R Observatory: Metrics for miclust version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

miclust

1.3.0Package record

Multiple Imputation in Cluster Analysis

0packages depend

3.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jose Barrera-GomezCRAN page ↗

Implementation of a framework for cluster analysis with selection of the final number of clusters and an optional variable selection procedure. The package is designed to integrate the results of multiple imputed datasets while accounting for the uncertainty that the imputations introduce in the final results. In addition, the package can also be used for a cluster analysis of the complete cases of a single dataset. The package also includes specific methods to summarize and plot the results. The methods are described in Basagana et al. (2013) doi:10.1093/aje/kws289.

Changes in 1.3.0

Minor changes:

Dependences:
The package is now completely independent of the irr package, which was previously used to internally calculate Cohen's Kappa (irr::kappa2). Now, Cohen's Kappa is calculated using a native base implementation to improve stability and maintainability. In addition, the Cohen's Kappa calculation is now faster.
Documentation:
Updated source code documentation to comply with the latest roxygen2 (v8.0.0) standards.
Improved README.Rmd plot rendering.
Integrated documentation for miclust() and its related methods print.miclust() and plot.miclust() into a single help page for a more fluid usage.
Integrated documentation for methods summary.miclust() and print.summary.miclust().
miclust:
The width of the verbose message has been reduced (now, breaks line each 20 imputations).
print.miclust:
Fix erratum in labels of the output of print.miclust.

Show all changes in 1.3.0Hide the rest of the changes in 1.3.0

plot.miclust:
New parameter metric, to select which metric is displayed. Defaults to "all", maintaining compatibility with the output from versions 1.2.8 and earlier. Other options are: "nclfreq" (percentage of times each number of clusters has been selected); "critcf" (critCF distribution for each number of clusters); "nvarfreq" (distribution of the number of selected variables), and "varsel" (percentage of appearance of the variables that remained in the final set of selected variables).
New parameters col.nclfreq, col.critcf, col.nvarfreq, and col.varsel, to customize the color used in the plots for metrics, "nclfreq", "critcf", "nvarfreq", and "varsel", respectively. Default values are consistent with results under versions 1.2.8 and earlier.
New parameter col.all. When specified, it overrides col.nclfreq, col.critcf, col.nvarfreq, and col.varsel, and applies that color across the entire panel. Default (NULL) is consistent with results under versions 1.2.8 and earlier.
summary.miclust:
Fix output errors related to within-cluster missingness of the selected variables.
Fix an internal error in summary.miclust() (originally triggered during kcca() execution inside assignprobandkappas()) that occurred when a specific imputation or the final assigned clustering result contained an empty cluster. Specifically, add a validation check in summary.miclust() to detect empty clusters across all imputations and the assigned cluster for the given k. The function now prints the affected cases and halts execution with a detailed error message.
An internal error in summary.miclust() (originally triggered during kcca() execution inside assignprobandkappas()) occurs when the final clustering for a given k and the set of selected variables results in an empty cluster within specific imputed datasets. This indicates that such a combination of k and selected variables is unable to find as many clusters as requested. A validation check has been added in summary.miclust() to detect these scenarios and halt execution with a detailed error message.
print.summary.miclust:
The Within-cluster summary section of the output has changed. To reduce the output width, the columns for missingness, mean, and standard deviation have been collapsed into a single column. The section label has been changed to Within-cluster summary [%miss.;mean;sd]. Separated columns (version <= 1.2.8 style) are still available in the summarybycluster element of the object.

From NEWS.md in the release

Install

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

install.packages("miclust", 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-miclust

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-miclust

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-miclust

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

13OK

CRAN check page ↗

Slowest check: 3.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.0

READMEYes · 317 wordsVignettesNoNEWSYes · 100% structured · mentions 1.3.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 6includes a package overview page
Examples that run: 60%3 run in a plain check · 2 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 33%

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #11,711 · ~9/day · ~264/mo

Releases R versions

Daily download trend is not available in this view yet.

39930 days

91390 days

3.2K1 year

Compare downloads with other packages →

Also on93 r2u5 autocran30 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing miclust adds 48 packages (27 with compiled code, 42 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB.

Depends (1)

R >= 4.1

Imports (7)

doBy combinat flexclustgraphicsmatrixStatsstatsutils

LinkingTo (0)

none

Suggests (3)

knitr xtable 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 (2)

Jose Barrera-Gomez

Author, Maintainer since 1.2.6 (2021)

Xavier Basagana

Author

Releases (4)

Pick two releases to compare their code metrics.

1.3.0Latest
record
2026-06-08 · current release · diff ↗
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
1.2.8
record
2022-02-07 · diff ↗
1.2.7
record
2021-09-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.6
record
2021-03-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-10
Total releases: 4 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1
Bundled data: 2.5 KB / 1 file
Download size: 166 KB

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' entry:

citation("miclust")

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

It points to 10.1093/aje/kws289.

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 miclust version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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