{ "_id": "6a1b19791d7bb097a0a0df7d", "Package": "ViralEntropR", "Title": "A Computational Pipeline for Entropy-Informed Detection of\nEmerging Viral Variants", "Version": "0.6.2", "Authors@R": "c(\nperson(\"Vadim\", \"Tyuryaev\", ,\"vadim.tyuryaev@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0008-1361-6265\")),\nperson(\"Jane\", \"Heffernan\", , \"jmheffer@yorku.ca\",\nrole = c(\"aut\")),\nperson(\"Hanna\", \"Jankowski\", , \"hkj@yorku.ca\",\nrole = c(\"aut\"))\n)", "Description": "Implements an entropy-informed pipeline for detecting\nemerging variants in viral amino acid sequence data, extending\nprior clustering-based approaches including hemagglutinin\nclustering methods (Li et al., 2015)\n. Provides a fully vectorized\nFASTA preprocessing toolkit covering header parsing, two-pass\ndate and country extraction, ambiguous-residue filtering, and\ninteger encoding under a 25-symbol amino acid alphabet.\nComputes per-site Shannon entropy across user-defined\ncumulative, sliding, or disjoint temporal partitions and\nclusters per-site entropy values using Gaussian mixture models\nvia 'mclust' (Scrucca et al., 2016) .\nQuantifies temporal distributional shifts between partitions\nusing the Hellinger distance (van der Vaart, 1998)\n, and detects temporal change\npoints non-parametrically using energy statistics (Matteson and\nJames, 2014) via 'ecp' or\nwild binary segmentation (Fryzlewicz, 2014)\n via 'HDcpDetect'. Per-site amino-acid\nfrequency tables and entropy trajectory plots characterize\nsequence composition and evolutionary dynamics across time. A\nconfigurable multi-variant simulation engine generates\nsynthetic sequence time series with known ground truth for\nbenchmarking detection pipelines. A curated dataset of\nSARS-CoV-2 Variants of Concern and Variants of Interest with\nassociated lineage and surveillance metadata is included, along\nwith a bundled National Center for Biotechnology Information\n(NCBI) Spike protein sample and vignettes demonstrating the\nfull workflow.", "License": "MIT + file LICENSE", "Language": "en-GB", "Date": "2026-05-07", "URL": "https://github.com/vadimtyuryaev/ViralEntropR,\nhttps://doi.org/10.5281/zenodo.19040165,\nhttps://vadimtyuryaev.github.io/ViralEntropR/", "BugReports": "https://github.com/vadimtyuryaev/ViralEntropR/issues", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr, R.rsp", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 17:04:07 UTC", "User": "root" }, "Author": "Vadim Tyuryaev [aut, cre] (ORCID:\n), Jane Heffernan [aut],\nHanna Jankowski [aut]", "Maintainer": "Vadim Tyuryaev ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-05-30 13:40:21 UTC", "RemoteUrl": "https://github.com/cran/ViralEntropR", "RemoteRef": "HEAD", "RemoteSha": "a9b293057a1d5b20f074216fc899da6ebdd0389b", "MD5sum": "06e7b27812529117d030bb5ff13af41b", "_user": "cran", "_type": "src", "_file": "ViralEntropR_0.6.2.tar.gz", "_fileid": "72645331e622a344d61aa6cd0b201edfc292aecbaf6bdc7b4f941346ec80c558", "_filesize": 2130854, "_sha256": "72645331e622a344d61aa6cd0b201edfc292aecbaf6bdc7b4f941346ec80c558", "_created": "2026-05-30T17:04:07.000Z", "_published": "2026-05-30T17:08:09.290Z", "_distro": "noble", "_jobs": [ { "job": 78664057488, "time": 170, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7309876890" }, { "job": 78664057485, "time": 195, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7309879472" }, { "job": 78663833459, "time": 221, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7309859886" }, { "job": 78664057481, "time": 136, "config": "wasm-release", "r": 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