R Observatory: Metrics for MBMethPred version 0.1.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MBMethPred

0.1.4.4Package record

Medulloblastoma Subgroups Prediction

0packages depend

3.1Kdownloads / year

63.4%test coverage

8/13flavors OK

Overview

About

Maintained by Edris Sharif RahmaniCRAN page ↗GitHub ↗Issues ↗

Utilizing a combination of machine learning models (Random Forest, Naive Bayes, K-Nearest Neighbor, Support Vector Machines, Extreme Gradient Boosting, and Linear Discriminant Analysis) and a deep Artificial Neural Network model, 'MBMethPred' can predict medulloblastoma subgroups, including wingless (WNT), sonic hedgehog (SHH), Group 3, and Group 4 from DNA methylation beta values. See Sharif Rahmani E, Lawarde A, Lingasamy P, Moreno SV, Salumets A and Modhukur V (2023), MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches. Front. Genet. 14:1233657. <doi: 10.3389/fgene.2023.1233657> for more details.

Install

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

install.packages("MBMethPred", 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("sharifrahmanie/MBMethPred")

Development version from sharifrahmanie/MBMethPred. 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-mbmethpred

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-MBMethPred

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-MBMethPred

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

5NOTE8OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Base packages in Suggests/Enhances imported in NAMESPACE:
  ‘stats’ ‘utils’

r-devel-windows-x86_64

Base packages in Suggests/Enhances imported in NAMESPACE:
  'stats' 'utils'

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘KNearestNeighborModel.Rd’ ‘LinearDiscriminantAnalysisModel.Rd’
  ‘NaiveBayesModel.Rd’ ‘NeuralNetworkModel.Rd’ ‘RandomForestModel.Rd’
  ‘SupportVectorMachineModel.Rd’ ‘XGBoostModel.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 5.4 min · r-oldrel-macos-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.4.4

READMEYes · 1,225 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 19
Examples that run: 79%15 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 3 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 16%

Vignettes (1)

MBMethPred introduction HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #13,453 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

37930 days

85190 days

3.1K1 year

Compare downloads with other packages →

Also on136 r2u1 autocran

How downloads are counted

Repository

sharifrahmanie/mbmethpred ↗Account: sharifrahmanie

0Stars

0Forks

0Open issues

0Open PRs

1Releases

38Commits

2Commit identities

38 commits · Last activity 2025-12-04

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: not measured

How these are measured

PracticesBeta

Checks run against github.com/sharifrahmanie/mbmethpred on 2026-10-18.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing MBMethPred adds 119 packages (61 with compiled code, 81 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.5.0

Imports (20)

stringr ggplot2parallelcaTools caret kerasMASSRtsne SNFtoolclassdplyr e1071 pROC randomForest readr reshape2 reticulate rgl tensorflow xgboost

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown testthatutilsstatsscales

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 (3)

Edris Sharif Rahmani

Author, Contributor, Maintainer since 0.1.0 (2022)

Vijayachitra Modhukur

Author, Contributor

Ankita Sunil Lawarde

Author, Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.4.4Latest
record
2025-12-04 · current release · diff ↗
0.1.4.3
record
2025-06-17 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.4.2
record
2023-09-18 · diff ↗
0.1.4
record
2023-07-11 · diff ↗
0.1.2
record
2023-07-03 · diff ↗
0.1.1
record
2023-07-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.0
record
2022-12-13
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-13
Total releases: 7 / 4 yrs
License: GPL
Minimum R: ≥ 3.5.0
Bundled data: 2.9 MB / 4 files
Download size: 3.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MBMethPred")

Format

Sharif Rahmani, E., Modhukur, V., & Sunil Lawarde, A. (2025). MBMethPred: Medulloblastoma Subgroups Prediction (Version 0.1.4.4) [Computer software]. https://doi.org/10.32614/CRAN.package.MBMethPred

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 MBMethPred version 0.1.4.4 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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