R Observatory: Metrics for MicrobiomeSurv version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MicrobiomeSurv

0.1.0

Biomarker Validation for Microbiome-Based Survival Classification and Prediction

0packages depend

1.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Thi Huyen NguyenFirst published 2023-10-121 releasesCRAN page ↗GitHub ↗

An approach to identify microbiome biomarker for time to event data by discovering microbiome for predicting survival and classifying subjects into risk groups. Classifiers are constructed as a linear combination of important microbiome and treatment effects if necessary. Several methods were implemented to estimate the microbiome risk score such as the LASSO method by Robert Tibshirani (1998) doi:10.1002/(SICI)1097-0258(19970228)16:4%3C385::AID-SIM380%3E3.0.CO;2-3, Elastic net approach by Hui Zou and Trevor Hastie (2005) doi:10.1111/j.1467-9868.2005.00503.x, supervised principle component analysis of Wold Svante et al. (1987) doi:10.1016/0169-7439(87)80084-9, and supervised partial least squares analysis by Inge S. Helland https://www.jstor.org/stable/4616159. 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 microbiome 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)

install.packages("MicrobiomeSurv", 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("N-T-Huyen/MicrobiomeSurv")

Development version from N-T-Huyen/MicrobiomeSurv. 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-microbiomesurv

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

2ERROR11OK

Failing flavors

ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

15

Dependencies · direct

Check history

ERROR2026-03-10
11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

1.7K

CRAN downloads in the past year

Rank #22,579 · ~5/day · ~141/mo

Releases R versions

Daily download trend is not available in this view yet.

10930 days

47590 days

1.7K1 year

Compare downloads with other packages →

Also on102 r2u

Repository

GitHub ↗ n-t-huyen/microbiomesurv

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2023-10-04

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/n-t-huyen/microbiomesurv on 2026-08-16.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (15)

graphicsstatsggplot2survivalsurvminer glmnetmethodssuperpc lmtest gplots tidyr dplyr microbiome plsgrDevices

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Thi Huyen Nguyen

Author, Maintainer

Authors (3)

Thi Huyen Nguyen

Author, Maintainer

Olajumoke Evangelina Owokotomo

Author

Ziv Shkedy

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2023-10-12
Total releases: 1 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 231 KB / 6 files
Download size: 413 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MicrobiomeSurv")

Format

Nguyen, T. H., Owokotomo, O. E., & Shkedy, Z. (2023). MicrobiomeSurv: Biomarker Validation for Microbiome-Based Survival Classification and Prediction (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MicrobiomeSurv

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 MicrobiomeSurv version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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