{ "_id": "6a107013acfb0bcc41cab890", "Package": "RADstackshelpR", "Title": "Optimize the De Novo Stacks Pipeline via R", "Version": "0.1.0", "Authors@R": "person(given = \"Devon\",\nfamily = \"DeRaad\",\nrole = c(\"aut\", \"cre\"),\nemail = \"devonderaad@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3105-985X\"))", "Description": "Offers a handful of useful wrapper functions which\nstreamline the reading, analyzing, and visualizing of variant\ncall format (vcf) files in R. This package was designed to\nfacilitate an explicit pipeline for optimizing Stacks (Rochette\net al., 2019) () parameters during de\nnovo (without a reference genome) assembly and variant calling\nof restriction-enzyme associated DNA sequence (RADseq) data.\nThe pipeline implemented here is based on the 2017 paper \"Lost\nin Parameter Space\" (Paris et al., 2017)\n() which establishes clear\nrecommendations for optimizing the parameters 'm', 'M', and\n'n', during the process of assembling loci.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 07:19:51 UTC", "User": "root" }, "Author": "Devon DeRaad [aut, cre]\n()", "Maintainer": "Devon DeRaad ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2021-08-19 08:10:07 UTC", "RemoteUrl": "https://github.com/cran/RADstackshelpR", "RemoteRef": "HEAD", "RemoteSha": "c8ab76ab58ad2063278fe2a075ca40ac6cbdd91d", 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"_host": "GitHub-Actions", "_upstream": "https://github.com/cran/RADstackshelpR", "_commit": { "id": "c8ab76ab58ad2063278fe2a075ca40ac6cbdd91d", "author": "Devon DeRaad ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1629360607 }, "_maintainer": { "name": "Devon DeRaad", "email": "devonderaad@gmail.com", "orcid": "0000-0003-3105-985X" }, "_registered": true, "_dependencies": [ { "package": "vcfR", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggridges", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 249, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RADstackshelpR" }, "_searchresults": 31, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/RADstackshelpR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2021-08-19" } ], "_exports": [ "optimize_bigM", "optimize_m", "optimize_n", "vis_depth", "vis_loci", "vis_snps" ], "_help": [ { "page": "optimize_bigM", "title": "Optimize the M parameter during denovo stacks assembly", "topics": [ "optimize_bigM" ] }, { "page": "optimize_m", "title": "Optimize the m parameter during denovo stacks assembly", "topics": [ "optimize_m" ] }, { "page": "optimize_n", "title": "Optimize the n parameter during denovo stacks assembly", "topics": [ "optimize_n" ] }, { "page": "vis_depth", "title": "Visualize the effect of varying the m parameter on the mean depth of each sample", "topics": [ "vis_depth" ] }, { "page": "vis_loci", "title": "Visualize the effect of varying a stacks parameter on the number of polymorphic loci retained", "topics": [ "vis_loci" ] }, { "page": "vis_snps", "title": "Visualize the effect of varying a stacks parameter on the number of SNPs retained", "topics": [ "vis_snps" ] } ], "_pkglogo": "https://github.com/cran/RADstackshelpR/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/cran/RADstackshelpR/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "cluster", "cpp11", "digest", "dplyr", "farver", "generics", "ggplot2", "ggridges", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memuse", "mgcv", "nlme", "permute", "pillar", "pinfsc50", "pkgconfig", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "withr" ], "_vignettes": [ { "source": "reproducible.vignette.Rmd", "filename": "reproducible.vignette.html", "title": "Reproducible example", "author": "Devon DeRaad", "engine": "knitr::rmarkdown", "headings": [ "This vignette/article is designed to provide a fully reproducible example of how to use the RADstackshelpR package to optimize STACKS parameters. Each bash code chunk gives a generic example of code you could use to execute the STACKS pipeline. Each R code chunk uses extremely light (20 samples, ~200 SNPs), toy vcf files which are distributed with the package, in order to provide fully reproducible examples for end-users. These chunks should run successfully if you have successfully installed the package.", "Demultiplex", "Iterate over potential values for the 'm' parameter in the 'ustacks' module", "Use RADstackshelpR to visualize the output of these 5 runs and determine the optimal value for the parameter 'm'.", "Iterate over potential values for the 'M' parameter in the 'ustacks' module", "Use RADstackshelpR to visualize the output of these 8 runs and determine the optimal value for the parameter 'M'.", "Iterate over potential values for the 'n' parameter in the 'cstacks' module", "Use RADstackshelpR to visualize the output of these 3 runs and determine the optimal value for 'n'." ], "created": "2021-08-19 08:10:07", "modified": "2021-08-19 08:10:07", "commits": 1 } ], "_score": 3.1903316981702914, "_indexed": true, "_nocasepkg": "radstackshelpr", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-05-07T07:22:08.000Z", "distro": "noble", "commit": "c8ab76ab58ad2063278fe2a075ca40ac6cbdd91d", "fileid": "90eb3197c48afcfbd7ce4c7c40a4e5663c606653048a3b15c4a2ca464aeeae8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/25481590776" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-05-07T07:21:59.000Z", "distro": "noble", "commit": "c8ab76ab58ad2063278fe2a075ca40ac6cbdd91d", "fileid": "413ca9f2a640513e40286cc166e046b640b03fa6212352f88048eb05af5df98f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/25481590776" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-05-22T15:02:23.000Z", "commit": "c8ab76ab58ad2063278fe2a075ca40ac6cbdd91d", "fileid": "f5a843027d16eab83fb70b24049258c1ba529b1af03ef1f244ece6aeb04ec91b", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25481590776" } ] }