R Observatory: Metrics for viralx version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

viralx

1.3.1Package record

Explainers for Regression Models in HIV Research

0packages depend

2.2Kdownloads / year

100.0%test coverage

13/13flavors OK

Overview

About

Maintained by Juan Pablo Acuña GonzálezCRAN page ↗GitHub ↗Issues ↗

A dedicated viral-explainer model tool designed to empower researchers in the field of HIV research, particularly in viral load and CD4 (Cluster of Differentiation 4) lymphocytes regression modeling. Drawing inspiration from the 'tidymodels' framework for rigorous model building of Max Kuhn and Hadley Wickham (2020) https://www.tidymodels.org, and the 'DALEXtra' tool for explainability by Przemyslaw Biecek (2020) doi:10.48550/arXiv.2009.13248. It aims to facilitate interpretable and reproducible research in biostatistics and computational biology for the benefit of understanding HIV dynamics.

Changes in 1.3.1

Added a NEWS.md file to track changes to the package.

From NEWS.md in the release

Install

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

install.packages("viralx", 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("juanv66x/viralx")

Development version from juanv66x/viralx. 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-viralx

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-viralx

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-viralx

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

13OK

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.1

READMEYes · 90 wordsVignettesNoNEWSYes · 67% structured · mentions 1.3.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16 (1 internal)includes a package overview page
Examples that run: 7%1 run in a plain check · 14 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #20,101 · ~6/day · ~180/mo

Releases R versions

Daily download trend is not available in this view yet.

27830 days

64690 days

2.2K1 year

Compare downloads with other packages →

Also on66 r2u4 autocran

How downloads are counted

Repository

juanv66x/viralx ↗Account: juanv66x

0Stars

0Forks

1Open issues

0Open PRs

0Releases

Last activity 2024-11-04

Responsiveness

not measured

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/juanv66x/viralx on 2026-10-11.

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing viralx adds 67 packages (27 with compiled code, 51 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (6)

DALEX DALEXtra parsnip recipesstatsworkflows

LinkingTo (0)

none

Suggests (8)

Cubist dplyr earth kknn rsample rules testthat (>= 3.0.0)vdiffr

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 (1)

Juan Pablo Acuña González

Author, Maintainer since 1.0.0 (2023)

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-07-04
1.3.1Latest
record
2025-07-04 · current release · diff ↗
archivedRemoved from CRAN
2025-05-15
requires archived package 'kknn'
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3.0
record
2024-03-29 · diff ↗ ·
added 1 export
glob_cr_vis
1.2.0
record
2024-01-21 · diff ↗ ·
added 5 exports
glob_knn_vis, viralx_knn, viralx_knn_glob, viralx_knn_shap, viralx_knn_vis
1.1.0
record
2023-09-13 · diff ↗ ·
added 2 exports
glob_nn_vis, viralx_nn_glob
1.0.0
record
2023-09-07
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-07
Total releases: 5 / 3 yrs
License: MIT + file LICENSE OSI · relicensed from GPL (>= 3) in 1.3.1
Minimum R: ≥ 4.1.0
Bundled data: 0.5 KB / 1 file
Download size: 21 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("viralx")

Format

Acuña González, J. P. (2025). viralx: Explainers for Regression Models in HIV Research (Version 1.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.viralx

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 viralx version 1.3.1 [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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