RADstackshelpR

0.1.0

Optimize the De Novo Stacks Pipeline via R

0packages depend

3.1Kdownloads / year

0.0%test coverage

10/13checks pass

Overview

About

Maintained by Devon DeRaadFirst published 2021-08-191 releasesCRAN page ↗

Offers a handful of useful wrapper functions which streamline the reading, analyzing, and visualizing of variant call format (vcf) files in R. This package was designed to facilitate an explicit pipeline for optimizing Stacks (Rochette et al., 2019) (doi:10.1111/mec.15253) parameters during de novo (without a reference genome) assembly and variant calling of restriction-enzyme associated DNA sequence (RADseq) data. The pipeline implemented here is based on the 2017 paper "Lost in Parameter Space" (Paris et al., 2017) (doi:10.1111/2041-210X.12775) which establishes clear recommendations for optimizing the parameters 'm', 'M', and 'n', during the process of assembling loci.

Install

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

install.packages("RADstackshelpR", 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-radstackshelpr

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-RADstackshelpR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

3NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 1.6 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.84

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 837 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

3.1K

CRAN downloads in the past year

Rank #13,826 · ~8/day · ~256/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

74690 days

3.1K1 year

Compare downloads with other packages →

Also on96 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

vcfR ggplot2 ggridges gridExtra

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Devon DeRaad

Author, Maintainer

Authors (1)

Devon DeRaad

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: 2021-08-19
Total releases: 1 / 5 yrs
License: MIT + file LICENSE OSI
Download size: 892 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →