updog

2.1.7

Flexible Genotyping for Polyploids

6packages depend

8.6Kdownloads / year

60.1%test coverage

9/13checks pass

Overview

About

Maintained by David GerardFirst published 2018-07-1014 releasesCRAN page ↗GitHub ↗

Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) doi:10.1534/genetics.118.301468 and Gerard and Ferrao (2020) doi:10.1093/bioinformatics/btz852 for details on the implemented methods.

Install

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

install.packages("updog", 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("dcgerard/updog")

Development version from dcgerard/updog. 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-updog

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-updog

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-updog

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

Health

CRAN checks

4NOTE9OK

Failing flavors

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

Slowest check: 6.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.21

60.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-16
10 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-11
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
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

Show 1 earlier snapshots

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

Documentation

READMEYes · 518 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 90%
Documented parameters: 97%
Return-value docs: 91%
References docs: 61%

Downloads

8.6K

CRAN downloads in the past year

Rank #4,398 · ~24/day · ~719/mo

Releases R versions

Daily download trend is not available in this view yet.

50530 days

2K90 days

8.6K1 year

Compare downloads with other packages →

Also on465 r2u30 autocran

Repository

GitHub ↗ dcgerard/updog

33Stars

10Forks

10Open issues

0Open PRs

0Releases

318Commits

2Contributors

License GPL-3.0 · 318 commits · Last activity 2026-03-17 · +3.1% stars, 30d

Stars over time

2025-04-03 · 282026-07-07 · 33

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/dcgerard/updog on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

revdep/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (12)

Rcpp RcppArmadillo assertthat ggplot2 reshape2 foreach future doFuture doRNGmethodsiterators parallelly

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (8)

covr testthat knitr rmarkdown VariantAnnotation GenomicRanges S4Vectors IRanges

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

1indirect

hwep segtest Qploidy ldsep mappoly polymapR

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

David Gerard

Author, Maintainer

Authors (1)

David Gerard

Author, Maintainer

Package Timeline

14 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.1.7Latest
2026-03-17 · current release · diff ↗
2.1.6
2025-09-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.1.5
2023-11-29 · diff ↗
2.1.4
2023-11-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.3
2022-10-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.2
2022-01-24 · diff ↗
2.1.1
2021-10-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.2
2020-07-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.0
2020-01-28 · diff ↗

Show 7 earlier events

1.1.3
2019-11-21 · diff ↗
1.1.1
2019-09-10 · diff ↗
1.1.0
2019-07-31 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.1
2018-07-27 · diff ↗
1.0.0
2018-07-10
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-10
Total releases: 14 / 8 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Bundled data: 6.1 KB / 2 files
Download size: 481 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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