{ "_id": "6a1afa491d7bb097a09fbeb3", "Package": "scoup", "Version": "1.7.0", "Date": "2026-03-17", "License": "GPL (>= 2)", "Authors@R": "c(person(\"Hassan\", \"Sadiq\", role=c(\"aut\",\"cre\",\"cph\"),\nemail=\"hassan.t.sadiq@gmail.com\",\ncomment=c(ORCID=\"0000-0003-0192-7134\")))", "Title": "Simulate Codons with Darwinian Selection Modelled as an OU\nProcess", "Description": "An elaborate molecular evolutionary framework that\nfacilitates straightforward simulation of codon genetic\nsequences subjected to different degrees and/or patterns of\nDarwinian selection. The model is built upon the fitness\nlandscape paradigm of Sewall Wright, as popularised by the\nmutation-selection model of Halpern and Bruno. This enables\nrealistic evolutionary process of living organisms to be\nreproducible seamlessly. For example, an Ornstein-Uhlenbeck\nfitness update algorithm is incorporated herein. Consequently,\notherwise complex biological processes, such as the effect of\nthe interplay between genetic drift and fitness landscape\nfluctuations on the inference of diversifying selection, may\nnow be investigated with minimal effort. Frequency-dependent\nand stochastic fitness landscape update techniques are\navailable.", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "biocViews": "Alignment, Classification, ComparativeGenomics, DataImport,\nGenetics, MathematicalBiology, ResearchField, Sequencing,\nSequenceMatching, Software, StatisticalMethod, WorkflowStep", "Contact": "", "URL": "https://github.com/thsadiq/scoup", "BugReports": "https://github.com/thsadiq/scoup/issues", "Packaged": { "Date": "2026-05-30 09:49:24 UTC", "User": "root" }, "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:51 UTC", "RemoteUrl": "https://github.com/bioc/scoup", "RemoteRef": "HEAD", "RemoteSha": "f62ca011d63ca3ef333daa38748b1148553bfac0", "NeedsCompilation": "no", "Author": "Hassan Sadiq [aut, cre, cph] (ORCID:\n)", "Maintainer": "Hassan Sadiq ", "MD5sum": "56351216a7b0880a886487bde6e7df52", "_user": "bioc", "_type": "src", "_file": "scoup_1.7.0.tar.gz", "_fileid": "c8c80998efe1287aab2a1e04ee54d4dca3023fcd38538a2dcefe647e0700a15e", "_filesize": 1307039, "_sha256": "c8c80998efe1287aab2a1e04ee54d4dca3023fcd38538a2dcefe647e0700a15e", "_created": "2026-05-30T09:49:24.000Z", "_published": "2026-05-30T14:55:05.252Z", "_jobs": [ { "job": 78640741274, "time": 155, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307526225" }, { "job": 78640741289, "time": 281, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307537485" }, { "job": 78640741281, "time": 234, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307533015" }, { "job": 78640741286, "time": 163, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309033179" }, { "job": 78640741282, "time": 199, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309037178" }, { "job": 78639983393, "time": 188, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307304749" }, { "job": 78640741275, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307523691" }, { "job": 78640741307, "time": 194, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307528479" }, { "job": 78640741308, "time": 162, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307524756" }, { "job": 78640741291, "time": 165, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307525061" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677156346", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scoup", "_commit": { "id": "f62ca011d63ca3ef333daa38748b1148553bfac0", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381431 }, "_maintainer": { "name": "Hassan Sadiq", "email": "hassan.t.sadiq@gmail.com", "login": "thsadiq", "description": "Mathematical statistics lecturer. Research interests: computational molecular biology (focus = natural selection modelling) and interesting data analyses!", "uuid": 177087441, "orcid": "0000-0003-0192-7134" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "Matrix", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "bookdown", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "yaml", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-24", "n": 27 }, { "week": "2025-25", "n": 2 }, { "week": "2025-27", "n": 4 }, { "week": "2025-32", "n": 11 }, { "week": "2026-06", 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