R Observatory: Metrics for sequoia version 3.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sequoia

3.2.0Package record

Pedigree Inference from SNPs

0packages depend

8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jisca HuismanCRAN page ↗Website ↗

Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (DOI:10.1111/1755-0998.12665) for more information.

Install

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

install.packages("sequoia", 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-sequoia

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-sequoia

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-sequoia

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

CRAN check page ↗

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

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.2.0

READMENoVignettesYes · 6 · dynamicNEWSYes · 100% structured · does not mention 3.2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 54
Examples that run: 77%33 run in a plain check · 10 never run
Exported functions with examples: 88%
Documented parameters: 95%
Return-value docs: 83%
Help pages citing references: 6%

Vignettes (6)

How these are measured

Downloads

8K

CRAN downloads in the past year

Rank #5,021 · ~22/day · ~663/mo

Releases R versions

Daily download trend is not available in this view yet.

63230 days

1.7K90 days

8K1 year

Compare downloads with other packages →

Also on444 r2u4 autocran

How downloads are counted

Repository

jiscah/jiscah.github.io ↗Account: JiscaH

1Stars

0Forks

0Open issues

0Open PRs

0Releases

57Commits

1Commit identities

57 commits · Last activity 2026-01-04

Responsiveness

not measured

Stars over time

2023-11-03 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/jiscah/jiscah.github.io on 2026-10-21.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-01-04

pkgdown site last built 2026-01-04, before release 3.2.0 (2026-01-09)

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing sequoia adds 3 packages (3 with compiled code, 2.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, cli 629 KB, plyr 392 KB.

Depends (1)

R >= 3.5.0

Imports (5)

plyrstatsutilsgraphicscli

LinkingTo (0)

none

Suggests (10)

openxlsx knitr rmarkdown bookdown kinship2 R.rsp hexbin data.table vcfR adegenet

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 (1)

Jisca Huisman

Author, Maintainer since 0.7.2 (2017)

Releases (25)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.2.0Latest
record
2026-01-09 · current release · diff ↗
3.1.3
record
2025-11-18 · diff ↗ ·
added 2 exports
CountOH, PlotPropAssigned
3.0.3
record
2025-08-19 · diff ↗ ·
removed 1 export
EstEr

added 3 exports
CalcParentProbs, Err_RADseq, LLtoProb
R
R 4.5.0 released · 2025-04-11
2.11.2
record
2024-05-28 · diff ↗
2.11.1
record
2024-05-27 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.9.0
record
2024-03-01 · diff ↗
2.8.3
record
2023-12-19 · diff ↗
2.7.2
record
2023-09-06 · diff ↗ ·
added 1 export
EstEr
2.5.6
record
2023-04-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.5.3
record
2023-03-21 · diff ↗ ·
removed 1 export
sequoia_report

added 2 exports
GetAncestors, GetDescendants
unarchivedReturned to CRAN
2023-01-08
2.4.1
record
2023-01-08 · diff ↗ ·
added 2 exports
PlotSeqSum, sequoia_report

Show 24 earlier eventsHide 24 earlier events

R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2021-12-06
check problems were not corrected in time
2.3.5
record
2021-05-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.3.4
record
2021-05-15 · diff ↗
2.3.3
record
2021-05-03 · diff ↗
2.3.2
record
2021-04-29 · diff ↗ ·
removed 1 export
GetRelCat

added 9 exports
CalcBYprobs, CalcPairLL, CalcRped, GetLLRAge, GetRelM, PlotPairLL, PlotPedComp, PlotRelPairs, getGenerations
unarchivedReturned to CRAN
2020-05-18
2.0.7
record
2020-05-18 · diff ↗ ·
added 6 exports
CalcMaxMismatch, CalcOHLLR, ComparePairs, ErrToM, PedPolish, getAssignCat
archivedRemoved from CRAN
2020-04-24
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
1.3.3
record
2019-06-20 · diff ↗
1.3.1
record
2019-06-14 · diff ↗ ·
removed 2 exports
MakeAgeprior, MergeFill

added 7 exports
CheckGeno, GetMaybeRel, GetRelCat, MakeAgePrior, MkGenoErrors, PlotAgePrior, SummarySeq
R
R 3.6.0 released · 2019-04-26
1.1.1
record
2018-08-13 · diff ↗ ·
removed 1 export
Merge

added 1 export
MergeFill
R
R 3.5.0 released · 2018-04-23
1.0.2
record
2018-04-01 · diff ↗
1.0.0
record
2018-03-29 · diff ↗ ·
added 9 exports
EstConf, FindFamilies, LHConvert, MakeAgeprior, Merge, PedStripFID, SnpStats, writeColumns, writeSeq
0.9.3
record
2017-07-25 · diff ↗
0.9.2
record
2017-07-18 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.8.1
record
2017-03-10 · diff ↗
0.7.2
record
2017-02-13
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-02-13
Total releases: 25 / 9 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 265 KB / 13 files
Download size: 2.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("sequoia")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 sequoia version 3.2.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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