{
  "_id": "6ac2395ed743750d376d716b",
  "Package": "SMASH",
  "Type": "Package",
  "Title": "Subclone Multiplicity Allocation and Somatic Heterogeneity",
  "Version": "1.0.0",
  "Date": "2025-02-07",
  "Authors@R": "person(\"Paul\",\"Little\",\nemail = \"pllittle321@gmail.com\",\nrole = c(\"aut\",\"cre\"))",
  "Description": "Cluster user-supplied somatic read counts with\ncorresponding allele-specific copy number and tumor purity to\ninfer feasible underlying intra-tumor heterogeneity in terms of\nnumber of subclones, multiplicity, and allocation (Little et\nal. (2019) <doi:10.1186/s13073-019-0643-9>).",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-04 11:26:59 UTC",
    "User": "root"
  },
  "Author": "Paul Little [aut, cre]",
  "Maintainer": "Paul Little <pllittle321@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-02-27 16:40:06 UTC",
  "RemoteUrl": "https://github.com/cran/SMASH",
  "RemoteRef": "HEAD",
  "RemoteSha": "f73c87275840edb5e66e8d389492dbedea8e84af",
  "_user": "cran",
  "_type": "src",
  "_file": "SMASH_1.0.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/25f520e1e55b1ee4d49a4d4bc84451b48aceb906d78277489850662e17f716e3",
  "_filesize": 838375,
  "_sha256": "25f520e1e55b1ee4d49a4d4bc84451b48aceb906d78277489850662e17f716e3",
  "_expires": "2027-01-12T11:32:43.000Z",
  "_created": "2026-10-04T11:26:59.000Z",
  "_published": "2026-10-04T11:32:46.640Z",
  "_jobs": [
    {
      "job": 111426062901,
      "time": 119,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11302331587"
    },
    {
      "job": 111426062837,
      "time": 135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11302266067"
    },
    {
      "job": 111426062961,
      "time": 136,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302246912"
    },
    {
      "job": 111426062881,
      "time": 160,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302715902"
    },
    {
      "job": 111425322591,
      "time": 268,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11301827173"
    },
    {
      "job": 111426062735,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11301912293"
    },
    {
      "job": 111426062825,
      "time": 202,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11301777739"
    },
    {
      "job": 111426062808,
      "time": 175,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11302336714"
    },
    {
      "job": 111426062802,
      "time": 292,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11301638733"
    },
    {
      "job": 111426062804,
      "time": 127,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302725213"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055",
  "_status": "success",
  "_upstream": "https://github.com/cran/SMASH",
  "_commit": {
    "id": "f73c87275840edb5e66e8d389492dbedea8e84af",
    "author": "Paul Little <pllittle321@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.0\n",
    "time": 1740674406
  },
  "_maintainer": {
    "name": "Paul Little",
    "email": "pllittle321@gmail.com"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "smarter",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 630,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 245,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SMASH"
  },
  "_searchresults": 18,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/SMASH.html"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2025-02-27"
    }
  ],
  "_exports": [
    "gen_ITH_RD",
    "gen_subj_truth",
    "grid_ITH_optim",
    "ITH_optim",
    "vis_GRID"
  ],
  "_datasets": [
    {
      "name": "eS",
      "title": "A collection of pre-defined subclone configurations.",
      "object": "eS",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "eS",
      "title": "A collection of pre-defined subclone configurations.",
      "topics": [
        "eS"
      ]
    },
    {
      "page": "gen_ITH_RD",
      "title": "gen_ITH_RD",
      "topics": [
        "gen_ITH_RD"
      ]
    },
    {
      "page": "gen_subj_truth",
      "title": "gen_subj_truth",
      "topics": [
        "gen_subj_truth"
      ]
    },
    {
      "page": "grid_ITH_optim",
      "title": "grid_ITH_optim",
      "topics": [
        "grid_ITH_optim"
      ]
    },
    {
      "page": "ITH_optim",
      "title": "ITH_optim",
      "topics": [
        "ITH_optim"
      ]
    },
    {
      "page": "vis_GRID",
      "title": "vis_GRID",
      "topics": [
        "vis_GRID"
      ]
    }
  ],
  "_rundeps": [
    "askpass",
    "base64enc",
    "bitops",
    "brew",
    "brio",
    "bslib",
    "cachem",
    "callr",
    "caTools",
    "cli",
    "clipr",
    "commonmark",
    "cpp11",
    "crayon",
    "credentials",
    "curl",
    "desc",
    "devtools",
    "diffobj",
    "digest",
    "downlit",
    "ellipsis",
    "evaluate",
    "fansi",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "gert",
    "ggplot2",
    "gitcreds",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr2",
    "ini",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "miniUI",
    "openssl",
    "otel",
    "pak",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "pkgdown",
    "pkgload",
    "plyr",
    "praise",
    "prettyunits",
    "processx",
    "profvis",
    "promises",
    "ps",
    "purrr",
    "R6",
    "ragg",
    "rappdirs",
    "rcmdcheck",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "rdtools",
    "reshape2",
    "rlang",
    "rmarkdown",
    "roxygen2",
    "rprojroot",
    "rstudioapi",
    "rversions",
    "S7",
    "sass",
    "scales",
    "sessioninfo",
    "shiny",
    "smarter",
    "sourcetools",
    "stringi",
    "stringr",
    "sys",
    "systemfonts",
    "testthat",
    "textshaping",
    "tibble",
    "tinytex",
    "urlchecker",
    "usethis",
    "utf8",
    "vctrs",
    "viridisLite",
    "waldo",
    "whisker",
    "withr",
    "xfun",
    "xml2",
    "xopen",
    "xtable",
    "yaml",
    "zip"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "intro.Rmd",
      "filename": "intro.html",
      "title": "Introduction",
      "author": "Paul Little",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Software",
        "Introduction",
        "Definitions",
        "Copy Number",
        "Cellular prevalence",
        "Variant Allele Frequency",
        "Simulation",
        "Optimization",
        "Known configuration",
        "Unknown configuration",
        "Downstream Applications",
        "Session Info",
        "References"
      ],
      "created": "2025-02-27 16:40:06",
      "modified": "2025-02-27 16:40:06",
      "commits": 1
    }
  ],
  "_score": 2.255272505103306,
  "_indexed": true,
  "_nocasepkg": "smash",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-10-04T11:28:58.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/0d8db1a627933081b7c7c91b2a7a9a65fb483f6dbd3da028362929154d70d3d8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-10-04T11:29:14.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/fc55bca51b64e93f3cf364177f8b9c22cd5f4a048e22adddce79ac25abb6dfc5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-10-04T11:29:13.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/50eb27d57971e2de41d84df6de18962059c9d6083272e1278b95c32f4a30c771",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-10-04T11:29:25.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/7578fc63835dcccf4a3b70f346d0b2bda94d1b067f386ef28f66e1601ec2653e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-10-04T11:29:42.000Z",
      "arch": "emscripten",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/2223d2e6815eeb4d64a495cb1a34d11c3e9940dad17803aa27cd93ff78ed9cc2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-10-04T11:29:57.000Z",
      "arch": "aarch64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/8060c5ec9121d959662812bd8a1005d64bfa38ee57ee4b2fdd551c1b185952f6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-10-04T11:28:30.000Z",
      "arch": "x86_64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/d30ace6844b13418df0a1577445ab49fa2002de347b533dcd1b84574ec30325e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-10-04T11:31:28.000Z",
      "arch": "aarch64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/fe3569326c795775b88e4b00d6809fa3934aa2eeb76d485c7e7133e0bb30466f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-10-04T11:28:26.000Z",
      "arch": "x86_64",
      "commit": "f73c87275840edb5e66e8d389492dbedea8e84af",
      "fileid": "https://r2.ropensci.org/82c6e3e6b8eb7bf14115703042fa813b7029bc76ec80125f7ac741ca262b48ec",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37198534055"
    }
  ]
}