whoa

0.0.2

Evaluation of Genotyping Error in Genotype-by-Sequencing Data

0packages depend

8.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Eric C. AndersonFirst published 2019-08-022 releasesCRAN page ↗

This is a small, lightweight package that lets users investigate the distribution of genotypes in genotype-by-sequencing (GBS) data where they expect (by and large) Hardy-Weinberg equilibrium, in order to assess rates of genotyping errors and the dependence of those rates on read depth. It implements a Markov chain Monte Carlo (MCMC) sampler using 'Rcpp' to compute a Bayesian estimate of what we call the heterozygote miscall rate for restriction-associated digest (RAD) sequencing data and other types of reduced representation GBS data. It also provides functions to generate plots of expected and observed genotype frequencies. Some background on these topics can be found in a recent paper "Recent advances in conservation and population genomics data analysis" by Hendricks et al. (2018) doi:10.1111/eva.12659, and another paper describing the MCMC approach is in preparation with Gordon Luikart and Thierry Gosselin.

Install

R (CRAN)Ubuntu (r2u)

install.packages("whoa", 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-whoa

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

Health

CRAN checks

13OK

Slowest check: 3.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 80%
References docs: 0%

Downloads

8.9K

CRAN downloads in the past year

Rank #4,621 · ~24/day · ~744/mo

Releases R versions

Daily download trend is not available in this view yet.

42230 days

2K90 days

8.9K1 year

Compare downloads with other packages →

Also on382 r2u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (8)

dplyr magrittr tibble tidyr Rcpp vcfR viridis ggplot2

LinkingTo (1)

Rcpp

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)

Eric C. Anderson

Author, Maintainer

Authors (1)

Eric C. Anderson

Author, Maintainer

Listed in earlier versions (1)

Anderson

no longer listed · 0.0.1 to 0.0.2

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.0.2Latest
2021-08-11 · current release · diff ↗
unarchivedReturned to CRAN
2021-08-11
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-07-05
requires archived package 'vcfR'
R
R 4.0.0 released · 2020-04-24
0.0.1
2019-08-02
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-02
Total releases: 2 / 7 yrs
License: CC0
Minimum R: ≥ 3.3.0
Bundled data: 172 KB / 2 files
Download size: 303 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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