{
  "_id": "6a1eeb50b401979e73412287",
  "Package": "HTRX",
  "Type": "Package",
  "Title": "Haplotype Trend Regression with eXtra Flexibility (HTRX)",
  "Version": "1.2.4",
  "Authors@R": "c(\nperson(\"Yaoling\", \"Yang\", email = \"yaoling.yang@bristol.ac.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4905-8097\")),\nperson(\"Daniel\", \"Lawson\", email = \"Dan.Lawson@bristol.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-5311-6213\")))",
  "Maintainer": "Yaoling Yang <yaoling.yang@bristol.ac.uk>",
  "Description": "Detection of haplotype patterns that include single\nnucleotide polymorphisms (SNPs) and non-contiguous haplotypes\nthat are associated with a phenotype. Methods for implementing\nHTRX are described in Yang Y, Lawson DJ (2023)\n<doi:10.1093/bioadv/vbad038> and Barrie W, Yang Y, Irving-Pease\nE.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-19 09:38:27 UTC",
    "User": "root"
  },
  "Author": "Yaoling Yang [aut, cre]\n(<https://orcid.org/0000-0003-4905-8097>), Daniel Lawson [aut]\n(<https://orcid.org/0000-0002-5311-6213>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-02-10 02:28:09 UTC",
  "RemoteUrl": "https://github.com/cran/HTRX",
  "RemoteRef": "HEAD",
  "RemoteSha": "79df34a6d8de197c9e04595206f4cb9f36d26e29",
  "MD5sum": "0a6072e566a5516ecca41334d811a1c8",
  "_user": "cran",
  "_type": "src",
  "_file": "HTRX_1.2.4.tar.gz",
  "_fileid": "6ed103e43257e8c6b882d8b47b910f97bfc070c8bf68d790e0668bc8d484b3a6",
  "_filesize": 646141,
  "_sha256": "6ed103e43257e8c6b882d8b47b910f97bfc070c8bf68d790e0668bc8d484b3a6",
  "_created": "2026-05-19T09:38:27.000Z",
  "_published": "2026-06-02T14:40:16.124Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79096884636,
      "time": 243,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7080035681"
    },
    {
      "job": 79096884962,
      "time": 159,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7080004913"
    },
    {
      "job": 79096883974,
      "time": 242,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7079946323"
    },
    {
      "job": 79096883220,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7360902659"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26088677600",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/HTRX",
  "_commit": {
    "id": "79df34a6d8de197c9e04595206f4cb9f36d26e29",
    "author": "Yaoling Yang <yaoling.yang@bristol.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.2.4\n",
    "time": 1707532089
  },
  "_maintainer": {
    "name": "Yaoling Yang",
    "email": "yaoling.yang@bristol.ac.uk",
    "orcid": "0000-0003-4905-8097"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "fastglm",
      "role": "Imports"
    },
    {
      "package": "caret",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "tune",
      "role": "Imports"
    },
    {
      "package": "recipes",
      "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": 183,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HTRX"
  },
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HTRX.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.7",
      "date": "2022-10-11"
    },
    {
      "version": "1.1.0",
      "date": "2022-11-24"
    },
    {
      "version": "1.2.1",
      "date": "2023-02-14"
    },
    {
      "version": "1.2.2",
      "date": "2023-03-27"
    },
    {
      "version": "1.2.4",
      "date": "2024-02-09"
    }
  ],
  "_exports": [
    "computeR2",
    "do_cumulative_htrx",
    "do_cumulative_htrx_step1",
    "do_cv",
    "do_cv_direct",
    "do_cv_step1",
    "extend_haps",
    "htrx_max",
    "htrx_nfeatures",
    "infer_fixedfeatures",
    "infer_step1",
    "kfold_split",
    "make_cumulative_htrx",
    "make_htr",
    "make_htrx",
    "make_snp",
    "mypredict",
    "themodel",
    "twofold_split"
  ],
  "_datasets": [
    {
      "name": "example_data_nosnp",
      "title": "Example covariate data",
      "object": "example_data_nosnp",
      "class": [
        "data.frame"
      ],
      "fields": [
        "outcome",
        "sex",
        "age",
        "PC1",
        "PC2",
        "PC3",
        "PC4",
        "PC5",
        "PC6",
        "PC7",
        "PC8",
        "PC9",
        "PC10",
        "PC11",
        "PC12",
        "PC13",
        "PC14",
        "PC15",
        "PC16",
        "PC17",
        "PC18"
      ],
      "rows": 5000,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_hap1",
      "title": "Example genotype data for the first genome",
      "object": "example_hap1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SNP1",
        "SNP2",
        "SNP3",
        "SNP4",
        "SNP5",
        "SNP6",
        "SNP7",
        "SNP8"
      ],
      "rows": 5000,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_hap2",
      "title": "Example genotype data for the second genome",
      "object": "example_hap2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SNP1",
        "SNP2",
        "SNP3",
        "SNP4",
        "SNP5",
        "SNP6",
        "SNP7",
        "SNP8"
      ],
      "rows": 5000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "HTRX-package",
      "title": "HTRX: Haplotype Trend Regression with eXtra flexibility",
      "topics": [
        "HTRX-package",
        "HTRX"
      ]
    },
    {
      "page": "computeR2",
      "title": "Compute variance explained by models",
      "topics": [
        "computeR2",
        "mypredict"
      ]
    },
    {
      "page": "data_split",
      "title": "Data split",
      "topics": [
        "data_split",
        "kfold_split",
        "twofold_split"
      ]
    },
    {
      "page": "do_cumulative_htrx",
      "title": "Cumulative HTRX on long haplotypes",
      "topics": [
        "do_cumulative_htrx",
        "do_cumulative_htrx_step1",
        "extend_haps",
        "make_cumulative_htrx"
      ]
    },
    {
      "page": "do_cv",
      "title": "Two-stage HTRX: Model selection on short haplotypes",
      "topics": [
        "do_cv",
        "do_cv_step1",
        "infer_fixedfeatures",
        "infer_step1"
      ]
    },
    {
      "page": "do_cv_direct",
      "title": "Direct HTRX: k-fold cross-validation on short haplotypes",
      "topics": [
        "do_cv_direct"
      ]
    },
    {
      "page": "example_data_nosnp",
      "title": "Example covariate data",
      "topics": [
        "example_data_nosnp"
      ]
    },
    {
      "page": "example_hap1",
      "title": "Example genotype data for the first genome",
      "topics": [
        "example_hap1"
      ]
    },
    {
      "page": "example_hap2",
      "title": "Example genotype data for the second genome",
      "topics": [
        "example_hap2"
      ]
    },
    {
      "page": "htrx_max",
      "title": "Maximum independent features for HTRX",
      "topics": [
        "htrx_max"
      ]
    },
    {
      "page": "htrx_nfeatures",
      "title": "Total number of features for HTRX",
      "topics": [
        "htrx_nfeatures"
      ]
    },
    {
      "page": "make_htrx",
      "title": "Generate haplotype data",
      "topics": [
        "make_htr",
        "make_htrx",
        "make_snp"
      ]
    },
    {
      "page": "themodel",
      "title": "Model fitting",
      "topics": [
        "themodel"
      ]
    }
  ],
  "_readme": "https://github.com/cran/HTRX/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "BH",
    "bigmemory",
    "bigmemory.sri",
    "bslib",
    "cachem",
    "caret",
    "class",
    "cli",
    "clock",
    "codetools",
    "cpp11",
    "data.table",
    "diagram",
    "dials",
    "DiceDesign",
    "digest",
    "dplyr",
    "e1071",
    "evaluate",
    "farver",
    "fastglm",
    "fastmap",
    "fontawesome",
    "foreach",
    "Formula",
    "fs",
    "furrr",
    "future",
    "future.apply",
    "GauPro",
    "generics",
    "ggplot2",
    "glmnet",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "highr",
    "htmltools",
    "ipred",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lattice",
    "lava",
    "lbfgs",
    "lifecycle",
    "listenv",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "mixopt",
    "modelenv",
    "ModelMetrics",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "parsnip",
    "pillar",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "pROC",
    "prodlim",
    "progressr",
    "proxy",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "recipes",
    "reshape2",
    "rlang",
    "rmarkdown",
    "rpart",
    "rsample",
    "S7",
    "sass",
    "scales",
    "sfd",
    "shape",
    "slider",
    "sparsevctrs",
    "splitfngr",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "tailor",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tinytex",
    "tune",
    "tzdb",
    "utf8",
    "uuid",
    "vctrs",
    "viridisLite",
    "warp",
    "withr",
    "workflows",
    "xfun",
    "yaml",
    "yardstick"
  ],
  "_vignettes": [
    {
      "source": "HTRX_vignette.Rmd",
      "filename": "HTRX_vignette.html",
      "title": "HTRX: an R package for learning non-contiguous haplotypes",
      "author": "Yaoling Yang, Daniel Lawson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Introduction",
        "2. Installation",
        "3. Data loading",
        "4. Haplotype selection within small regions",
        "4.1 Creating haplotype data",
        "4.2 Selecting haplotypes",
        "5. Haplotype selection for large regions",
        "References"
      ],
      "created": "2023-02-14 08:50:14",
      "modified": "2024-02-10 02:28:09",
      "commits": 3
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "htrx",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.4",
      "date": "2026-05-19T09:42:29.000Z",
      "distro": "noble",
      "commit": "79df34a6d8de197c9e04595206f4cb9f36d26e29",
      "fileid": "9f7d98e69519f3ff22bc57933c1f749a38455d143a01a82bdb4d709edd9abdae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26088677600"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.4",
      "date": "2026-05-19T09:41:02.000Z",
      "distro": "noble",
      "commit": "79df34a6d8de197c9e04595206f4cb9f36d26e29",
      "fileid": "c2dee4b6810d00e62cee788ee26624d6d5f74cdb47b36ba0b43d19f65d8128c5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26088677600"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.4",
      "date": "2026-06-02T14:38:59.000Z",
      "commit": "79df34a6d8de197c9e04595206f4cb9f36d26e29",
      "fileid": "768d2e4cc426b257e824b924eb9db5b5062c8770dbd921461a090ccbce8cc001",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26088677600"
    }
  ]
}