MMD

1.0.0

Minimal Multilocus Distance (MMD) for Source Attribution and Loci Selection

0packages depend

2.1Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Francisco Perez-RecheFirst published 2021-01-261 releasesCRAN page ↗

The aim of the package is two-fold: (i) To implement the MMD method for attribution of individuals to sources using the Hamming distance between multilocus genotypes. (ii) To select informative genetic markers based on information theory concepts (entropy, mutual information and redundancy). The package implements the functions introduced by Perez-Reche, F. J., Rotariu, O., Lopes, B. S., Forbes, K. J. and Strachan, N. J. C. Mining whole genome sequence data to efficiently attribute individuals to source populations. Scientific Reports 10, 12124 (2020) doi:10.1038/s41598-020-68740-6. See more details and examples in the README file.

Install

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

install.packages("MMD", 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-mmd

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

# 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-MMD

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 1.6 min · r-devel-linux-x86_64-fedora-clang

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

2.1K

CRAN downloads in the past year

Rank #21,591 · ~6/day · ~176/mo

MMD Releases R versions

Daily download trend is not available in this view yet.

16630 days

53890 days

2.1K1 year

Compare downloads with other packages →

Also on88 r2u13 autocran

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

e1071 plyr bigmemory

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Francisco Perez-Reche

Author, Maintainer

Authors (1)

Francisco Perez-Reche

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-01-26
Total releases: 1 / 5 yrs
License: GPL-3 OSI
Download size: 39 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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