R Observatory: Metrics for allelematch version 3.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

allelematch

3.0.0Package record

Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present

0packages dependsuggested by 1

5.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Todd CrossCRAN page ↗

Tools for the identification of unique multilocus genotypes when both genotyping error and missing data may be present. Includes a data pre-screening utility to analyze pairwise locus overlap and protect against underlying mathematical sorting constraints. Targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, particularly in non-invasive wildlife sampling applications). Functions explicitly incorporate missing data and can tolerate allele mismatches created by genotyping error. If you use this package, please cite the original publication in Molecular Ecology Resources (Galpern et al., 2012), the details for which can be generated using citation('allelematch'). The complete user manual and analytical tutorials are included locally as an R vignette and can be accessed within an active R session using vignette('allelematch').

Install

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

install.packages("allelematch", 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-allelematch

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-allelematch

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-allelematch

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: 2.0 min · r-oldrel-macos-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 3.0.0

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

Help pages: 11includes a package overview page
Examples that run: 0%9 never run
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 73%

Vignettes (1)

The ALLELEMATCH Package for R: Supplementary Documentation with Tutorials HTML

How these are measured

Downloads

5.1K

CRAN downloads in the past year

Rank #5,964 · ~14/day · ~423/mo

Releases R versions

Daily download trend is not available in this view yet.

47130 days

1.4K90 days

5.1K1 year

Compare downloads with other packages →

Also on172 r2u23 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing allelematch adds 1 package (0 with compiled code, 23 KB of source tarballs). Heaviest: dynamicTreeCut 23 KB.

Depends (2)

R >= 3.5.0dynamicTreeCut

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

amregtest

How these are counted

Code & Tests

Datasets

People & History

People (6)

Todd Cross

Maintainer since 2.5.1 (2019) · added in 2.5.1

Paul Galpern

Author

Pete Hettinga

Author · added in 2.5.5

Micheline Manseau

Author · added in 2.5.5

Karen Smith

Author · added in 2.5.5

Paul Wilson

Author · added in 2.5.5

Previously maintained by Paul Galpern (2.0 to 2.5).

Listed in earlier versions (1)

Katie Zarn

no longer listed · 2.5.1

Releases (12)

Pick two releases to compare their code metrics.

3.0.0Latest
record
2026-07-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.6.0
record
2025-07-26 · diff ↗
2.5.5
record
2025-07-26 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.5.4
record
2024-03-28 · diff ↗
2.5.3
record
2023-08-24 · diff ↗
2.5.2
record
2023-05-19 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-04-15
2.5.1
record
2019-04-15 · diff ↗

Show 15 earlier eventsHide 15 earlier events

archivedRemoved from CRAN
2019-01-26
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
2.5
record
2014-09-19 · diff ↗
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
2.03
record
2013-01-14 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.02
record
2012-02-21 · diff ↗
2.01
record
2012-01-11 · diff ↗ ·
added 1 export
pattern:.
R
R 2.14.0 released · 2011-10-31
2.0
record
2011-10-08
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-10-08
Total releases: 12 / 15 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 22 KB / 5 files
Download size: 9.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("allelematch")

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 allelematch version 3.0.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →