R Observatory: Metrics for mikropml version 1.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mikropml

1.7.1Package record

User-Friendly R Package for Supervised Machine Learning Pipelines

0packages depend

6.6Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Kelly SovacoolCRAN page ↗GitHub ↗Website ↗Issues ↗

An interface to build machine learning models for classification and regression problems. 'mikropml' implements the ML pipeline described by Topçuoğlu et al. (2020) doi:10.1128/mBio.00434-20 with reasonable default options for data preprocessing, hyperparameter tuning, cross-validation, testing, model evaluation, and interpretation steps. See the website https://www.schlosslab.org/mikropml/ for more information, documentation, and examples.

Changes in 1.7.1

Allow training_frac equal to 1... really this time! (#360, @pschloss)
Note: the maximum xgboost version supported is 1.7 (see #362).
A container is now available in ghcr (#364, #366, @kelly-sovacool).
see <https://github.com/SchlossLab/mikropml/pkgs/container/mikropml>.

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("SchlossLab/mikropml")

Development version from SchlossLab/mikropml. Installs pak first if it is not already available.

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-mikropml

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-mikropml

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-mikropml

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

2ERROR11OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package required but not available: ‘TreeSummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 14.2 min · r-oldrel-windows-x86_64

Status changes

ERROR11 OK, 2 ERRORNow
ERROR8 OK, 3 NOTE, 3 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7.1

READMEYes · 587 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.7.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JOSS paper

Help pages: 103 (58 internal)includes a package overview page
Examples that run: 26%20 run in a plain check · 56 never run
Exported functions with examples: 94%
Documented parameters: 100%
Return-value docs: 94%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #4,519 · ~18/day · ~550/mo

Releases R versions

Daily download trend is not available in this view yet.

65730 days

1.8K90 days

6.6K1 year

Compare downloads with other packages →

Also on165 r2u12 autocran2.3K conda_forge

How downloads are counted

Repository

schlosslab/mikropml ↗Organization: SchlossLab

65Stars

22Forks

11Open issues

2Open PRs

15Releases

2,573Commits

23Commit identities

machine-learningr-packagerstats

2,573 commits · Last activity 2026-08-29 · 0% stars, 30d · Default branch at 1.7.1.9000, ahead of CRAN 1.7.1 (checked 2026-10-11) · Discussions: 12 posts

Responsiveness

How these are sampled

PRs merged (all time): 98%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-07-30 · 592026-08-10 · 65

How these are measured

PracticesBeta

18 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/schlosslab/mikropml on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (5)

Code of conductContributing guideIssue templatesPR templateSupport guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-29 · The repository has a site deploy workflow

pkgdown site last built 2026-08-28

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Research and citation (2)

CITATION.cffcodemeta.json

Automation and maintenance (1)

pre-commit

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

33 external dependencies (excludes base and recommended)

Installing mikropml adds 75 packages (43 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 4 more not on CRAN are not measured.

Depends (1)

R >= 4.1.0

Imports (18)

caret dplyr e1071 glmnet kernlabmethodsMLmetrics randomForest rlangrpartS4Vectors SingleCellExperimentstatsSummarizedExperiment tidyselect TreeSummarizedExperimentutilsxgboost

LinkingTo (0)

none

Suggests (19)

assertthat doFuture forcats foreach furrr future future.apply ggplot2 knitr progress progressr purrr rmarkdown roxygen2 rsample styler testthat tidyr usethis

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 (10)

Kelly Sovacool

Author, Maintainer since 0.0.1 (2020)

Author

Author

Author

Author

Author

Contributor · added in 1.0.0

Tuomas Borman

Contributor · added in 1.7.0

Nick Lesniak

Contributor

Sarah Lucas

Contributor · added in 1.1.0

Releases (16)

Pick two releases to compare their code metrics.

1.7.1Latest
record
2026-08-28 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.7.0
record
2025-10-29 · diff ↗
1.6.2
record
2025-08-22 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.6.1
record
2023-08-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6.0
record
2023-04-15 · diff ↗ ·
added 3 exports
bootstrap_performance, calc_balanced_precision, calc_mean_perf
1.5.0
record
2023-01-16 · diff ↗ ·
added 6 exports
calc_baseline_precision, calc_mean_prc, calc_mean_roc, calc_model_sensspec, plot_mean_prc, plot_mean_roc
1.4.0
record
2022-10-16 · diff ↗
1.3.0
record
2022-05-20 · diff ↗ ·
added 2 exports
compare_models, permute_p_value
R
R 4.2.0 released · 2022-04-22
1.2.2
record
2022-02-03 · diff ↗
1.2.1
record
2022-01-30 · diff ↗
1.2.0
record
2021-11-11 · diff ↗

Show 7 earlier eventsHide 7 earlier events

1.1.1
record
2021-09-14 · diff ↗ ·
removed 1 export
get_corr_feats

added 1 export
group_correlated_features
1.1.0
record
2021-08-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.0
record
2021-05-14 · diff ↗ ·
added 2 exports
remove_singleton_columns, replace_spaces
0.0.2
record
2020-12-03 · diff ↗
0.0.1
record
2020-11-23
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-23
Total releases: 16 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.2 MB / 14 files
Download size: 2.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("mikropml")

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

It points to 10.21105/joss.03073.

The repository also keeps a CITATION.cff.

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 mikropml version 1.7.1 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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