R Observatory: Metrics for pedprobr version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pedprobr

1.1.1Package record

Probability Computations on Pedigrees

9packages dependsuggested by 1

9.7Kdownloads / year

72.6%test coverage

13/13flavors OK

Overview

About

Maintained by Magnus Dehli VigelandCRAN page ↗GitHub ↗Issues ↗

An implementation of the Elston-Stewart algorithm for calculating pedigree likelihoods given genetic marker data (Elston and Stewart (1971) doi:10.1159/000152448). The standard algorithm is extended to allow inbred founders. 'pedprobr' is part of the 'pedsuite', a collection of packages for pedigree analysis in R. In particular, 'pedprobr' depends on 'pedtools' for pedigree manipulations and 'pedmut' for mutation modelling. For more information, see 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).

Changes in 1.1.1

Allow theta = 0 in functions that do not support theta correction.
lumpAlleles() gains an argument observed for alleles that should not be lumped.
Fix ordering in oneMarkerDistribution() when target individuals are interleaved across pedigree components.

From NEWS.md in the release

Install

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

install.packages("pedprobr", 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("magnusdv/pedprobr")

Development version from magnusdv/pedprobr. 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-pedprobr

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-pedprobr

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-pedprobr

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: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 420 wordsVignettesNoNEWSYes · 100% structured · mentions 1.1.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 11 (1 internal)includes a package overview page
Examples that run: 100%9 run in a plain check (1 of them under a condition)
Exported functions with examples: 90%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 18%

How these are measured

Downloads

9.7K

CRAN downloads in the past year

Rank #4,298 · ~27/day · ~809/mo

Releases R versions

Daily download trend is not available in this view yet.

80530 days

2K90 days

9.7K1 year

Compare downloads with other packages →

Also on142 r2u2 autocran

How downloads are counted

Repository

magnusdv/pedprobr ↗Account: magnusdv

4Stars

0Forks

0Open issues

1Open PRs

17Releases

287Commits

1Commit identities

License file reads as GPL-2.0 · 287 commits · Last activity 2026-09-24

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 38
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-02-20 · 42026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/magnusdv/pedprobr on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing pedprobr adds 10 packages (4 with compiled code, 2.1 MB of source tarballs). Heaviest: kinship2 484 KB, knitr 479 KB, lpSolve 457 KB.

Depends (2)

R >= 4.2.0pedtools

Imports (1)

pedmut

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

9direct

2indirect

Depends 1 · Imports 8

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

forrel dvir pedbuildr simDNAmixtures KLINK paramlink2 pedsuite famnesia segregatr

Suggests, most downloaded first

mispitools

How these are counted

Code & Tests

People & History

People (1)

Magnus Dehli Vigeland

Author, Maintainer since 0.1.0 (2019)

Releases (18)

Pick two releases to compare their code metrics.

1.1.1Latest
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2026-09-11 · current release · diff ↗
1.1.0
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2026-06-22 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.1
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2025-05-07 · diff ↗
1.0.0
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2025-05-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.9.5
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2025-03-19 · diff ↗
0.9.4
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2024-05-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.9.3
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2024-04-02 · diff ↗
0.9.2
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2024-02-28 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.8.0
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2023-04-13 · diff ↗ ·
added 2 exports
haldane, kosambi
0.7.1
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2023-02-13 · diff ↗
0.7.0
record
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22

Show 10 earlier eventsHide 10 earlier events

0.6.1
record
2022-01-05 · diff ↗
0.6.0
record
2022-01-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.5.0
record
2021-03-27 · diff ↗
0.4.0
record
2020-11-13 · diff ↗ ·
added 4 exports
checkMerlin, likelihood2, lumpAlleles, setMutationModel
0.3
record
2020-07-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.0
record
2020-03-21 · diff ↗ ·
added 1 export
merlin
0.1.0
record
2019-11-01
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-11-01
Total releases: 18 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Download size: 71 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("pedprobr")

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

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 pedprobr version 1.1.1 [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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