R Observatory: Metrics for MMD version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MMD

1.0.0Package record

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

0packages depend

2.2Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Francisco Perez-RecheCRAN 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)Fedora (COPR)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. 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-MMD

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-MMD

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) MMD_attr.Rd:62: Lost braces; missing escapes or markup?
    62 | \item Probability of attribution of each unknown individual to each source $p_{u,s}$
       |                                                                               ^

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (1)

Tutorial for the R MMD package HTML

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #22,124 · ~6/day · ~180/mo

Releases R versions

Daily download trend is not available in this view yet.

21430 days

59990 days

2.2K1 year

Compare downloads with other packages →

Also on65 r2u4 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing MMD adds 8 packages (6 with compiled code, 17 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, plyr 392 KB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Francisco Perez-Reche

Author, Maintainer since 1.0.0 (2021)

Releases (1)

R
R 4.6.0 released · 2026-04-24
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.0Latest
record
2021-01-26 · current release
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-26
Total releases: 1 / 5 yrs
License: GPL-3 OSI
Download size: 39 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MMD")

Format

Perez-Reche, F. (2021). MMD: Minimal Multilocus Distance (MMD) for Source Attribution and Loci Selection (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MMD

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 MMD version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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