{
  "_id": "6a102b26acfb0bcc41c923f3",
  "Package": "PopPsiSeqR",
  "Type": "Package",
  "Title": "Process and Visualize Evolve & Resequence Experiments",
  "Version": "1.0.0",
  "Date": "2025-11-19",
  "Authors@R": "person(\"Charles\", \"Soeder\", , \"csoeder@email.unc.edu\", role = c(\"aut\", \"cre\", \"cph\"))",
  "Description": "Handle data from evolve and resequence experiments.\nMeasured allele frequencies (e.g., from variants called from\nhigh-throughput sequencing data) are compared using an update\nof the PsiSeq algorithm (Earley, Eric and Corbin Jones (2011)\n<doi:10.1534/genetics.111.129445>). Functions for saving and\nloading important files are also included, as well as functions\nfor basic data visualization.",
  "URL": "https://github.com/csoeder/PopPsiSeq,\nhttps://github.com/csoeder/PopPsiSeqR",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "BugReports": "https://github.com/csoeder/PopPsiSeqR/issues",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev libbz2-dev libgit2-dev\nlibicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev",
  "Repository": "https://csoeder.r-universe.dev",
  "Date/Publication": "2025-12-03 17:39:22 UTC",
  "RemoteUrl": "https://github.com/csoeder/poppsiseqr",
  "RemoteRef": "HEAD",
  "RemoteSha": "7a673839521de704d68050a85dbef39942d18825",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 06:48:04 UTC",
    "User": "root"
  },
  "Author": "Charles Soeder [aut, cre, cph]",
  "Maintainer": "Charles Soeder <csoeder@email.unc.edu>",
  "MD5sum": "2a3bc1cb6ed7413518127b4e583302cc",
  "_user": "csoeder",
  "_type": "src",
  "_file": "PopPsiSeqR_1.0.0.tar.gz",
  "_fileid": "7a5556d9a2eba45bac6e938d1e4de1ea93a1e9c399b6887d1c1cd36adfa1d515",
  "_filesize": 2609726,
  "_sha256": "7a5556d9a2eba45bac6e938d1e4de1ea93a1e9c399b6887d1c1cd36adfa1d515",
  "_created": "2026-05-13T06:48:04.000Z",
  "_published": "2026-05-22T10:08:38.205Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77358627268,
      "time": 238,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6963445025"
    },
    {
      "job": 77358627295,
      "time": 248,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6963448910"
    },
    {
      "job": 77358627394,
      "time": 228,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6963608960"
    },
    {
      "job": 77358627358,
      "time": 225,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6963573830"
    },
    {
      "job": 77358626571,
      "time": 283,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6963386934"
    },
    {
      "job": 77358626522,
      "time": 193,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157993510"
    },
    {
      "job": 77358627316,
      "time": 172,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6963429413"
    },
    {
      "job": 77358627473,
      "time": 223,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6963441623"
    },
    {
      "job": 77358627221,
      "time": 159,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6963426664"
    }
  ],
  "_buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/csoeder/poppsiseqr",
  "_commit": {
    "id": "7a673839521de704d68050a85dbef39942d18825",
    "author": "charles Soeder <csoeder@charless-Laptop.local>",
    "committer": "charles Soeder <csoeder@charless-Laptop.local>",
    "message": "minor updates; administrative bump\n",
    "time": 1764783562
  },
  "_maintainer": {
    "name": "Charles Soeder",
    "email": "csoeder@email.unc.edu"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "ggbio",
      "version": ">= 1.56.1",
      "role": "Imports"
    },
    {
      "package": "withr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "devtools",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "csoeder",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-31",
      "n": 6
    },
    {
      "week": "2025-49",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_userbio": {
    "uuid": 9089178,
    "type": "user",
    "name": "Charles Soeder"
  },
  "_downloads": {
    "count": 322,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PopPsiSeqR"
  },
  "_devurl": "https://github.com/csoeder/poppsiseqr",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PopPsiSeqR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/csoeder/poppsiseqr",
  "_realowner": "csoeder",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2025-08-20"
    },
    {
      "version": "1.0.2",
      "date": "2026-01-12"
    }
  ],
  "_exports": [
    "%>%",
    "export.freqshft",
    "freqShifter",
    "import.freqtbl",
    "import.smvshift",
    "subTractor",
    "windowedFrequencyShift.plotter"
  ],
  "_help": [
    {
      "page": "export.freqshft",
      "title": "Save the shifted frequencies",
      "topics": [
        "export.freqshft"
      ]
    },
    {
      "page": "freqShifter",
      "title": "Frequency Shift Calculator",
      "topics": [
        "freqShifter"
      ]
    },
    {
      "page": "import.freqtbl",
      "title": "Load Merged Allele Frequency Table",
      "topics": [
        "import.freqtbl"
      ]
    },
    {
      "page": "import.smvshift",
      "title": "Load Smoothed Frequency Shift",
      "topics": [
        "import.smvshift"
      ]
    },
    {
      "page": "subTractor",
      "title": "Subtractor",
      "topics": [
        "subTractor"
      ]
    },
    {
      "page": "windowedFrequencyShift.plotter",
      "title": "Data displayer",
      "topics": [
        "windowedFrequencyShift.plotter"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "brew",
    "brio",
    "BSgenome",
    "bslib",
    "cachem",
    "callr",
    "checkmate",
    "cigarillo",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "colorspace",
    "commonmark",
    "cpp11",
    "crayon",
    "credentials",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "desc",
    "devtools",
    "dichromat",
    "diffobj",
    "digest",
    "downlit",
    "dplyr",
    "ellipsis",
    "ensembldb",
    "evaluate",
    "fansi",
    "farver",
    "fastmap",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "gert",
    "ggbio",
    "ggplot2",
    "gh",
    "gitcreds",
    "glue",
    "graph",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "ini",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "nnet",
    "openssl",
    "OrganismDbi",
    "otel",
    "pak",
    "patchwork",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "pkgdown",
    "pkgload",
    "plyr",
    "png",
    "praise",
    "prettyunits",
    "processx",
    "profvis",
    "promises",
    "ProtGenerics",
    "ps",
    "purrr",
    "R6",
    "ragg",
    "rappdirs",
    "RBGL",
    "rcmdcheck",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "roxygen2",
    "rpart",
    "rprojroot",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "rversions",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "sessioninfo",
    "shiny",
    "snow",
    "sourcetools",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "testthat",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "UCSC.utils",
    "urlchecker",
    "usethis",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "waldo",
    "whisker",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xopen",
    "xtable",
    "XVector",
    "yaml",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "PopPsiSeq_and_Helpers.Rmd",
      "filename": "PopPsiSeq_and_Helpers.html",
      "title": "PopPsiSeq and Helper Functions",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Hybridize/Select/Backcross/Resequence Experiments",
        "Building and Loading Example Data",
        "Sitewise Calculations",
        "Smoothing by Window",
        "Data Visualization",
        "Comparing and Contrasting Results",
        "Bibliography"
      ],
      "created": "2025-04-04 14:25:21",
      "modified": "2025-07-28 20:31:11",
      "commits": 4
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "poppsiseqr",
  "_universes": [
    "csoeder"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-13T06:51:12.000Z",
      "distro": "noble",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "ce484512dfecbdb1192d78bba178af51be737ba5e5515fa6b9376b6230cf8cfe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-13T06:51:24.000Z",
      "distro": "noble",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "bbb873f6c162ce4c82c465fffe831d4c7850058dd012fe6453b7934317cdd9d7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-13T07:02:03.000Z",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "7e9ad556c3b7ece4bd8ac5d9bb7b6d2651b20a14b037afd6ae7276be1d2bc455",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-13T06:59:49.000Z",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "819c73dad5334bd11e4d4c7284635187cd36ba52a1044a9bbb21c0b66287177d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-13T06:49:53.000Z",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "4151bcd8a3ec9c5b986eacd2b5102efe78bed6611d7e6d57853f9e1f4fd268ff",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-13T06:51:02.000Z",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "d8a748ad44d6430ea3fc3790ef871333897a6f8b0d2a92057947db71db635292",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-13T06:49:47.000Z",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "555afdb667e5518cd1cd8596735d76796d5008365b864a92bb41b6f5da6b3ae9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-05-22T10:08:17.000Z",
      "commit": "7a673839521de704d68050a85dbef39942d18825",
      "fileid": "d55bb460e2a3503e3fb3bd16b0644c80e3dbb9642dfc394a0370724ff13b41c4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/csoeder/actions/runs/25783012000"
    }
  ]
}