R Observatory: Metrics for polyRAD version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

polyRAD

2.0.1Package record

Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

0packages dependsuggested by 2

6.2Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Lindsay V. ClarkCRAN page ↗GitHub ↗Declared funder: U.S. National Science Foundation

Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) doi:10.1534/g3.118.200913, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) doi:10.1186/s12859-022-04635-9. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) doi:10.1101/2020.01.11.902890.

Changes in 2.0.1

Bug fix in TestOverdispersion when the optimal value is the minimum tested.
VCF2RADdata now can make use of .csi indices on VCFs that are already bgzipped.
Bug fix in Export_MAPpoly relating to how ploidy is coded.
Bug fix in AddAlleleFreqByTaxa if only one PC is used.
Update readStacks for new file formats.
Update Bioconductor links to pass CRAN checks

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("polyRAD", 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("lvclark/polyRAD")

Development version from lvclark/polyRAD. 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-polyrad

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

Health

CRAN checks

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  polyRAD/inst/doc/isolocus_sorting.R (.Dim: 1, .Dimnames: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.

CRAN check page ↗

Slowest check: 5.3 min · r-devel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE10 OK, 3 NOTE2026-07-16
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-25

Show 1 earlier changeHide 1 earlier change

WARNING8 OK, 3 NOTE, 3 WARNING2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

README· In the repository, left out of the releaseVignettesYes · 2 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 2.0.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 49
Examples that run: 96%46 run in a plain check · 2 never run
Exported functions with examples: 98%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 29%

Vignettes (2)

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #5,440 · ~17/day · ~515/mo

Releases R versions

Daily download trend is not available in this view yet.

51330 days

1.5K90 days

6.2K1 year

Compare downloads with other packages →

Also on406 r2u

How downloads are counted

Repository

lvclark/polyrad ↗Account: lvclark

33Stars

11Forks

4Open issues

0Open PRs

16Releases

716Commits

2Commit identities

bioinformaticsrdna-sequencinggenotyping-by-sequencinggenotype-likelihoodsrad-seqrad-sequencingsnp-genotyping

716 commits · Last activity 2026-03-22 · 0% stars, 30d · Discussions: 9 posts

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 29
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-26 · 302026-07-07 · 33

How these are measured

PracticesBeta

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

Checks run against github.com/lvclark/polyrad on 2026-10-18.

Governance and community (2)

Code of conductPR template

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing polyRAD adds 3 packages (3 with compiled code, 13 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, fastmatch 18 KB. 1 more not on CRAN is not measured.

Depends (2)

R >= 3.5.0methods

Imports (4)

fastmatch pcaMethods Rcpp stringi

LinkingTo (1)

Rcpp

Suggests (18)

rrBLUP Rsamtools GenomeInfoDb Biostrings GenomicRanges VariantAnnotation SummarizedExperiment S4Vectors IRanges BiocGenerics knitr rmarkdown GenomicFeatures ggplot2 adegenet txdbmaker polymapR BSgenome

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

polymapR BIGr

How these are counted

Code & Tests

Datasets

People & History

People (2)

Lindsay V. Clark

Author, Maintainer since 0.5-0 (2018)

U.S. National Science Foundation

Funder

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.1Latest
record
2026-03-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.0.0
record
2022-11-06 · diff ↗ ·
removed 1 export
AddPriorTimesLikelihood

added 4 exports
ExamineGenotype, GetTaxaByPloidy, GetTaxaPloidy, SetTaxaPloidy
R
R 4.2.0 released · 2022-04-22
1.6
record
2022-02-15 · diff ↗
1.5
record
2021-09-03 · diff ↗ ·
added 4 exports
ExpectedHindHeMapping, Export_polymapR_probs, readDArTag, SimGenotypesMapping
R
R 4.1.0 released · 2021-05-18
1.4
record
2021-03-23 · diff ↗ ·
added 1 export
Export_adegenet_genind
1.3
record
2021-01-06 · diff ↗ ·
added 4 exports
ExpectedHindHe, Export_Structure, SimAlleleDepth, SimGenotypes
1.2
record
2020-05-12 · diff ↗ ·
added 9 exports
AddDepthSamplingPermutations, EstimateParentalGenotypes, HindHe, HindHeMapping, InbreedingFromHindHe, MergeIdenticalHaplotypes, RADdata2VCF, readProcessSamMulti, readProcessIsoloci
R
R 4.0.0 released · 2020-04-24
1.1
record
2019-06-04 · diff ↗ ·
added 5 exports
Export_GWASpoly, Export_MAPpoly, MergeTaxaDepth, RemoveUngenotypedLoci, SubsetByPloidy
R
R 3.6.0 released · 2019-04-26

Show 3 earlier eventsHide 3 earlier events

1.0
record
2018-11-20 · diff ↗ ·
added 5 exports
AddGenotypePriorProb_Even, Export_polymapR, readTASSELGBSv2, RemoveHighDepthLoci, TestOverdispersion
0.5-0
record
2018-08-02
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-02
Total releases: 10 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 173 KB / 3 files
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("polyRAD")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1534/g3.118.200913, 10.1186/s12859-022-04635-9.

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 polyRAD version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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