{
  "_id": "6a2130ddcd65a98ecbd25230",
  "Package": "asmbPLS",
  "Type": "Package",
  "Title": "Predicting and Classifying Patient Phenotypes with Multi-Omics\nData",
  "Version": "1.0.1",
  "Date": "2023-11-28",
  "Authors@R": "c(\nperson(\"Runzhi\", \"Zhang\", role = c(\"aut\", \"cre\"), email = \"runzhi.zhang@ufl.edu\"),\nperson(\"Susmita\", \"Datta\", role = c(\"aut\", \"ths\"), email = \"susmita.datta@ufl.edu\"))",
  "Description": "Adaptive Sparse Multi-block Partial Least Square, a\nsupervised algorithm, is an extension of the Sparse Multi-block\nPartial Least Square, which allows different quantiles to be\nused in different blocks of different partial least square\ncomponents to decide the proportion of features to be retained.\nThe best combinations of quantiles can be chosen from a set of\nuser-defined quantiles combinations by cross-validation. By\ndoing this, it enables us to do the feature selection for\ndifferent blocks, and the selected features can then be further\nused to predict the outcome. For example, in biomedical\napplications, clinical covariates plus different types of omics\ndata such as microbiome, metabolome, mRNA data, methylation\ndata, copy number variation data might be predictive for\npatients outcome such as survival time or response to therapy.\nDifferent types of data could be put in different blocks and\nalong with survival time to fit the model. The fitted model can\nthen be used to predict the survival for the new samples with\nthe corresponding clinical covariates and omics data. In\naddition, Adaptive Sparse Multi-block Partial Least Square\nDiscriminant Analysis is also included, which extends Adaptive\nSparse Multi-block Partial Least Square for classifying the\ncategorical outcome.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "Author": "Runzhi Zhang [aut, cre], Susmita Datta [aut, ths]",
  "Maintainer": "Runzhi Zhang <runzhi.zhang@ufl.edu>",
  "Config/pak/sysreqs": "cmake make libicu-dev",
  "Repository": "https://runzhiz.r-universe.dev",
  "Date/Publication": "2024-03-21 14:04:53 UTC",
  "RemoteUrl": "https://github.com/runzhiz/asmbpls",
  "RemoteRef": "HEAD",
  "RemoteSha": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-04 07:51:06 UTC",
    "User": "root"
  },
  "MD5sum": "7bf8666f1d68d8c2c201b35e11727d5d",
  "_user": "runzhiz",
  "_type": "src",
  "_file": "asmbPLS_1.0.1.tar.gz",
  "_fileid": "366286bed32d0c7b43c38b3bfe71e8ce6166d0cf2eb06a57053c948e4a404125",
  "_filesize": 1658998,
  "_sha256": "366286bed32d0c7b43c38b3bfe71e8ce6166d0cf2eb06a57053c948e4a404125",
  "_created": "2026-06-04T07:51:06.000Z",
  "_published": "2026-06-04T08:01:33.427Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79474172120,
      "time": 272,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7406043835"
    },
    {
      "job": 79474171968,
      "time": 248,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7406035370"
    },
    {
      "job": 79474172132,
      "time": 275,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7406044701"
    },
    {
      "job": 79474172019,
      "time": 226,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7406028282"
    },
    {
      "job": 79474171997,
      "time": 200,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7406010791"
    },
    {
      "job": 79474171979,
      "time": 447,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7406093077"
    },
    {
      "job": 79474172029,
      "time": 245,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7406026537"
    },
    {
      "job": 79474172003,
      "time": 438,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7406090229"
    },
    {
      "job": 79472995342,
      "time": 457,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7405952960"
    },
    {
      "job": 79474172034,
      "time": 190,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7406016260"
    },
    {
      "job": 79474172072,
      "time": 282,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7406045946"
    },
    {
      "job": 79474172014,
      "time": 266,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7406041045"
    },
    {
      "job": 79474171962,
      "time": 279,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7406045663"
    }
  ],
  "_buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/runzhiz/asmbpls",
  "_commit": {
    "id": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
    "author": "Runzhi Zhang <runzhi.zhang@ufl.edu>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
    "time": 1711029893
  },
  "_maintainer": {
    "name": "Runzhi Zhang",
    "email": "runzhi.zhang@ufl.edu",
    "login": "runzhiz",
    "description": "Runzhi Zhang's projects",
    "uuid": 71341239
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.8",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "runzhiz",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "runzhiz",
      "count": 92,
      "uuid": 71341239
    }
  ],
  "_userbio": {
    "uuid": 71341239,
    "type": "user",
    "name": "Runzhi Zhang",
    "description": "Runzhi Zhang's projects"
  },
  "_downloads": {
    "count": 251,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/asmbPLS"
  },
  "_devurl": "https://github.com/runzhiz/asmbpls",
  "_searchresults": 20,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/asmbPLS.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/runzhiz/asmbpls",
  "_realowner": "runzhiz",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2023-04-17"
    }
  ],
  "_exports": [
    "asmbPLS.cv",
    "asmbPLS.fit",
    "asmbPLS.predict",
    "asmbPLSDA.cv",
    "asmbPLSDA.fit",
    "asmbPLSDA.predict",
    "asmbPLSDA.vote.fit",
    "asmbPLSDA.vote.predict",
    "mbPLS.fit",
    "meanimp",
    "plotCor",
    "plotPLS",
    "plotRelevance",
    "quantileComb",
    "to.categorical"
  ],
  "_datasets": [
    {
      "name": "asmbPLS.example",
      "title": "Example data for asmbPLS algorithm",
      "object": "asmbPLS.example",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "asmbPLSDA.example",
      "title": "Example data for asmbPLS-DA algorithm",
      "object": "asmbPLSDA.example",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "asmbPLS-package",
      "title": "Predicting and Classifying Patient Phenotypes with Multi-Omics Data",
      "topics": [
        "asmbPLS-package",
        "asmbPLS"
      ]
    },
    {
      "page": "asmbPLS.cv",
      "title": "Cross-validation for asmbPLS to find the best combinations of quantiles for prediction",
      "topics": [
        "asmbPLS.cv"
      ]
    },
    {
      "page": "asmbPLS.example",
      "title": "Example data for asmbPLS algorithm",
      "topics": [
        "asmbPLS.example"
      ]
    },
    {
      "page": "asmbPLS.fit",
      "title": "asmbPLS for block-structured data",
      "topics": [
        "asmbPLS.fit"
      ]
    },
    {
      "page": "asmbPLS.predict",
      "title": "Using an asmbPLS model for prediction of new samples",
      "topics": [
        "asmbPLS.predict"
      ]
    },
    {
      "page": "asmbPLSDA.cv",
      "title": "Cross-validation for asmbPLS-DA to find the best combinations of quantiles for classification",
      "topics": [
        "asmbPLSDA.cv"
      ]
    },
    {
      "page": "asmbPLSDA.example",
      "title": "Example data for asmbPLS-DA algorithm",
      "topics": [
        "asmbPLSDA.example"
      ]
    },
    {
      "page": "asmbPLSDA.fit",
      "title": "asmbPLS-DA for block-structured data",
      "topics": [
        "asmbPLSDA.fit"
      ]
    },
    {
      "page": "asmbPLSDA.predict",
      "title": "Using an asmbPLS-DA model for classification of new samples",
      "topics": [
        "asmbPLSDA.predict"
      ]
    },
    {
      "page": "asmbPLSDA.vote.fit",
      "title": "asmbPLS-DA vote model fit",
      "topics": [
        "asmbPLSDA.vote.fit"
      ]
    },
    {
      "page": "asmbPLSDA.vote.predict",
      "title": "Using an asmbPLS-DA vote model for classification of new samples",
      "topics": [
        "asmbPLSDA.vote.predict"
      ]
    },
    {
      "page": "mbPLS.fit",
      "title": "mbPLS for block-structured data",
      "topics": [
        "mbPLS.fit"
      ]
    },
    {
      "page": "meanimp",
      "title": "Mean imputation for the survival time",
      "topics": [
        "meanimp"
      ]
    },
    {
      "page": "plotCor",
      "title": "Graphical output for the asmbPLS-DA framework",
      "topics": [
        "plotCor"
      ]
    },
    {
      "page": "plotPLS",
      "title": "PLS plot for asmbPLS-DA",
      "topics": [
        "plotPLS"
      ]
    },
    {
      "page": "plotRelevance",
      "title": "Relevance plot for asmbPLS-DA",
      "topics": [
        "plotRelevance"
      ]
    },
    {
      "page": "quantileComb",
      "title": "Create the quantile combination set for asmbPLS and asmbPLS-DA",
      "topics": [
        "quantileComb"
      ]
    },
    {
      "page": "to.categorical",
      "title": "Converts a class vector to a binary class matrix",
      "topics": [
        "to.categorical"
      ]
    }
  ],
  "_readme": "https://github.com/runzhiz/asmbpls/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "boot",
    "broom",
    "car",
    "carData",
    "cli",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "Deriv",
    "doBy",
    "dplyr",
    "farver",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "polynom",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rstatix",
    "S7",
    "scales",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "asmbPLS_tutorial.Rmd",
      "filename": "asmbPLS_tutorial.html",
      "title": "Tutorial for asmbPLS package",
      "author": "Runzhi Zhang, Ph.D.Department of BiostatisticsUniversity of Florida",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Requirements",
        "asmbPLS",
        "Example data for asmbPLS algorithm",
        "Cross Validation",
        "Model Fit",
        "Prediction",
        "asmbPLS-DA",
        "Example data for asmbPLS-DA algorithm",
        "Classification",
        "Vote Function",
        "Visualization",
        "Correlation between different blocks",
        "PLS plot",
        "Relevance plot"
      ],
      "created": "2023-03-30 23:03:10",
      "modified": "2023-04-11 00:42:38",
      "commits": 4
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "asmbpls",
  "_universes": [
    "runzhiz"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-04T07:55:13.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "5941ff12154ec609d3403dd94a3c48fd8316c659f958439aa89b1e4a7ed75a65",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-04T07:55:07.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "a4b2a039336dcb4c0292f980d78203e52d8098e723bb8f451e042b65be7b141f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-04T07:55:18.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "a76ddaa548691e915d50642ccb0e70ccc0a7b9b63431e63b4d58af52e0770a83",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-04T07:55:06.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "ea9846a91dfad5a5b60840e22b0c45d6b7acf6d20e042a716463a1d0110ce4eb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-04T07:54:56.000Z",
      "arch": "aarch64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "fa5e166be2850c3924d760077390cde3386055e9340d2d241dc0813e0e10b459",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-04T07:57:09.000Z",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "f5c167e3199acdfbad28729f4f571aabb604339c7830576f0f468406bf63930b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-04T07:55:08.000Z",
      "arch": "aarch64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "eea3998669c89aa38c241f127161e3faf30ca936ed8169bf1720865ea05d1bf9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-04T07:56:13.000Z",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "21bedf5973977a55663f555ffecff556fb1a0b89d2c713a6fcac249d9c964cdb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-06-04T07:55:00.000Z",
      "arch": "emscripten",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "5c757a7b1147ffa5274fe47a96cca309017af8af737340ad020113a2f8c9e0c2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-04T07:54:15.000Z",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "c7925f97ae103d79fa07a85b42f7a98fac87840726d5f35a2a6e4a83ec23334b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-04T07:54:23.000Z",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "d4f843b7c241a6689af8702fe01d03d9230378c28c7114de42b47662c3a816e3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-04T07:54:10.000Z",
      "arch": "x86_64",
      "commit": "2c60ca2e2bad5df79fad1af8fa83e8442d890832",
      "fileid": "bebb2ce7e0ec3b85c868fe4bfaeb1b8d7fb65ab47bff8e9ed2d0349d64acde8a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/runzhiz/actions/runs/26938203709"
    }
  ]
}