{ "_id": "6adf2fd8b29d1aafda550ccc", "Package": "MetaEntropy", "Title": "Functional Shannon Entropy for Virome Mutational Analysis", "Version": "1.4", "Date": "2026-08-31", "Authors@R": "c( person(\"Leandro Roberto\", \"Jones\", email = \"lrj000@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5877-4194\")),\nperson(\"Julieta Marina\", \"Manrique\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-8712-6666\")))", "Description": "Estimates Shannon entropy, per gene and per genomic\nposition, associated with non-synonymous mutation frequencies\nin viral populations, such as wastewater samples. The package\nuses codon translations for functional insights. Each amino\nacid can be treated as an individual state, resulting in a\n20-state entropy computation, or grouped into one of six\nphysicochemical classes, adding further functional context.\nProvides normalized values (0-1 scale) to facilitate the direct\ncomparison of different genomic positions or total functional\nentropy across multiple metagenomes. Designed to analyze\nmutational data using tabular 'Single Nucleotide Variant' (SNV)\nfrequency tables generated by variant callers (e.g., 'iVar' or\n'LoFreq'), operating independently of consensus sequence\nestimation and multiple sequence alignment.", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "License": "MIT + file LICENSE", "Config/roxygen2/version": "8.1.0", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-26 10:44:14 UTC", "User": "root" }, "Author": "Leandro Roberto Jones [aut, cre] (ORCID:\n), Julieta Marina\nManrique [aut] (ORCID: )", "Maintainer": "Leandro Roberto Jones ", "Repository": "https://jones-lr.r-universe.dev", "Date/Publication": "2026-09-03 14:10:02 UTC", "RemoteUrl": "https://github.com/cran/MetaEntropy", "RemoteRef": "HEAD", "RemoteSha": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "_user": "jones-lr", "_type": "src", "_file": "MetaEntropy_1.4.tar.gz", "_fileid": "https://r2.ropensci.org/a35ba60c62ef62c3fd924c0c7039aaa9d45232e3fd7b5e3f8e87d1f9d7d5a1f0", "_filesize": 783287, "_sha256": "a35ba60c62ef62c3fd924c0c7039aaa9d45232e3fd7b5e3f8e87d1f9d7d5a1f0", "_expires": "2027-02-03T10:47:50.000Z", "_created": "2026-10-26T10:44:14.000Z", "_published": "2026-10-26T10:47:52.363Z", "_upstream": "https://github.com/cran/MetaEntropy", "_status": "success", "_maintainer": { "name": "Leandro Roberto Jones", "email": "lrj000@gmail.com", "login": "jones-lr", "description": "", "uuid": 260074809, "orcid": "0000-0002-5877-4194" }, "_jobs": [ { "job": 121527713707, "time": 120, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12643797292" }, { "job": 121527713689, "time": 127, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12644570833" }, { "job": 121527713694, "time": 160, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12643962660" }, { "job": 121527713773, "time": 179, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12643653785" }, { "job": 121526531887, "time": 165, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12644171808" }, { "job": 121527714296, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12643683391" }, { "job": 121527713976, "time": 88, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12644316864" }, { "job": 121527713729, "time": 74, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12644306096" }, { "job": 121527713959, "time": 80, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12644626021" } ], "_buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570", "_commit": { "id": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "author": "Leandro Roberto Jones ", "committer": "cran-robot ", "message": "version 1.4\n", "time": 1788444602 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "beeswarm", "role": "Imports" }, { "package": "ggbeeswarm", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-10", "n": 1 }, { "week": "2026-11", "n": 1 }, { "week": "2026-36", "n": 1 } ], "_tags": [ { "name": "1.2", "date": "2026-03-03" }, { "name": "1.3", "date": "2026-03-09" }, { "name": "1.4", "date": "2026-09-03" } ], "_stars": 0, "_contributors": [ { "user": "jones-lr", "count": 3, "uuid": 260074809 } ], "_userbio": { "uuid": 260074809, "type": "user", "name": "JONES-LR", "followers": 0 }, "_downloads": { "count": 244, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MetaEntropy" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/MetaEntropy.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "jones-lr", "_cranurl": false, "_releases": [ { "version": "1.2", "date": "2026-03-03" }, { "version": "1.3", "date": "2026-03-09" }, { "version": "1.4", "date": "2026-09-08" } ], "_exports": [ "assessHotSpot", "getEntropySignature", "heatmap_entropyProfiles", "showMutations" ], "_datasets": [ { "name": "intraHostVariants", "title": "SNVs from multiple organs of individuals with postmortem SARS-CoV-2 detection", "object": "intraHostVariants", "class": [ "data.frame" ], "fields": [ "case", "organ", "CHROM", "POS", "linkage", "depth", "REF", "ALT", "GENE", "protein", "ref_codon", "alt_codon", "aa_position", "ref_aa", "alt_aa", "alt_aa_freq" ], "rows": 213, "table": true, "tojson": true }, { "name": "mn908947.3", "title": "CDS topology and length of Wuhan-Hu-1 reference strain", "object": "mn908947.3", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "wWater", "title": "Data from first and third COVID-19 waves in Trelew ", "object": "wWater", "class": [ "data.frame" ], "fields": [ "wave", "position", "linkage", "ref", "alt", "protein", "aa_position", "ref_aa", "alt_aa", "alt_aa_freq" ], "rows": 148, "table": true, "tojson": true } ], "_help": [ { "page": "as.data.frame.entropyProfile", "title": "Coerce 'entropyProfile' to a Data Frame", "topics": [ "as.data.frame.entropyProfile" ] }, { "page": "assessHotSpot", "title": "Evaluates Entropy Hotspot", "topics": [ "assessHotSpot" ] }, { "page": "createPositionSummary", "title": "Summarize variants and frequencies at a genome position", "topics": [ "createPositionSummary" ] }, { "page": "createStorage", "title": "Build a structure representing amino acid categories.", "topics": [ "createStorage" ] }, { "page": "entropyProfile", "title": "Create (empty) object of class \"entropyProfile\"", "topics": [ "entropyProfile" ] }, { "page": "fillPosition", "title": "Translate amino acid frequencies into category frequencies", "topics": [ "fillPosition" ] }, { "page": "getEntropySignature", "title": "Infer Entropy Signature", "topics": [ "getEntropySignature" ] }, { "page": "getPosEntropy", "title": "Calculates aminoacidic entropy resulting from SNVs present in a specific locus", "topics": [ "getPosEntropy" ] }, { "page": "heatmap_entropyProfiles", "title": "Graphically compare entropy profiles", "topics": [ "heatmap_entropyProfiles" ] }, { "page": "intraHostVariants", "title": "SNVs from multiple organs of individuals with postmortem SARS-CoV-2 detection", "topics": [ "intraHostVariants" ] }, { "page": "mn908947.3", "title": "CDS topology and length of Wuhan-Hu-1 reference strain", "topics": [ "mn908947.3" ] }, { "page": "plot.entropyProfile", "title": "Plot entropy signatures", "topics": [ "plot.entropyProfile" ] }, { "page": "print.profileSummary", "title": "Print method for 'profileSummary' objects", "topics": [ "print.profileSummary" ] }, { "page": "print.tidyMutations", "title": "Print method for 'tidyMutations' objects", "topics": [ "print.tidyMutations" ] }, { "page": "showMutations", "title": "Summarize mutations", "topics": [ "showMutations" ] }, { "page": "summary.entropyProfile", "title": "Summarize entropy profile", "topics": [ "summary.entropyProfile" ] }, { "page": "wWater", "title": "Data from first and third COVID-19 waves in Trelew ", "topics": [ "wWater" ] } ], "_readme": "https://github.com/cran/MetaEntropy/raw/HEAD/README.md", "_rundeps": [ "beeswarm", "cli", "cpp11", "dplyr", "evaluate", "farver", "generics", "ggbeeswarm", "ggplot2", "glue", "gtable", "highr", "isoband", "knitr", "labeling", "lifecycle", "magrittr", "patchwork", "pillar", "pkgconfig", "R6", "RColorBrewer", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "vipor", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "intraHostVariants.Rmd", "filename": "intraHostVariants.html", "title": "intraHostVariants: SNVs from Multiple Anatomical Sites", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data Structure and Characteristics", "Package Integration", "Create a custom genome", "Entropy computation", "Profiles comparison", "References" ], "created": "2026-09-03 14:10:02", "modified": "2026-09-03 14:10:02", "commits": 1 }, { "source": "overview.Rmd", "filename": "overview.html", "title": "Overview of MetaEntropy", "engine": "knitr::rmarkdown", "headings": [ "Motivation", "Input data", "Worked example: SARS-CoV-2 immune escape", "Loading packages", "Conceptual framework and data", "Entropy signatures", "Omicron sublineages in more detail", "Integrating Biological Signal via Entropy", "References" ], "created": "2026-03-03 10:00:38", "modified": "2026-09-03 14:10:02", "commits": 2 } ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "metaentropy", "_universes": [ "jones-lr" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4", "date": "2026-10-26T10:46:05.000Z", "distro": "resolute", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/7924de7453b79f95822e89c380b362afcfe987efa0a6c69da4a7f3325908cc99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.6.1", "os": "linux", "version": "1.4", "date": "2026-10-26T10:46:09.000Z", "distro": "resolute", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/f753734dfa2ee28d2cbcb5415baf0f19813c3d6222089dcc72cddd54d0d949ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.5.3", "os": "mac", "version": "1.4", "date": "2026-10-26T10:46:27.000Z", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/3192291e35189fe81d69cdad91b408ec3ebc5ecc5f4c3c0df6391da350d2789c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.6.1", "os": "mac", "version": "1.4", "date": "2026-10-26T10:46:33.000Z", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/fe299b31ba7c98680c3d08e8db4dddc6ae36b7d5468088638ac8487606774fa7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.6.0", "os": "wasm", "version": "1.4", "date": "2026-10-26T10:46:07.000Z", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/646e9ddeac7e604e26674a4591daf435ba989561e622fa26a3b50ce51866f6f4", "status": "success", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.7.0", "os": "win", "version": "1.4", "date": "2026-10-26T10:45:24.000Z", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/b8774dff0c30c75fac40e4ebb79417ea90caf204db2968aa3f85809837d51089", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.5.3", "os": "win", "version": "1.4", "date": "2026-10-26T10:45:22.000Z", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/3d036ef48fb0ff0d54c0958140259592449ac051c6e3b41097ea918fc0785b33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" }, { "r": "4.6.1", "os": "win", "version": "1.4", "date": "2026-10-26T10:45:22.000Z", "commit": "9fdb9ebe35fb97535f2e19510fcae516c9e59466", "fileid": "https://r2.ropensci.org/3b6344b45e9c029a919a709c9e2c93d614e4a37237595e2ea4bdd0e2bb770d33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jones-lr/actions/runs/40309345570" } ] }