R Observatory: Metrics for SIP version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SIP

0.1.0

Single-Iteration Permutation for Large-Scale Biobank Data

0packages depend

1.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Aubrey AnnisFirst published 2025-12-091 releasesCRAN page ↗GitHub ↗

A single, phenome-wide permutation of large-scale biobank data. When a large number of phenotypes are analyzed in parallel, a single permutation across all phenotypes followed by genetic association analyses of the permuted data enables estimation of false discovery rates (FDRs) across the phenome. These FDR estimates provide a significance criterion for interpreting genetic associations in a biobank context. For the basic permutation of unrelated samples, this package takes a sample-by-variable file with ID, genotypic covariates, phenotypic covariates, and phenotypes as input. For data with related samples, it also takes a file with sample pair-wise identity-by-descent information. The function outputs a permuted sample-by-variable file ready for genome-wide association analysis. See Annis et al. (2021) doi:10.21203/rs.3.rs-873449/v1 for details.

Install

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

install.packages("SIP", 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("acannis/SIP")

Development version from acannis/SIP. 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-sip

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-SIP

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-SIP

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

Health

CRAN checks

13OK

Slowest check: 1.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,229 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 42%
Return-value docs: 100%
References docs: 0%

Downloads

1.4K

CRAN downloads in the past year

Rank #23,212 · ~4/day · ~117/mo

Releases R versions

Daily download trend is not available in this view yet.

8030 days

43890 days

1.4K1 year

Compare downloads with other packages →

Also on71 r2u14 autocran

Repository

GitHub ↗ acannis/sip

0Stars

1Forks

0Open issues

0Open PRs

0Releases

34Commits

2Contributors

34 commits · Last activity 2026-06-26

Forks over time

2025-10-28 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/acannis/sip on 2026-08-09.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (3)

statsdata.table ggplot2

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 (1)

Maintainer (1)

Aubrey Annis

Author, Maintainer

Authors (1)

Aubrey Annis

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-09
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 1.4 MB / 3 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SIP")

Format

Annis, A. (2025). SIP: Single-Iteration Permutation for Large-Scale Biobank Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SIP

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 SIP version 0.1.0 [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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