{
  "_id": "6acc9d74a14063b82c3a6dfd",
  "Package": "BioMoR",
  "Type": "Package",
  "Title": "Bioinformatics Modeling with Recursion and Autoencoder-Based\nEnsemble",
  "Version": "0.1.0",
  "Authors@R": "person(given = \"MD.\",\nfamily = \"Arshad\",\nemail = \"arshad10867c@gmail.com\",\nrole = c(\"aut\", \"cre\"))",
  "Description": "Provides tools for bioinformatics modeling using recursive\ntransformer-inspired architectures, autoencoders, random\nforests, XGBoost, and stacked ensemble models. Includes\nutilities for cross-validation, calibration, benchmarking, and\nthreshold optimization in predictive modeling workflows.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "make libicu-dev",
  "Repository": "https://sulkysubject37.r-universe.dev",
  "Date/Publication": "2025-12-14 09:14:13 UTC",
  "RemoteUrl": "https://github.com/sulkysubject37/biomor",
  "RemoteRef": "HEAD",
  "RemoteSha": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-12 08:36:10 UTC",
    "User": "root"
  },
  "Author": "MD. Arshad [aut, cre]",
  "Maintainer": "MD. Arshad <arshad10867c@gmail.com>",
  "_user": "sulkysubject37",
  "_type": "src",
  "_file": "BioMoR_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c3c6a8554255a82da8c8f38d1230c41327e6f5e7b2c7574a91acabfbf4707157",
  "_filesize": 103973,
  "_sha256": "c3c6a8554255a82da8c8f38d1230c41327e6f5e7b2c7574a91acabfbf4707157",
  "_expires": "2027-01-20T08:42:25.000Z",
  "_created": "2026-10-12T08:36:10.000Z",
  "_published": "2026-10-12T08:42:27.917Z",
  "_buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114728931922,
      "time": 254,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11736690056"
    },
    {
      "job": 114728931866,
      "time": 196,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11736190239"
    },
    {
      "job": 114728931913,
      "time": 113,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11735224815"
    },
    {
      "job": 114728932058,
      "time": 176,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11736375125"
    },
    {
      "job": 114727889314,
      "time": 180,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11735244329"
    },
    {
      "job": 114728931827,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11735429585"
    },
    {
      "job": 114728932094,
      "time": 244,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11735674909"
    },
    {
      "job": 114728932023,
      "time": 292,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11736590244"
    },
    {
      "job": 114728931986,
      "time": 329,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11736110709"
    }
  ],
  "_upstream": "https://github.com/sulkysubject37/biomor",
  "_commit": {
    "id": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
    "author": "MD. Arshad <98695355+Sulkysubject37@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update citation for BioMoR package version",
    "time": 1765703653
  },
  "_maintainer": {
    "name": "MD. Arshad",
    "email": "arshad10867c@gmail.com",
    "login": "sulkysubject37",
    "twitter": "@sulkysubject",
    "description": "Enthusiast, bioinformatician, musician, literature nerd, and an average photographer",
    "uuid": 98695355
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "caret",
      "role": "Imports"
    },
    {
      "package": "recipes",
      "role": "Imports"
    },
    {
      "package": "themis",
      "role": "Imports"
    },
    {
      "package": "xgboost",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "pROC",
      "role": "Imports"
    },
    {
      "package": "randomForest",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "PRROC",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    },
    {
      "package": "yardstick",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "sulkysubject37",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-50",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "autoencoder",
    "benchmarking",
    "bioinformatics",
    "calibration",
    "deep-learning",
    "ensemble-learning",
    "feature",
    "machine-learning",
    "mixture-of-recursions"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "sulkysubject37",
      "count": 5,
      "uuid": 98695355
    }
  ],
  "_userbio": {
    "uuid": 98695355,
    "type": "user",
    "name": "MD. Arshad",
    "followers": 5,
    "description": "Enthusiast, bioinformatician, musician, literature nerd, and an average photographer"
  },
  "_downloads": {
    "count": 274,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BioMoR"
  },
  "_devurl": "https://github.com/sulkysubject37/biomor",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BioMoR.html",
    "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/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/sulkysubject37/biomor",
  "_realowner": "sulkysubject37",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-10-03"
    },
    {
      "version": "0.1.1",
      "date": "2025-12-11"
    }
  ],
  "_exports": [
    "biomor_benchmark",
    "brier_score",
    "compute_f1_threshold",
    "get_cv_control",
    "get_embeddings",
    "prepare_model_data",
    "train_autoencoder",
    "train_rf",
    "train_xgb_caret"
  ],
  "_help": [
    {
      "page": "biomor_benchmark",
      "title": "Benchmark a trained model",
      "topics": [
        "biomor_benchmark"
      ]
    },
    {
      "page": "biomor_run_pipeline",
      "title": "Run full BioMoR pipeline",
      "topics": [
        "biomor_run_pipeline"
      ]
    },
    {
      "page": "brier_score",
      "title": "Compute Brier Score",
      "topics": [
        "brier_score"
      ]
    },
    {
      "page": "calibrate_model",
      "title": "Calibrate model probabilities",
      "topics": [
        "calibrate_model"
      ]
    },
    {
      "page": "compute_f1_threshold",
      "title": "Compute optimal threshold for maximum F1 score",
      "topics": [
        "compute_f1_threshold"
      ]
    },
    {
      "page": "get_cv_control",
      "title": "Get caret cross-validation control",
      "topics": [
        "get_cv_control"
      ]
    },
    {
      "page": "get_embeddings",
      "title": "Get Embeddings from Autoencoder (stub)",
      "topics": [
        "get_embeddings"
      ]
    },
    {
      "page": "prepare_model_data",
      "title": "Prepare dataset for modeling",
      "topics": [
        "prepare_model_data"
      ]
    },
    {
      "page": "train_autoencoder",
      "title": "Train Autoencoder (stub)",
      "topics": [
        "train_autoencoder"
      ]
    },
    {
      "page": "train_biomor",
      "title": "Train BioMoR Autoencoder",
      "topics": [
        "train_biomor"
      ]
    },
    {
      "page": "train_rf",
      "title": "Train a Random Forest model with caret",
      "topics": [
        "train_rf"
      ]
    },
    {
      "page": "train_xgb_caret",
      "title": "Train an XGBoost model with caret",
      "topics": [
        "train_xgb_caret"
      ]
    }
  ],
  "_readme": "https://github.com/sulkysubject37/biomor/raw/HEAD/README.md",
  "_rundeps": [
    "caret",
    "class",
    "cli",
    "clock",
    "codetools",
    "cpp11",
    "data.table",
    "diagram",
    "digest",
    "dplyr",
    "e1071",
    "farver",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "ipred",
    "isoband",
    "iterators",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "ModelMetrics",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "pillar",
    "pkgconfig",
    "plyr",
    "pROC",
    "prodlim",
    "progressr",
    "proxy",
    "purrr",
    "R6",
    "RANN",
    "RColorBrewer",
    "Rcpp",
    "recipes",
    "reshape2",
    "rlang",
    "ROSE",
    "rpart",
    "S7",
    "scales",
    "shape",
    "sparsevctrs",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "themis",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xgboost"
  ],
  "_vignettes": [
    {
      "source": "biomor-autoencoder.Rmd",
      "filename": "biomor-autoencoder.html",
      "title": "BioMoR Autoencoder",
      "engine": "knitr::rmarkdown",
      "headings": [
        "title: \"BioMoR Autoencoder and Embeddings\"output: rmarkdown::html_vignettevignette: >%\\VignetteIndexEntry"
      ],
      "created": "2025-09-21 09:20:09",
      "modified": "2025-09-21 09:20:09",
      "commits": 1
    },
    {
      "source": "biomor-benchmarking.Rmd",
      "filename": "biomor-benchmarking.html",
      "title": "BioMoR Benchmarking",
      "engine": "knitr::rmarkdown",
      "headings": [
        "title: \"BioMoR Benchmarking Tutorial\"output: rmarkdown::html_vignettevignette: >%\\VignetteIndexEntry"
      ],
      "created": "2025-09-21 09:20:09",
      "modified": "2025-09-21 09:20:09",
      "commits": 1
    },
    {
      "source": "biomor-intro.Rmd",
      "filename": "biomor-intro.html",
      "title": "Introduction to BioMoR",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2025-09-21 09:20:09",
      "modified": "2025-09-21 09:20:09",
      "commits": 1
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "biomor",
  "_universes": [
    "sulkysubject37"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-12T08:39:18.000Z",
      "distro": "resolute",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/f683629f785705c63be37b7cbdae7cc78600bdd59f8c7e4f379a9fe397d48496",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-10-12T08:38:25.000Z",
      "distro": "resolute",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/3fa39e7cb14f7b8a6ec254048d4138a82d91894fd5f2b9f5f94425fad380b571",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-12T08:37:47.000Z",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/3c3c44114da62c599ffc26c214611aa08529f03eb610e813b8f5bae4f3346319",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-10-12T08:38:13.000Z",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/29dde3687244c65392a7e121a49203abccd3dc4675f422482997f2dea0517b3e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-10-12T08:38:39.000Z",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/ff9c6e8b2fefe57c167749380eaafbe133e87041fe6893a0c2e7fe19c3bf9112",
      "status": "success",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-12T08:37:34.000Z",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/e5b49e19a651272adcc79aaf02c1e49d31892c7bb0a88ee5cc82897dbde5d416",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-12T08:37:42.000Z",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/10d304cd517e38e88867924901fe1c83b493b4c53f456aaddc1b4e72c231a18a",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-10-12T08:37:30.000Z",
      "commit": "d6f15437d13b82e6ad5596c66fc7b2e8bfbdef7f",
      "fileid": "https://r2.ropensci.org/851668387f2cdc57e3bb9231977d485f5f34ea9c5c77c3daba4243250813046a",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/sulkysubject37/actions/runs/38224265474"
    }
  ]
}