{
  "_id": "6ada6fd9c9cc1e56bbac4ecc",
  "Package": "miaTime",
  "Type": "Package",
  "Title": "Microbiome Time Series Analysis",
  "Version": "1.3.2",
  "Authors@R": "c(person(given = \"Leo\", family = \"Lahti\", role = c(\"aut\"),\nemail = \"leo.lahti@iki.fi\",\ncomment = c(ORCID = \"0000-0001-5537-637X\")),\nperson(given = \"Tuomas\", family = \"Borman\", role = c(\"aut\", \"cre\"),\nemail = \"tuomas.v.borman@utu.fi\",\ncomment = c(ORCID = \"0000-0002-8563-8884\")),\nperson(given = \"Yagmur\", family = \"Simsek\", role = c(\"aut\"),\nemail = \"yagmur.simsek@hsrw.org\"),\nperson(given = \"Sudarshan\", family = \"Shetty\", role = c(\"ctb\"),\nemail = \"sudarshanshetty9@gmail.com\"),\nperson(given = \"Chouaib\", family = \"Benchraka\", role = c(\"ctb\")),\nperson(given = \"Muluh\", family = \"Muluh\", role = c(\"ctb\")),\nperson(given = \"Ali\", family = \"Hajj\", role = c(\"ctb\"))\n)",
  "Description": "The `miaTime` package provides tools for microbiome time\nseries analysis based on (Tree)SummarizedExperiment\ninfrastructure.",
  "biocViews": "Microbiome, Software, Sequencing",
  "License": "Artistic-2.0 | file LICENSE",
  "URL": "https://github.com/microbiome/miaTime",
  "BugReports": "https://github.com/microbiome/miaTime/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libglpk-dev make libgsl0-dev libicu-dev\nlibuv1-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-22 13:27:03 UTC",
  "RemoteUrl": "https://github.com/bioc/miaTime",
  "RemoteRef": "HEAD",
  "RemoteSha": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-22 19:33:52 UTC",
    "User": "root"
  },
  "Author": "Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>),\nTuomas Borman [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8563-8884>),\nYagmur Simsek [aut],\nSudarshan Shetty [ctb],\nChouaib Benchraka [ctb],\nMuluh Muluh [ctb],\nAli Hajj [ctb]",
  "Maintainer": "Tuomas Borman <tuomas.v.borman@utu.fi>",
  "_user": "bioc",
  "_type": "src",
  "_file": "miaTime_1.3.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/8f9385f0a7a26df95cf19b041f8d8a3965c077447907d52e6f155d7dfa2d326a",
  "_filesize": 6859281,
  "_sha256": "8f9385f0a7a26df95cf19b041f8d8a3965c077447907d52e6f155d7dfa2d326a",
  "_expires": "2027-01-30T20:19:34.000Z",
  "_created": "2026-10-22T19:33:52.000Z",
  "_published": "2026-10-22T20:19:36.964Z",
  "_upstream": "https://github.com/bioc/miaTime",
  "_status": "success",
  "_maintainer": {
    "name": "Tuomas Borman",
    "email": "tuomas.v.borman@utu.fi",
    "orcid": "0000-0002-8563-8884"
  },
  "_jobs": [
    {
      "job": 120042800993,
      "time": 232,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12452758487"
    },
    {
      "job": 120042801284,
      "time": 768,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12454281565"
    },
    {
      "job": 120042801303,
      "time": 522,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12453621404"
    },
    {
      "job": 120042801142,
      "time": 313,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12456420577"
    },
    {
      "job": 120042801065,
      "time": 449,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12456266020"
    },
    {
      "job": 120038452464,
      "time": 495,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12451649734"
    },
    {
      "job": 120042800996,
      "time": 168,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12452568996"
    },
    {
      "job": 120042801123,
      "time": 335,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12452469721"
    },
    {
      "job": 120042801322,
      "time": 369,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12453910789"
    },
    {
      "job": 120042801341,
      "time": 492,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12454185725"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499",
  "_commit": {
    "id": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
    "author": "Muluh <127390183+0xMuluh@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "add getSurvival (#112)\n\nSigned-off-by: Daena Rys <rysdaena8@gmail.com>\nCo-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>\nCo-authored-by: Tuomas Borman <tvborm@utu.fi>",
    "time": 1792675623
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "mia",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "TreeSummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "lubridate",
      "role": "Suggests"
    },
    {
      "package": "miaViz",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "scater",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "vegan",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-40",
      "n": 1
    },
    {
      "week": "2026-43",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.3.1",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.2.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "microbiome",
    "software",
    "sequencing"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "antagomir",
      "count": 103,
      "uuid": 1228382
    },
    {
      "user": "yagmursimsekk",
      "count": 67,
      "uuid": 55834139
    },
    {
      "user": "0xmuluh",
      "count": 20,
      "uuid": 127390183
    },
    {
      "user": "tuomasborman",
      "count": 17,
      "uuid": 60338854
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "microsud",
      "count": 4,
      "uuid": 16476233
    },
    {
      "user": "chouaibb",
      "count": 2,
      "uuid": 86964562
    },
    {
      "user": "alihajj20",
      "count": 1,
      "uuid": 160850403
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    },
    {
      "user": "ake123",
      "count": 1,
      "uuid": 40662956
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 479,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 320,
    "source": "https://www.bioconductor.org/packages/stats/bioc/miaTime"
  },
  "_devurl": "https://github.com/microbiome/miatime",
  "_searchresults": 42,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/miaTime.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/microbiome/miatime",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addBaselineDivergence",
    "addBimodality",
    "addShortTermChange",
    "addStability",
    "addStepwiseDivergence",
    "addSurvival",
    "getBaselineDivergence",
    "getBimodality",
    "getShortTermChange",
    "getStability",
    "getStepwiseDivergence",
    "getSurvival"
  ],
  "_datasets": [
    {
      "name": "crohn_survival",
      "title": "Survival microbiome data from 150 individuals with longitudinal measurements",
      "object": "crohn_survival",
      "file": "crohn_survival.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "hitchip1006",
      "title": "HITChip Atlas with 1006 Western Adults",
      "object": "hitchip1006",
      "file": "hitchip1006.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HMP_2019_ibdmdb",
      "title": "HMP_2019_ibdmdb",
      "object": "HMP_2019_ibdmdb",
      "file": "HMP_2019_ibdmdb.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Kumaraswamy2024",
      "title": "Kumaraswamy2024",
      "object": "Kumaraswamy2024",
      "file": "Kumaraswamy2024.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "minimalgut",
      "title": "Human Gut Minimal Microbiome Profiling Data",
      "object": "minimalgut",
      "file": "minimalgut.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SilvermanAGutData",
      "title": "SilvermanAGutData",
      "object": "SilvermanAGutData",
      "file": "SilvermanAGutData.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "temporalMicrobiome20",
      "title": "Gut Microbiome Profiling 20 Belgian Women",
      "object": "temporalMicrobiome20",
      "file": "temporalMicrobiome20.rda",
      "class": [
        "TreeSummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "miaTime-package",
      "title": "'miaTime' Package.",
      "topics": [
        "miaTime-package",
        "miaTime"
      ]
    },
    {
      "page": "getShortTermChange",
      "title": "Short term changes in abundance",
      "topics": [
        "addShortTermChange",
        "addShortTermChange,SummarizedExperiment-method",
        "getShortTermChange",
        "getShortTermChange,SummarizedExperiment-method"
      ]
    },
    {
      "page": "crohn_survival",
      "title": "Survival microbiome data from 150 individuals with longitudinal measurements",
      "topics": [
        "crohn_survival"
      ]
    },
    {
      "page": "getBaselineDivergence",
      "title": "Beta diversity between the baseline and later time steps",
      "topics": [
        "addBaselineDivergence",
        "addBaselineDivergence,SummarizedExperiment-method",
        "getBaselineDivergence",
        "getBaselineDivergence,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getBimodality",
      "title": "Calculate coefficient of bimodality.",
      "topics": [
        "addBimodality",
        "addBimodality,SummarizedExperiment-method",
        "getBimodality",
        "getBimodality,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getStability",
      "title": "Estimate stability",
      "topics": [
        "addStability",
        "addStability,SummarizedExperiment-method",
        "getStability",
        "getStability,SummarizedExperiment-method"
      ]
    },
    {
      "page": "getStepwiseDivergence",
      "title": "Beta diversity between consecutive time steps",
      "topics": [
        "addStepwiseDivergence",
        "addStepwiseDivergence,SummarizedExperiment-method",
        "getStepwiseDivergence",
        "getStepwiseDivergence,ANY-method"
      ]
    },
    {
      "page": "getSurvival",
      "title": "Survival analysis",
      "topics": [
        "addSurvival",
        "addSurvival,SummarizedExperiment-method",
        "getSurvival",
        "getSurvival,SummarizedExperiment-method"
      ]
    },
    {
      "page": "hitchip1006",
      "title": "HITChip Atlas with 1006 Western Adults",
      "topics": [
        "hitchip1006"
      ]
    },
    {
      "page": "HMP_2019_ibdmdb",
      "title": "HMP_2019_ibdmdb",
      "topics": [
        "HMP_2019_ibdmdb"
      ]
    },
    {
      "page": "Kumaraswamy2024",
      "title": "Kumaraswamy2024",
      "topics": [
        "Kumaraswamy2024"
      ]
    },
    {
      "page": "minimalgut",
      "title": "Human Gut Minimal Microbiome Profiling Data",
      "topics": [
        "minimalgut"
      ]
    },
    {
      "page": "SilvermanAGutData",
      "title": "SilvermanAGutData",
      "topics": [
        "SilvermanAGutData"
      ]
    },
    {
      "page": "temporalMicrobiome20",
      "title": "Gut Microbiome Profiling 20 Belgian Women",
      "topics": [
        "temporalMicrobiome20"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/miaTime/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ape",
    "assorthead",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bluster",
    "cli",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "DBI",
    "DECIPHER",
    "decontam",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "DirichletMultinomial",
    "dplyr",
    "dqrng",
    "ecodive",
    "farver",
    "FNN",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggrepel",
    "glmnet",
    "glue",
    "gridExtra",
    "gtable",
    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mgcv",
    "mia",
    "MultiAssayExperiment",
    "nlme",
    "permute",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "purrr",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppEigen",
    "RcppML",
    "RcppProgress",
    "Rdpack",
    "reshape2",
    "rlang",
    "RSpectra",
    "rsvd",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "ScaledMatrix",
    "scales",
    "scater",
    "scuttle",
    "Seqinfo",
    "shape",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidytree",
    "treeio",
    "TreeSummarizedExperiment",
    "utf8",
    "uwot",
    "vctrs",
    "vegan",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "XVector",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "miaTime.Rmd",
      "filename": "miaTime.html",
      "title": "miaTime: Microbiome Time Series Analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Load the package",
        "Divergence between time points",
        "Types of divergence provided",
        "Purpose",
        "Practical application",
        "Visualize time series",
        "Session info"
      ],
      "created": "2021-11-21 13:01:50",
      "modified": "2025-08-04 07:17:03",
      "commits": 16
    }
  ],
  "_score": 6.78161178249315,
  "_indexed": true,
  "_nocasepkg": "miatime",
  "_universes": [
    "bioc",
    "microbiome"
  ],
  "_previous": "1.3.1",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.2",
      "date": "2026-10-22T19:42:43.000Z",
      "distro": "resolute",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/b6e4880255c002fd402a15b78465ce78a7ec8ee116e3a23d0206bcd0f1a2e08e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.3.2",
      "date": "2026-10-22T19:39:33.000Z",
      "distro": "resolute",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/1db9199694d62b5d4e79a732ab85fe894735bd66ff80045ef6f7e152391cc46d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.2",
      "date": "2026-10-22T20:13:03.000Z",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/df77a85ca41906a4fa2e0390212531dcdac73ac2442e773ba77dba0b9702de25",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.3.2",
      "date": "2026-10-22T20:13:41.000Z",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/02e0c40df2d880b924cf137fb7ff3daf95e82bdb64482eb06940d4287575e364",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.2",
      "date": "2026-10-22T19:37:23.000Z",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/d0d7e87bbae551842796d63719ab1efe789b88a8636ad5acdd208a09b6c780f9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.2",
      "date": "2026-10-22T19:36:17.000Z",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/e8c9988a1dcdbff6b02f4d42008c233c1c7f9d62b70b64ec2b25d33daa39c23a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.2",
      "date": "2026-10-22T19:36:14.000Z",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/3983acb673bf7a069d0c56b9833516291508b25ecc5ca11e14842012a52951a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.3.2",
      "date": "2026-10-22T19:37:36.000Z",
      "commit": "534c76d28cf77ba29781b4e58c86f94ed28f38fa",
      "fileid": "https://r2.ropensci.org/f516c7c711caedbc11eb5a9c048eb8a0fc53af62f66e89dd7e75961e429001d1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39840036499"
    }
  ]
}