R Observatory: Metrics for MetabolicSurv version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MetabolicSurv

1.1.2Package record

A Biomarker Validation Approach for Classification and Predicting Survival Using Metabolomics Signature

0packages depend

2.6Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Olajumoke Evangelina OwokotomoCRAN page ↗GitHub ↗Issues ↗

An approach to identifies metabolic biomarker signature for metabolic data by discovering predictive metabolite for predicting survival and classifying patients into risk groups. Classifiers are constructed as a linear combination of predictive/important metabolites, prognostic factors and treatment effects if necessary. Several methods were implemented to reduce the metabolomics matrix such as the principle component analysis of Wold Svante et al. (1987) doi:10.1016/0169-7439(87)80084-9 , the LASSO method by Robert Tibshirani (1998) doi:10.1002/(SICI)1097-0258(19970228)16:4%3C385::AID-SIM380%3E3.0.CO;2-3, the elastic net approach by Hui Zou and Trevor Hastie (2005) doi:10.1111/j.1467-9868.2005.00503.x. Sensitivity analysis on the quantile used for the classification can also be accessed to check the deviation of the classification group based on the quantile specified. Large scale cross validation can be performed in order to investigate the mostly selected predictive metabolites and for internal validation. During the evaluation process, validation is accessed using the hazard ratios (HR) distribution of the test set and inference is mainly based on resampling and permutations technique.

Install

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

install.packages("MetabolicSurv", 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("OlajumokeEvangelina/MetabolicSurv")

Development version from OlajumokeEvangelina/MetabolicSurv. 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-metabolicsurv

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-MetabolicSurv

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-MetabolicSurv

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

13NOTE

Check messages

NOTERd filesr-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-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) CVLasoelacox.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:74-76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:82-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CVLasoelacox.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly

CRAN check page ↗

Slowest check: 4.0 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNo

Help pages: 57includes a package overview page
Examples that run: 44%11 run in a plain check · 14 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 9% with a bibliography file

Vignettes (1)

MetabolicSurv: A Biomarker Validation approach for Classification and Predicting Survival Using Metabolomic Signature HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #14,690 · ~7/day · ~218/mo

Releases R versions

Daily download trend is not available in this view yet.

35830 days

80290 days

2.6K1 year

Compare downloads with other packages →

Also on88 r2u5 autocran40 c2d4u

How downloads are counted

Repository

olajumokeevangelina/metabolicsurv ↗Account: OlajumokeEvangelina

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2019-08-06 · The default branch showed an older version (1.1.0) than CRAN on 2026-10-11

Responsiveness

not measured

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/olajumokeevangelina/metabolicsurv on 2026-10-11.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

GitHub Pages site last deployed 2019-08-06

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing MetabolicSurv adds 120 packages (61 with compiled code, 115 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (13)

superpc glmnet matrixStats survminersurvivalrms tidyr pls Rdpackmethodsstatsggplot2 dplyr

LinkingTo (0)

none

Suggests (2)

knitr 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)

Olajumoke Evangelina Owokotomo

Author, Maintainer since 1.0.0 (2019)

Ziv Shkedy

Contributor

Releases (4)

Pick two releases to compare their code metrics.

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
unarchivedReturned to CRAN
2021-06-11
1.1.2Latest
record
2021-06-11 · current release · diff ↗ ·
removed 2 exports
CVSim, QuantileAnalysis

added 2 exports
CVSimet, ms
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-08-26
requires archived package 'superpc'
1.1.1
record
2020-08-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
record
2019-08-05 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.0
record
2019-01-31
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-01-31
Total releases: 4 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.2 KB / 1 file
Download size: 201 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MetabolicSurv")

Format

Owokotomo, O. E., & Shkedy, Z. (2021). MetabolicSurv: A Biomarker Validation Approach for Classification and Predicting Survival Using Metabolomics Signature (Version 1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.MetabolicSurv

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 MetabolicSurv version 1.1.2 [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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