURE format. Methods for population cross-validation are described in Jombart (2008) doi:10.1093/bioinformatics/btn129.

Install

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

install.packages("snpAIMeR", 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("OksanaVe/snpAIMeR")

Development version from OksanaVe/snpAIMeR. 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-snpaimer

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-snpAIMeR

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-snpAIMeR

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

Health

CRAN checks

13OK

Slowest check: 1.2 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.06

7.8%

Coverage · measured lines

100%

Documentation · exports

14

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 418 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.1K

CRAN downloads in the past year

Rank #19,080 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

13030 days

57390 days

2.1K1 year

Compare downloads with other packages →

Also on98 r2u14 autocran

Repository

GitHub ↗ oksanave/snpaimer

0Stars

1Forks

0Open issues

0Open PRs

0Releases

57Commits

3Contributors

57 commits · Last activity 2024-07-09

Forks over time

2023-01-26 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

Checks run against github.com/oksanave/snpaimer on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (14)

adegenet doParallel dplyr forcats foreach ggplot2graphicsmagrittrparallelreadr tidyrutilswithr yaml

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Kim Vertacnik

Maintainer, Author

Authors (3)

Kim Vertacnik

Maintainer, Author

Julian Dupuis

Author

Oksana Vernygora

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.1.1Latest
2024-02-20 · current release · diff ↗
2.1.0
2023-12-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-17
Total releases: 2 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Download size: 7.3 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("snpAIMeR")

Format

Vertacnik, K., Dupuis, J., & Vernygora, O. (2024). snpAIMeR: Assess the Diagnostic Power of Genomic Marker Combinations (Version 2.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.snpAIMeR

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 snpAIMeR version 2.1.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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