{
  "_id": "6ae3175f327abcdf86866508",
  "Package": "PCMBaseCpp",
  "Type": "Package",
  "Title": "Fast Likelihood Calculation for Phylogenetic Comparative Models",
  "Version": "0.1.12",
  "Authors@R": "c(person(\"Venelin\", \"Mitov\", email = \"vmitov@gmail.com\",\ncomment = '<a href=\"https://venelin.github.io\">venelin.github.io</a>',\nrole = c(\"aut\", \"cre\", \"cph\")))",
  "Maintainer": "Venelin Mitov <vmitov@gmail.com>",
  "Description": "Provides a C++ backend for multivariate phylogenetic\ncomparative models implemented in the R-package 'PCMBase'. Can\nbe used in combination with 'PCMBase' to enable fast and\nparallel likelihood calculation. Implements the pruning\nlikelihood calculation algorithm described in Mitov et al.\n(2020) <doi:10.1016/j.tpb.2019.11.005>. Uses the 'SPLITT' C++\nlibrary for parallel tree traversal described in Mitov and\nStadler (2018) <doi:10.1111/2041-210X.13136>.",
  "Encoding": "UTF-8",
  "License": "GPL (>= 3.0)",
  "LazyData": "true",
  "ByteCompile": "yes",
  "NeedsCompilation": "yes",
  "URL": "https://github.com/venelin/PCMBaseCpp, https://venelin.github.io",
  "BugReports": "https://github.com/venelin/PCMBaseCpp/issues",
  "VignetteBuilder": "knitr, rmarkdown",
  "RoxygenNote": "7.3.2",
  "Packaged": {
    "Date": "2026-10-29 09:45:32 UTC",
    "User": "root"
  },
  "Author": "Venelin Mitov [aut, cre, cph] (<a\nhref=\"https://venelin.github.io\">venelin.github.io</a>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-02-28 21:38:52 UTC",
  "RemoteUrl": "https://github.com/cran/PCMBaseCpp",
  "RemoteRef": "HEAD",
  "RemoteSha": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
  "_user": "cran",
  "_type": "src",
  "_file": "PCMBaseCpp_0.1.12.tar.gz",
  "_fileid": "https://r2.ropensci.org/16155832429a36f1d270e995d5a6e6c306a8962c513bd400523df965cd597478",
  "_filesize": 1156309,
  "_sha256": "16155832429a36f1d270e995d5a6e6c306a8962c513bd400523df965cd597478",
  "_expires": "2027-02-06T09:52:29.000Z",
  "_created": "2026-10-29T09:45:32.000Z",
  "_published": "2026-10-29T09:52:31.162Z",
  "_upstream": "https://github.com/cran/PCMBaseCpp",
  "_status": "success",
  "_maintainer": {
    "name": "Venelin Mitov",
    "email": "vmitov@gmail.com",
    "login": "venelin",
    "description": "PK/PD Modeling Consultant and Software Architect",
    "uuid": 15032497
  },
  "_jobs": [
    {
      "job": 123374482052,
      "time": 233,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12887633357"
    },
    {
      "job": 123374482534,
      "time": 212,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12887712709"
    },
    {
      "job": 123374482131,
      "time": 230,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12888525054"
    },
    {
      "job": 123374482272,
      "time": 204,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12887757179"
    },
    {
      "job": 123372256844,
      "time": 302,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12887059824"
    },
    {
      "job": 123374482051,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12887996517"
    },
    {
      "job": 123374482164,
      "time": 335,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12887049997"
    },
    {
      "job": 123374482197,
      "time": 277,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12887179622"
    },
    {
      "job": 123374482396,
      "time": 319,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12887976806"
    },
    {
      "job": 123374482138,
      "time": 311,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12888026801"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180",
  "_commit": {
    "id": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
    "author": "Venelin Mitov <vmitov@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.12\n",
    "time": 1772314732
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "PCMBase",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.1.12",
      "date": "2026-02-28"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "venelin",
      "count": 8,
      "uuid": 15032497
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 634,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 444,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PCMBaseCpp"
  },
  "_devurl": "https://github.com/venelin/pcmbasecpp",
  "_searchresults": 96,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PCMBaseCpp.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/venelin/pcmbasecpp",
  "_realowner": "venelin",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.5",
      "date": "2019-10-06"
    },
    {
      "version": "0.1.6",
      "date": "2019-11-11"
    },
    {
      "version": "0.1.7",
      "date": "2019-11-21"
    },
    {
      "version": "0.1.8",
      "date": "2020-02-23"
    },
    {
      "version": "0.1.9",
      "date": "2020-03-23"
    },
    {
      "version": "0.1.10",
      "date": "2025-04-27"
    },
    {
      "version": "0.1.11",
      "date": "2025-05-04"
    },
    {
      "version": "0.1.12",
      "date": "2026-02-28"
    }
  ],
  "_exports": [
    "BenchmarkRvsCpp",
    "MiniBenchmarkRvsCpp",
    "PCMBaseCppIsADevRelease",
    "PCMInfoCpp",
    "PCMParamGetFullVector",
    "PCMTreePreorderCpp"
  ],
  "_datasets": [
    {
      "name": "benchmarkData",
      "title": "Data for performing a benchmark",
      "object": "benchmarkData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "tree",
        "model",
        "X",
        "ll",
        "modelOU",
        "llOU",
        "modelBM",
        "llBM"
      ],
      "rows": 4,
      "table": false,
      "tojson": false
    },
    {
      "name": "benchmarkResults",
      "title": "Results from running a performance benchmark on a personal computer including the time for parameter transformation",
      "object": "benchmarkResults",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "k",
        "modelType",
        "options",
        "N",
        "R",
        "mapping",
        "type",
        "PCMBase.Lmr.mode",
        "logLik",
        "logLikCpp",
        "timeR",
        "timeCpp",
        "IdRun"
      ],
      "rows": 168,
      "table": false,
      "tojson": true
    },
    {
      "name": "benchmarkResultsNoTransform",
      "title": "Results from running a performance benchmark on a personal computer excluding the time for parameter transformation",
      "object": "benchmarkResultsNoTransform",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "k",
        "modelType",
        "options",
        "N",
        "R",
        "mapping",
        "type",
        "PCMBase.Lmr.mode",
        "logLik",
        "logLikCpp",
        "timeR",
        "timeCpp",
        "IdRun"
      ],
      "rows": 168,
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "benchmarkData",
      "title": "Data for performing a benchmark",
      "topics": [
        "benchmarkData"
      ]
    },
    {
      "page": "benchmarkResults",
      "title": "Results from running a performance benchmark on a personal computer including the time for parameter transformation",
      "topics": [
        "benchmarkResults"
      ]
    },
    {
      "page": "benchmarkResultsNoTransform",
      "title": "Results from running a performance benchmark on a personal computer excluding the time for parameter transformation",
      "topics": [
        "benchmarkResultsNoTransform"
      ]
    },
    {
      "page": "BenchmarkRvsCpp",
      "title": "A log-likelihood calculation time comparison for different numbers of traits and option-sets",
      "topics": [
        "BenchmarkRvsCpp"
      ]
    },
    {
      "page": "MiniBenchmarkRvsCpp",
      "title": "Evaluate the likelihood calculation times for example trees and data",
      "topics": [
        "MiniBenchmarkRvsCpp"
      ]
    },
    {
      "page": "PCListInt",
      "title": "Converts the logical matrix pc into a list of vectors denoting the (0-based) TRUE-indices in each column",
      "topics": [
        "PCListInt"
      ]
    },
    {
      "page": "PCMBaseCppIsADevRelease",
      "title": "Check if the PCMBaseCpp version correpsonds to a dev release",
      "topics": [
        "PCMBaseCppIsADevRelease"
      ]
    },
    {
      "page": "PCMInfoCpp",
      "title": "A S3 generic for creating C++ backend objects given a model, data and a tree.",
      "topics": [
        "PCMInfoCpp"
      ]
    },
    {
      "page": "PCMParamGetFullVector",
      "title": "Get a vector with all model parameters unrolled",
      "topics": [
        "PCMParamGetFullVector"
      ]
    },
    {
      "page": "PCMTreePreorderCpp",
      "title": "Fast preorder of the edges in a tree",
      "topics": [
        "PCMTreePreorderCpp"
      ]
    }
  ],
  "_readme": "https://github.com/cran/PCMBaseCpp/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ape",
    "cli",
    "cpp11",
    "data.table",
    "digest",
    "expm",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "Matrix",
    "mvtnorm",
    "nlme",
    "PCMBase",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr",
    "xtable"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "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": "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"
    }
  ],
  "_vignettes": [
    {
      "source": "PCMBaseCpp.Rmd",
      "filename": "PCMBaseCpp.html",
      "title": "Getting started with the PCMBaseCpp R-package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How to use the package?",
        "Passing the function PCMInfoCpp as a metaI argument of PCMLik and/or PCMCreateLikelihood",
        "Passing the meta-information object returned by PCMInfoCpp as a metaI argument of PCMLik and PCMCreateLikelihood"
      ],
      "created": "2019-11-21 15:10:05",
      "modified": "2026-02-28 21:38:52",
      "commits": 3
    }
  ],
  "_score": 3.681241237375587,
  "_indexed": false,
  "_nocasepkg": "pcmbasecpp",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://venelin.r-universe.dev/PCMBaseCpp",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.12",
      "date": "2026-10-29T09:48:01.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/2eedc090a9cbeaca62f6d509fcdecab61c2f2af802312a8801539eff1527e497",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.12",
      "date": "2026-10-29T09:48:14.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/14726c6f2da8efdafef90db3bd2dd3a4642d243df6d1cac1c29d8c264f451189",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.12",
      "date": "2026-10-29T09:47:59.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/14db0dff20476d7ec41b2092bd194334331af06bad72891068930b1dc12e035a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.12",
      "date": "2026-10-29T09:48:14.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/dcf0d300561636ea0c4b0ea5bd0b0bc85ebe2640e7b20fa62a27cb31ec279a6c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.12",
      "date": "2026-10-29T09:48:14.000Z",
      "arch": "emscripten",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/3cbf485b32abc5d4247be16689c80888bda135f520115e8b5574e7e3cb2cdb38",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.12",
      "date": "2026-10-29T09:49:14.000Z",
      "arch": "aarch64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/3377964e6054cfeb00d2f6dd3023949193c7f78e320eb209b73ec44470117967",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.12",
      "date": "2026-10-29T09:47:28.000Z",
      "arch": "x86_64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/b34f7c05e73976e07ffbfb4ac18c73ae2f856e71dd196e41f3b5079e43298683",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.12",
      "date": "2026-10-29T09:49:09.000Z",
      "arch": "aarch64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/ecd6252366babdac979d58bec02a8e3e6fdec73456b21b45e6794a2b96d76d8a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.12",
      "date": "2026-10-29T09:47:41.000Z",
      "arch": "x86_64",
      "commit": "0a9a941dff289d365ddca92080b632c8ac2c3ae8",
      "fileid": "https://r2.ropensci.org/0470acd36528021f8e50651a9f1ffa013ea60afa800862e5c57898fbd525d017",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/40851567180"
    }
  ]
}