R Observatory: Metrics for MIML version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MIML

0.1.0Package record

Machine Learning Imputation, Clustering and Survival Analysis for Longitudinal Proteomic Data

0packages depend

335downloads / year

51.7%test coverage

13/13flavors OK

Overview

About

Maintained by Neelesh KumarCRAN page ↗

Imputes missing biomarker measurements in a wide longitudinal serum panel with gradient-boosted decision trees, groups the completed panel by Bayesian consensus clustering, and compares the resulting patient subgroups by Kaplan-Meier, log-rank and Cox analysis. The imputation learner is described in Ke et al. (2017) https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision-tree and the clustering method in Lock and Dunson (2013) doi:10.1093/bioinformatics/btt425. Imputed values are conditional-mean predictions, so the procedure is a machine-learning single imputation; the completions carry no between-imputation variance and must not be pooled by Rubin's rules. Two panels from Gene Expression Omnibus accession 'GSE65622' are included, one for each survival endpoint.

Changes in 0.1.0

First release.

miml_rfs() runs the published workflow on RFS_data.
miml_mfs() runs it on MFS_data.
RFS_data and MFS_data: 80 patients, 288 patient-visits, 507 protein biomarkers, about 10.3 percent missing, from GEO accession GSE65622.

From NEWS.md in the release

Install

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

install.packages("MIML", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

# 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-MIML

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-MIML

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: 1.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK5 OK2026-10-01

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMENoVignettesNoNEWSYes · 67% structured · mentions 0.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5 (1 internal)includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 20%

How these are measured

Downloads

335

CRAN downloads in the past year

Rank #25,293 · ~1/day · ~28/mo

MIML Releases R versions

Daily download trend is not available in this view yet.

33530 days

33590 days

3351 year

Compare downloads with other packages →

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing MIML adds 4 packages (3 with compiled code, 8.5 MB of source tarballs). Heaviest: data.table 5.7 MB, lightgbm 1.7 MB, jsonlite 1.0 MB.

Depends (1)

R >= 4.1.0

Imports (5)

lightgbm data.tablesurvivalstatsutils

LinkingTo (0)

none

Suggests (2)

BCClong testthat

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 (4)

Neelesh Kumar

Author, Maintainer since 0.1.0 (2026)

Atanu Bhattacharjee

Author

Tanmoy Majumdar

Author

Gajendra K. Vishwakarma

Author

Listed in earlier versions (1)

Gajendra K.

no longer listed · 0.1.0

Releases (1)

0.1.0Latest
record
2026-09-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-09-30
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.6 MB / 2 files
Download size: 1.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MIML")

Format

Kumar, N., Bhattacharjee, A., Majumdar, T., & Vishwakarma, G. K. (2026). MIML: Machine Learning Imputation, Clustering and Survival Analysis for Longitudinal Proteomic Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MIML

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 MIML version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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