R Observatory: Metrics for SOMMD version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SOMMD

0.1.2Package record

Self Organising Maps for the Analysis of Molecular Dynamics Data

1packages depend

2.1Kdownloads / year

29.3%test coverage

13/13flavors OK

Overview

About

Maintained by Stefano MottaCRAN page ↗

Processes data from Molecular Dynamics simulations using Self Organising Maps. Features include the ability to read different input formats. Trajectories can be analysed to identify groups of important frames. Output visualisation can be generated for maps and pathways. Methodological details can be found in Motta S et al (2022) doi:10.1021/acs.jctc.1c01163. I/O functions for xtc format files were implemented using the 'xdrfile' library available under open source license. The relevant information can be found in inst/COPYRIGHT.

Install

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

install.packages("SOMMD", 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-sommd

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-SOMMD

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Additional issues

rchk

CRAN check page ↗

Slowest check: 3.4 min · r-devel-windows-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 0.1.2

READMEYes · 126 wordsVignettesNoNEWSYes · 67% structured · does not mention 0.1.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 36
Examples that run: 96%25 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 96%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #20,409 · ~6/day · ~175/mo

Releases R versions

Daily download trend is not available in this view yet.

20430 days

65490 days

2.1K1 year

Compare downloads with other packages →

Also on340 r2u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing SOMMD adds 13 packages (9 with compiled code, 13 MB of source tarballs). Heaviest: igraph 4.8 MB, Rcpp 1.8 MB, bio3d 1.5 MB.

Depends (1)

R >= 3.5.0

Imports (6)

bio3d kohonen abindclustermethodsigraph

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

MDaRes

How these are counted

Code & Tests

Datasets

People & History

People (4)

Stefano Motta

Alessandro Pandini

Author, Copyright holder

Erik Lindahl

Contributor

Author of xdrfile C library

David van der Spoel

Contributor

Author of xdrfile C library

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.2Latest
record
2024-10-02 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-02
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 746 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("SOMMD")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1021/acs.jctc.1c01163.

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 SOMMD version 0.1.2 [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.

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