R Observatory: Metrics for ViralEntropR version 0.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ViralEntropR needs HDcpDetect, which is past its CRAN deadline of Oct 12 to fix its check problems.

ViralEntropR

0.6.2Package record

A Computational Pipeline for Entropy-Informed Detection of Emerging Viral Variants

0packages depend

1.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Vadim TyuryaevCRAN page ↗GitHub ↗Website ↗Issues ↗

Implements an entropy-informed pipeline for detecting emerging variants in viral amino acid sequence data, extending prior clustering-based approaches including hemagglutinin clustering methods (Li et al., 2015) doi:10.1142/9789814667944_0018. Provides a fully vectorized FASTA preprocessing toolkit covering header parsing, two-pass date and country extraction, ambiguous-residue filtering, and integer encoding under a 25-symbol amino acid alphabet. Computes per-site Shannon entropy across user-defined cumulative, sliding, or disjoint temporal partitions and clusters per-site entropy values using Gaussian mixture models via 'mclust' (Scrucca et al., 2016) doi:10.32614/RJ-2016-021. Quantifies temporal distributional shifts between partitions using the Hellinger distance (van der Vaart, 1998) doi:10.1017/CBO9780511802256, and detects temporal change points non-parametrically using energy statistics (Matteson and James, 2014) doi:10.1080/01621459.2013.849605 via 'ecp' or wild binary segmentation (Fryzlewicz, 2014) doi:10.1214/14-AOS1245 via 'HDcpDetect'. Per-site amino-acid frequency tables and entropy trajectory plots characterize sequence composition and evolutionary dynamics across time. A configurable multi-variant simulation engine generates synthetic sequence time series with known ground truth for benchmarking detection pipelines. A curated dataset of SARS-CoV-2 Variants of Concern and Variants of Interest with associated lineage and surveillance metadata is included, along with a bundled National Center for Biotechnology Information (NCBI) Spike protein sample and vignettes demonstrating the full workflow.

Changes in 0.6.2

Additional CRAN feedback addressed in resubmission:
The \dontrun{} block in the sarscov2_variants dataset example that calls References$display() (which requires DT, in Suggests) was missed in the prior audit. The block is now wrapped in if (interactive() && requireNamespace("DT", quietly = TRUE)), the CRAN-recommended pattern for examples that depend on Suggests packages and are intended for interactive use.

From NEWS.md in the release

Install

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

install.packages("ViralEntropR", 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("vadimtyuryaev/ViralEntropR")

Development version from vadimtyuryaev/ViralEntropR. 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-viralentropr

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-ViralEntropR

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-ViralEntropR

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: 2.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-05-31

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6.2

READMEYes · 2,546 wordsVignettesYes · 3 · staticNEWSYes · 100% structured · mentions 0.6.2Citation fileNoWebsiteYes · pkgdown

Description cites an R Journal article

Help pages: 23 (4 internal)includes a package overview page
Examples that run: 79%15 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 4% with a bibliography file

Vignettes (3)

How these are measured

Downloads

1.4K

CRAN downloads in the past year

Rank #16,974 · ~4/day · ~117/mo

Releases R versions

Daily download trend is not available in this view yet.

25930 days

74190 days

1.4K1 year

Compare downloads with other packages →

Also on23 r2u3 autocran

How downloads are counted

Repository

vadimtyuryaev/viralentropr ↗Account: vadimtyuryaev

0Stars

0Forks

0Open issues

0Open PRs

0Releases

bioinformaticschange-point-detectionclusteringcomputational-biologycovid-19fastafunctional-data-analysisgaussian-mixture-models

Last activity 2026-05-31

Responsiveness

not measured

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/vadimtyuryaev/viralentropr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-31 · The repository has a site deploy workflow

pkgdown site last built 2026-05-31

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 3 practices

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing ViralEntropR adds 55 packages (32 with compiled code, 54 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5.0

Imports (13)

ggplot2grDevicesHDcpDetect ecp kableExtra lubridate magrittr mclust rlangstatsstringrutilszoo

LinkingTo (0)

none

Suggests (9)

Biostrings DT dplyr here knitr readxl rmarkdown R.rsp testthat

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

HDcpDetectdeadline passed Oct 12

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Vadim Tyuryaev

Author, Maintainer since 0.6.2 (2026)

Jane Heffernan

Author

Hanna Jankowski

Author

Releases (1)

0.6.2Latest
record
2026-05-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-05-30
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 46 KB / 1 file
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ViralEntropR")

Format

Tyuryaev, V., Heffernan, J., & Jankowski, H. (2026). ViralEntropR: A Computational Pipeline for Entropy-Informed Detection of Emerging Viral Variants (Version 0.6.2) [Computer software]. https://doi.org/10.32614/CRAN.package.ViralEntropR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

The repository also keeps a CITATION.cff.

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 ViralEntropR version 0.6.2 [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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