allelematch

3.0.0

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

1packages depend

5.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Todd CrossFirst published 2011-10-0812 releasesCRAN 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.

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).

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

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

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 73%

Downloads

5.2K

CRAN downloads in the past year

Rank #7,733 · ~14/day · ~436/mo

Releases R versions

Daily download trend is not available in this view yet.

60230 days

1.3K90 days

5.2K1 year

Compare downloads with other packages →

Also on198 r2u63 autocran

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0dynamicTreeCut

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

amregtest

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Todd Cross

Maintainer · added in 2.5.1

Authors (5)

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

Listed in earlier versions (1)

Katie Zarn

no longer listed · 2.5.1

Package Timeline

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

3.0.0Latest
2026-07-24 · current release · diff ↗
2.6.0
2026-07-05 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.5.5
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
2024-03-28 · diff ↗
2.5.3
2023-08-24 · diff ↗
2.5.2
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
2.5.1
2019-04-15 · diff ↗
unarchivedReturned to CRAN
2019-04-15

Show 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
2014-09-19 · diff ↗
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
2.03
2013-01-14 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.02
2012-02-21 · diff ↗
2.01
2012-01-11 · diff ↗
R
R 2.14.0 released · 2011-10-31
2.0
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: 57 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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