R Observatory: Metrics for SweepDiscovery version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SweepDiscovery

0.1.1Package record

Selective Sweep Discovery Tool

0packages depend

1.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Abhik SarkarCRAN page ↗

Selective sweep is a biological phenomenon in which genetic variation between neighboring beneficial mutant alleles is swept away due to the effect of genetic hitchhiking. Detection of selective sweep is not well acquainted as well as it is a laborious job. This package is a user friendly approach for detecting selective sweep in genomic regions. It uses a Random Forest based machine learning approach to predict selective sweep from VCF files as an input. Input of this function, train data and new data, can be computed using the project https://github.com/AbhikSarkar1999/SweepDiscovery in 'GitHub'. This package has been developed by using the concept of Pavlidis and Alachiotis (2017) doi:10.1186/s40709-017-0064-0.

Install

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

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

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

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-sweepdiscovery

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-SweepDiscovery

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-SweepDiscovery

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

Additional issues

donttest

CRAN check page ↗

Slowest check: 51 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-10
WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 0%1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #24,389 · ~5/day · ~156/mo

Releases R versions

Daily download trend is not available in this view yet.

17130 days

50690 days

1.9K1 year

Compare downloads with other packages →

Also on79 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing SweepDiscovery adds 1 package (1 with compiled code, 80 KB of source tarballs). Heaviest: randomForest 80 KB.

Depends (1)

R >= 3.5.0

Imports (3)

statsutilsrandomForest

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Abhik Sarkar

Author, Maintainer since 0.1.1 (2023)

Saikath Das

Author

Dwijesh Chandra Mishra

Author

Dipro Sinha

Author

Md Yeasin

Author

Releases (1)

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
0.1.1Latest
record
2023-12-14 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-14
Total releases: 1 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 1.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SweepDiscovery")

Format

Sarkar, A., Das, S., Mishra, D. C., Sinha, D., & Yeasin, M. (2023). SweepDiscovery: Selective Sweep Discovery Tool (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SweepDiscovery

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 SweepDiscovery version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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