R Observatory: Metrics for MasterBayes version 2.59

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MasterBayes

2.59Package record

Maximum Likelihood and Markov Chain Monte Carlo (MCMC) Methods for Pedigree Reconstruction and Analysis

0packages depend

4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jarrod HadfieldCRAN page ↗

The primary aim of 'MasterBayes' is to use Markov chain Monte Carlo (MCMC) techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data (Hadfield et al. (2006) doi:10.1111/j.1365-294X.2006.03050.x). Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled 'C++' for efficiency.

Install

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

install.packages("MasterBayes", 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-masterbayes

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-MasterBayes

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-MasterBayes

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: 5.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-03-20

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.59

READMENoVignettesYes · 1 · staticNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 33includes a package overview page
Examples that run: 81%22 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 90%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 58%

Vignettes (1)

MasterBayes Tutorial PDF

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #6,022 · ~11/day · ~332/mo

Releases R versions

Daily download trend is not available in this view yet.

50230 days

1.4K90 days

4K1 year

Compare downloads with other packages →

Also on341 r2u191 autocran136 c2d4u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing MasterBayes adds 13 packages (5 with compiled code, 3.2 MB of source tarballs). Heaviest: mvtnorm 1.0 MB, kinship2 484 KB, knitr 479 KB.

Depends (4)

coda genetics gtools kinship2

Imports (2)

methodsstats

LinkingTo (0)

none

Suggests (0)

none

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 (4)

Jarrod Hadfield

Author, Maintainer since 1.0 (2006)

Andrew D. Martin

Contributor, Copyright holder · added in 2.59

Original author of modified C++ Scythe code

Daniel Pemstein

Contributor, Copyright holder · added in 2.59

Original author of modified C++ Scythe code

Kevin M. Quinn

Contributor, Copyright holder · added in 2.59

Original author of modified C++ Scythe code

Releases (29)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-03-19
2.59Latest
record
2026-03-19 · 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
archivedRemoved from CRAN
2023-02-25
issues were not corrected in time
unarchivedReturned to CRAN
2022-06-22
2.58
record
2022-06-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2022-04-16
check problems were not corrected despite reminders
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-06-25
2.57
record
2020-06-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2019-12-15
check issues were not corrected despite multiple reminders

Show 46 earlier eventsHide 46 earlier events

R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
2.55
record
2017-07-29 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.54
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2016-10-26 · diff ↗
2.53.1
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2016-09-07 · diff ↗
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
2.52
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2014-12-04 · diff ↗
R
R 3.1.0 released · 2014-04-10
2.51
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2014-03-20 · diff ↗
2.50.2
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2013-11-15 · diff ↗
2.50.1
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2013-05-21 · diff ↗
R
R 3.0.0 released · 2013-04-03
2.50
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2012-07-15 · diff ↗
2.49
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2012-07-06 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.48
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2012-03-15 · diff ↗
2.47
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2012-01-15 · diff ↗
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
2.46
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2010-12-18 · diff ↗
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
2.45
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2009-11-12 · diff ↗ ·
added 2 exports
insertPed, consensusG
R
R 2.10.0 released · 2009-10-26
2.44
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2009-07-21 · diff ↗
R
R 2.9.0 released · 2009-04-17
2.43
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2009-04-14 · diff ↗
2.42
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2009-03-06 · diff ↗ ·
removed 1 export
order.ped

added 1 export
orderPed
2.41
record
2008-12-02 · diff ↗
R
R 2.8.0 released · 2008-10-20
2.22
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2008-06-13 · diff ↗
R
R 2.7.0 released · 2008-04-22
2.21
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2008-04-10 · diff ↗ ·
added 1 export
autocorrP
2.4
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2008-09-04 · diff ↗
2.3
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2008-06-16 · diff ↗
2.2
record
2008-04-07 · diff ↗ ·
added 1 export
post.pairs
2.1
record
2007-11-27 · diff ↗
R
R 2.6.0 released · 2007-10-03
R
R 2.5.0 released · 2007-04-24
2.0
record
2006-12-15 · diff ↗ ·
added 3 exports
genotypeD, is.genotypeD, modeG
1.01
record
2006-10-17 · diff ↗
R
R 2.4.0 released · 2006-10-03
1.0
record
2006-10-02
R
R 2.3.0 released · 2006-04-24

Package metadata

First published: 2006-10-02
Total releases: 29 / 20 yrs
License: GPL (>= 2) OSI
Bundled data: 8.4 KB / 2 files
Download size: 2.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("MasterBayes")

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 MasterBayes version 2.59 [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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