{
  "_id": "6a10243cacfb0bcc41c8db1a",
  "Package": "microbiomeDASim",
  "Type": "Package",
  "Title": "Microbiome Differential Abundance Simulation",
  "Version": "1.27.0",
  "Author": "Justin Williams, Hector Corrada Bravo, Jennifer Tom, Joseph\nNathaniel Paulson",
  "Maintainer": "Justin Williams <williazo@ucla.edu>",
  "Description": "A toolkit for simulating differential microbiome data\ndesigned for longitudinal analyses. Several functional forms\nmay be specified for the mean trend. Observations are drawn\nfrom a multivariate normal model. The objective of this package\nis to be able to simulate data in order to accurately compare\ndifferent longitudinal methods for differential abundance.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.0.2",
  "VignetteBuilder": "knitr",
  "biocViews": "Microbiome, Visualization, Software",
  "BugReports": "https://github.com/williazo/microbiomeDASim/issues",
  "URL": "https://github.com/williazo/microbiomeDASim",
  "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:52 UTC",
  "RemoteUrl": "https://github.com/bioc/microbiomeDASim",
  "RemoteRef": "HEAD",
  "RemoteSha": "aefd984661283df0461ec00c0516f60def40aeab",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 09:52:18 UTC",
    "User": "root"
  },
  "MD5sum": "4f417d8e44d1f387a9747fc26bbebf01",
  "_user": "bioc",
  "_type": "src",
  "_file": "microbiomeDASim_1.27.0.tar.gz",
  "_fileid": "795bc068f4d550b7dbb9afd7f0c058ac96d64505d1dfee09c43b7eadf33b6b47",
  "_filesize": 1758700,
  "_sha256": "795bc068f4d550b7dbb9afd7f0c058ac96d64505d1dfee09c43b7eadf33b6b47",
  "_created": "2026-05-13T09:52:18.000Z",
  "_published": "2026-05-22T09:39:08.453Z",
  "_jobs": [
    {
      "job": 77354292981,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6966972786"
    },
    {
      "job": 77354293114,
      "time": 301,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6967012811"
    },
    {
      "job": 77354293099,
      "time": 314,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6967016015"
    },
    {
      "job": 77354292717,
      "time": 229,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6967328603"
    },
    {
      "job": 77354292820,
      "time": 201,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6967319208"
    },
    {
      "job": 77354292047,
      "time": 271,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6966904013"
    },
    {
      "job": 77354292181,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157458688"
    },
    {
      "job": 77354292840,
      "time": 268,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6966999612"
    },
    {
      "job": 77354292788,
      "time": 278,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6967003484"
    },
    {
      "job": 77354293087,
      "time": 230,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6966986756"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/microbiomeDASim",
  "_commit": {
    "id": "aefd984661283df0461ec00c0516f60def40aeab",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380652
  },
  "_maintainer": {
    "name": "Justin Williams",
    "email": "williazo@ucla.edu",
    "login": "williazo",
    "uuid": 25311057
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "tmvtnorm",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "phyloseq",
      "role": "Imports"
    },
    {
      "package": "metagenomeSeq",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microbiome",
    "visualization",
    "software"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "williazo",
      "count": 44,
      "uuid": 25311057
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 332,
    "source": "https://www.bioconductor.org/packages/stats/bioc/microbiomeDASim"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/williazo/microbiomedasim",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/microbiomeDASim.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/williazo/microbiomedasim",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "gen_norm_microbiome",
    "gen_norm_microbiome_obs",
    "ggplot_spaghetti",
    "mean_trend",
    "mvrnorm_corr_gen",
    "mvrnorm_sim",
    "mvrnorm_sim_obs",
    "simulate2MRexperiment",
    "simulate2phyloseq"
  ],
  "_help": [
    {
      "page": "form_beta_check",
      "title": "Beta Specification Check",
      "topics": [
        "form_beta_check"
      ]
    },
    {
      "page": "gen_norm_microbiome",
      "title": "Generate Longitduinal Differential Abundance from Multivariate Normal",
      "topics": [
        "gen_norm_microbiome"
      ]
    },
    {
      "page": "gen_norm_microbiome_obs",
      "title": "Generate Longitduinal Differential Abundance from Multivariate Normal with Observed Data",
      "topics": [
        "gen_norm_microbiome_obs"
      ]
    },
    {
      "page": "ggplot_spaghetti",
      "title": "Spaghetti Plots using 'ggplot2'",
      "topics": [
        "ggplot_spaghetti"
      ]
    },
    {
      "page": "mean_trend",
      "title": "Function for Generating Various Longitudinal Mean Trends",
      "topics": [
        "mean_trend"
      ]
    },
    {
      "page": "mvrnorm_corr_gen",
      "title": "Generate Multivariate Random Normal Longitudinal Data",
      "topics": [
        "mvrnorm_corr_gen"
      ]
    },
    {
      "page": "mvrnorm_sim",
      "title": "Simulate Microbiome Longitudinal Data from Multivariate Random Normal",
      "topics": [
        "mvrnorm_sim"
      ]
    },
    {
      "page": "mvrnorm_sim_obs",
      "title": "Simulate Microbiome Longitudinal Data from Multivariate Random Normal with Observed Data",
      "topics": [
        "mvrnorm_sim_obs"
      ]
    },
    {
      "page": "simulate2MRexperiment",
      "title": "Convert simulated output to MRexperiment object",
      "topics": [
        "simulate2MRexperiment"
      ]
    },
    {
      "page": "simulate2phyloseq",
      "title": "Convert simulated output to phyloseq object",
      "topics": [
        "simulate2phyloseq"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/microbiomeDASim/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "ape",
    "Biobase",
    "BiocGenerics",
    "biomformat",
    "Biostrings",
    "bitops",
    "caTools",
    "cli",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "digest",
    "farver",
    "foreach",
    "generics",
    "ggplot2",
    "glmnet",
    "glue",
    "gmm",
    "gplots",
    "gtable",
    "gtools",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "metagenomeSeq",
    "mgcv",
    "multtest",
    "mvtnorm",
    "nlme",
    "pbapply",
    "permute",
    "phyloseq",
    "pixmap",
    "pkgconfig",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "reshape2",
    "rlang",
    "S4Vectors",
    "S7",
    "sandwich",
    "scales",
    "Seqinfo",
    "shape",
    "sp",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "tmvtnorm",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "Wrench",
    "XVector",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "microbiomeDASim.Rnw",
      "filename": "microbiomeDASim.pdf",
      "title": "microbiomeDASim",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2019-08-26 17:46:05",
      "modified": "2020-01-15 04:22:11",
      "commits": 6
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "microbiomedasim",
  "_universes": [
    "bioc",
    "williazo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-13T09:55:43.000Z",
      "distro": "noble",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "3e533486c67ed9d3edce701fe96d6b20ff85b47054896a3c97da2fc8d8561ee8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-13T09:55:54.000Z",
      "distro": "noble",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "256238f2249acc34fb44c046663865faa5db330e1f755c405a20f7d82aaffcf1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-13T10:10:58.000Z",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "ca8b146195000b05b0a9f50202b9d8defcada884cb9c0a4cf40e158229785902",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-13T10:10:23.000Z",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "0ce759d9e62ae6937cfe0ec8ff34c2f174401117a0cf0010c46252b290cf66aa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-13T09:54:38.000Z",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "2bb283f302998a893b8c82fbf3ed13154e60fe3f718db6bd06072f4259e5ff8a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-13T09:53:56.000Z",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "58438dd43ef169c65a941c6ab76881a8509eb933a8a681aa020d781073e8bb05",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-13T09:54:04.000Z",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "c136d319be609420db41aac12f9f9008f8da1fa201f6e27d7d50fe56c31557cc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-05-22T09:38:44.000Z",
      "commit": "aefd984661283df0461ec00c0516f60def40aeab",
      "fileid": "5fea2bfe3c6172c195d626ef615690d26d7ae497c7bcfec4cec9ccc477c22c0e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25791457947"
    }
  ]
}