R Observatory: Metrics for parallelpam version 1.4.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

parallelpam

1.4.3

Parallel Partitioning-Around-Medoids (PAM) for Big Sets of Data

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Juan DomingoFirst published 2022-11-246 releasesCRAN page ↗

Application of the Partitioning-Around-Medoids (PAM) clustering algorithm described in Schubert, E. and Rousseeuw, P.J.: "Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms." Information Systems, vol. 101, p. 101804, (2021). doi:10.1016/j.is.2021.101804. It uses a binary format for storing and retrieval of matrices developed for the 'jmatrix' package but the functionality of 'jmatrix' is included here, so you do not need to install it. Also, it is used by package 'scellpam', so if you have installed it, you do not need to install this package. PAM can be applied to sets of data whose dissimilarity matrix can be very big. It has been tested with up to 100.000 points. It does this with the help of the code developed for other package, 'jmatrix', which allows the matrix not to be loaded in 'R' memory (which would force it to be of double type) but it gets from disk, which allows using float (or even smaller data types). Moreover, the dissimilarity matrix is calculated in parallel if the computer has several cores so it can open many threads. The initial part of the PAM algorithm can be done with the BUILD or LAB algorithms; the BUILD algorithm has been implemented in parallel. The optimization phase implements the FastPAM1 algorithm, also in parallel. Finally, calculation of silhouette is available and also implemented in parallel.

Install

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

install.packages("parallelpam", 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-parallelpam

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-parallelpam

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-parallelpam

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

Health

CRAN checks

13OK

Slowest check: 5.8 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-08
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 4 earlier snapshots

OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #17,188 · ~7/day · ~216/mo

Releases R versions

Daily download trend is not available in this view yet.

12930 days

62590 days

2.6K1 year

Compare downloads with other packages →

Also on384 r2u16 autocran

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

Rcpp memuse

LinkingTo (1)

Rcpp

Suggests (2)

knitrcluster

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Juan Domingo

Author, Maintainer

Authors (1)

Juan Domingo

Author, Maintainer

Contributors (1)

Guillermo Ayala

Contributor

Funders (1)

Spanish Ministry of Science and Innovation, MCIN/AEI <doi:10.13039/501100011033>

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.4.3Latest
2024-07-15 · current release · diff ↗
1.4.2
2024-07-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4
2023-10-09 · diff ↗
1.3
2023-06-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.1
2023-01-08 · diff ↗
1.0
2022-11-24
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-11-24
Total releases: 6 / 4 yrs
License: GPL (>= 2) OSI
Download size: 155 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("parallelpam")

Format

Domingo, J., Spanish Ministry of Science and Innovation, MCIN/AEI <doi:10.13039/501100011033>, & Ayala, G. (2024). parallelpam: Parallel Partitioning-Around-Medoids (PAM) for Big Sets of Data (Version 1.4.3) [Computer software]. https://doi.org/10.32614/CRAN.package.parallelpam

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 parallelpam version 1.4.3 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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