R Observatory: Metrics for Coxmos version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Coxmos

1.1.5Package record

Cox MultiBlock Survival

0packages depend

3.7Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Pedro SalgueroCRAN page ↗GitHub ↗Issues ↗

This software package provides Cox survival analysis for high-dimensional and multiblock datasets. It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis, including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression, Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies, and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources for interpreting results. While references are available within the corresponding functions, key literature is mentioned below. Terry M Therneau (2024) https://CRAN.R-project.org/package=survival, Noah Simon et al. (2011) doi:10.18637/jss.v039.i05, Philippe Bastien et al. (2005) doi:10.1016/j.csda.2004.02.005, Philippe Bastien (2008) doi:10.1016/j.chemolab.2007.09.009, Philippe Bastien et al. (2014) doi:10.1093/bioinformatics/btu660, Kassu Mehari Beyene and Anouar El Ghouch (2020) doi:10.1002/sim.8671, Florian Rohart et al. (2017) doi:10.1371/journal.pcbi.1005752.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("Coxmos", 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("BiostatOmics/Coxmos")

Development version from BiostatOmics/Coxmos. 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-coxmos

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

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 package in Suggests/Enhances imported in NAMESPACE:
  ‘grDevices’

r-devel-windows-x86_64

Base package in Suggests/Enhances imported in NAMESPACE:
  'grDevices'

CRAN check page ↗

Slowest check: 14.8 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-09-12
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08

Show 3 earlier changesHide 3 earlier changes

OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.5

READMEYes · 352 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Description cites a JSS article

Help pages: 107 (12 internal)
Examples that run: 93%76 run in a plain check · 6 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 23% with a bibliography file

Vignettes (2)

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #5,244 · ~10/day · ~308/mo

Releases R versions

Daily download trend is not available in this view yet.

70230 days

1.6K90 days

3.7K1 year

Compare downloads with other packages →

Also on445 r2u

How downloads are counted

Repository

biostatomics/coxmos ↗Organization: BiostatOmics

2Stars

0Forks

1Open issues

0Open PRs

4Releases

280Commits

1Commit identities

License file reads as GPL-3.0 · DESCRIPTION declares CC BY 4.0 · 280 commits · Last activity 2026-02-24 · 0% stars, 30d · Default branch at 1.2.0, ahead of CRAN 1.1.5 (checked 2026-10-22)

Responsiveness

not measured

Stars over time

2025-02-19 · 12026-07-07 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/biostatomics/coxmos on 2026-10-22.

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Installing Coxmos adds 126 packages (68 with compiled code, 98 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 4.1.0

Imports (23)

caret cowplot furrr future ggrepel ggplot2 ggpubr glmnetMASSmixOmicsmethodspatchwork progress purrr Rdpack scattermorestatssurvcompsurvivalsurvminer svglite tidyrutils

LinkingTo (0)

none

Suggests (9)

ggforcegrDevicesknitr nsROC RColorConesa risksetROC rmarkdown smoothROCtime survivalROC

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 (6)

Pedro Salguero

Author, Maintainer, Reviewer · added in 1.1.5

Contributor

Contributor

Contributor

Contributor

Sonia Tarazona Campos

Thesis advisor

Maintainer since 1.0.0 (2024)

Listed in earlier versions (2)

Ana Conesa Cegarra

no longer listed · 1.0.0 to 1.1.3

Pedro Salguero García

no longer listed · 1.0.0 to 1.1.3

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.5Latest
record
2025-09-22 · current release · diff ↗ ·
added 1 export
transformIllegalChars
1.1.3
record
2025-06-02 · diff ↗ ·
removed 1 export
plot_PLS_Coxmos

added 6 exports
coxmos, cv.coxmos, cv.mb.coxmos, getTrainTest, mb.coxmos, plot_sPLS_Coxmos
R
R 4.5.0 released · 2025-04-11
1.1.2
record
2025-03-05 · diff ↗ ·
removed 4 exports
plot_LP.multipleObservations, plot_LP.multipleObservations.list, plot_pseudobeta_newObservation, plot_pseudobeta_newObservation.list

added 4 exports
plot_multipleObservations.LP, plot_multipleObservations.LP.list, plot_observation.pseudobeta, plot_observation.pseudobeta.list
1.1.1
record
2025-02-06 · diff ↗
1.1.0
record
2025-01-18 · diff ↗ ·
removed 6 exports
cv.splsdacox_dynamic, cv.splsdrcox_dynamic, save_ggplot.svg, save_ggplot_lst.svg, splsdacox_dynamic, splsdrcox_dynamic

added 16 exports
cv.isb.splsdacox, cv.isb.splsdrcox_penalty, cv.sb.splsdacox, cv.sb.splsdrcox_penalty, cv.splsdacox, cv.splsdrcox_penalty, eval_Coxmos_model_per_variable.list, getDesign.MB, isb.splsdacox, isb.splsdrcox, isb.splsdrcox_penalty, isb.splsicox, sb.splsdacox, sb.splsdrcox_penalty, splsdacox, splsdrcox_penalty
R
R 4.4.0 released · 2024-04-24
1.0.2
record
2024-03-25 · diff ↗
1.0.1
record
2024-03-22 · diff ↗
1.0.0
record
2024-03-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-03-12
Total releases: 8 / 2 yrs
License: CC BY 4.0
Minimum R: ≥ 4.1.0
Bundled data: 906 KB / 4 files
Download size: 2.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Coxmos")

Format

Salguero, P., Araújo, A., Mehari Beyene, K., Meira Machado, L., Sestelo, M., & Tarazona Campos, S. (2025). Coxmos: Cox MultiBlock Survival (Version 1.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.Coxmos

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 Coxmos version 1.1.5 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →