{
  "_id": "6a21b263cd65a98ecbd3a5cb",
  "Package": "tima",
  "Title": "Taxonomically Informed Metabolite Annotation",
  "Version": "2.13.0.9000",
  "Authors@R": "c(\nperson(given = \"Adriano\",\nfamily = \"Rutz\",\nemail = \"adafede@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0443-9902\")),\nperson(given = \"Pierre-Marie\",\nfamily = \"Allard\",\nemail = \"pierre-marie.allard@unifr.ch\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3389-2191\"))\n)",
  "Maintainer": "Adriano Rutz <adafede@gmail.com>",
  "Description": "TIMA provides a reproducible workflow for taxonomically\ninformed metabolite annotation from feature tables, MS/MS\nspectra, and optional external resources such as SIRIUS and\nGNPS outputs. It combines mass, spectral, taxonomic, and\nstructural evidence into a transparent scoring framework that\ncan be inspected step-by-step. The package targets metabolomics\npractitioners who need configurable, scriptable, and documented\nannotation pipelines for research and production settings.",
  "License": "AGPL (>= 3)",
  "URL": "https://github.com/taxonomicallyinformedannotation/tima,\nhttps://taxonomicallyinformedannotation.github.io/tima-shinylive,\nhttps://taxonomicallyinformedannotation.github.io/tima",
  "BugReports": "https://github.com/taxonomicallyinformedannotation/tima/issues",
  "SystemRequirements": "python (>= 3.12, < 3.15)",
  "VignetteBuilder": "quarto",
  "ByteCompile": "TRUE",
  "Collate": "'logs_utils.R' 'errors_utils.R' 'validations_utils.R'\n'safe_fread.R' 'add_xrefs_to_annotations.R' 'adduct_universe.R'\n'adduct_universe_config.R' 'constants.R'\n'adduct_universe_formula.R' 'adducts_utils.R' 'round_reals.R'\n'mass_evidence.R' 'harmonize_adducts.R' 'parse_yaml_params.R'\n'parse_cli_params.R' 'pkg_system_file.R' 'get_default_paths.R'\n'get_path.R' 'get_params.R' 'dists_utils.R' 'decorate_masses.R'\n'parse_adduct.R' 'calculate_mass_of_m.R' 'annotate_masses.R'\n'annotate_masses_consistency.R' 'annotate_masses_coverage.R'\n'annotate_masses_enforcement.R' 'annotate_masses_features.R'\n'annotate_masses_hypothesis.R' 'columns_utils.R'\n'annotate_spectra.R' 'assert_utils.R'\n'benchmark_metrics_utils.R' 'benchmark_taxize_spectra.R'\n'c_wrappers.R' 'sanitize_spectrum_matrix.R'\n'calculate_similarity.R' 'calculate_entropy_and_similarity.R'\n'load_yaml_files.R' 'go_to_cache.R' 'create_dir.R'\n'change_params_small.R' 'clean_bio.R' 'summarize_results.R'\n'filter_high_evidence_only.R' 'clean_chemo.R'\n'clean_chemo_preprocessing.R' 'clean_chemo_candidates.R'\n'complement_metadata_structures.R' 'copy_backbone.R'\n'create_components.R' 'predicates_utils.R' 'create_edges.R'\n'sanitize_spectra.R' 'read_mgf_opti.R' 'import_spectra.R'\n'get_spectra_ids.R' 'create_edges_spectra.R' 'decorate_bio.R'\n'decorate_chemo.R' 'evidence_validation_utils.R'\n'export_output.R' 'export_params.R' 'export_spectra_rds.R'\n'extract_spectra.R' 'fake_ecmdb.R' 'fake_hmdb.R' 'fake_lotus.R'\n'fake_pubchemlite.R' 'filter_annotations.R'\n'get_compounds_xrefs.R' 'retry_utils.R' 'get_file.R'\n'get_example_sirius.R' 'get_example_files.R'\n'get_gnps_tables.R' 'get_last_version_from_zenodo.R'\n'get_organism_taxonomy_ott.R' 'globals.R'\n'harmonize_names_sirius.R' 'harmonize_spectra.R' 'install.R'\n'mass_evidence_hypothesis.R' 'mass_evidence_utils.R'\n'move_file_safely.R' 'mztab_app_utils.R' 'mztab_schema_utils.R'\n'mztab_parser.R' 'mztab_validate.R'\n'pre_harmonize_names_sirius.R' 'process_smiles.R'\n'select_annotations_columns.R' 'prepare_annotations_gnps.R'\n'prepare_annotations_mzmine.R' 'read_mztab.R'\n'prepare_annotations_mztab.R' 'select_sirius_columns.R'\n'read_from_sirius_zip.R' 'prepare_annotations_sirius.R'\n'prepare_annotations_sirius_utils.R'\n'prepare_annotations_spectra.R' 'prepare_features_components.R'\n'prepare_features_edges.R' 'rts_utils.R'\n'prepare_features_tables.R' 'prepare_libraries_rt.R'\n'select_sop_columns.R' 'prepare_libraries_sop_bigg.R'\n'prepare_libraries_sop_closed.R'\n'prepare_libraries_sop_ecmdb.R'\n'prepare_libraries_sop_hmdb_like.R'\n'prepare_libraries_sop_hmdb.R' 'prepare_libraries_sop_lotus.R'\n'split_tables_sop.R' 'prepare_libraries_sop_merged.R'\n'prepare_libraries_sop_merged_utils.R'\n'prepare_libraries_sop_pubchemlite.R'\n'prepare_libraries_spectra.R' 'prepare_params.R'\n'prepare_taxa.R' 'replace_id.R' 'run_app.R' 'run_tima.R'\n'sanitize_data.R' 'sanitize_data_utils.R' 'tima-package.R'\n'transform_score_sirius_csi.R' 'validate_inputs.R'\n'validations_params.R' 'weights_utils.R' 'weight_chemo.R'\n'weight_bio.R' 'weight_annotations.R'\n'weight_annotations_utils.R' 'write_mztab.R'\n'write_mztab_comments.R' 'write_mztab_merge.R'\n'write_mztab_metadata.R' 'write_mztab_tables.R'",
  "Config/roxygen2/markdown": "TRUE",
  "Config/roxygen2/version": "8.0.0",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "biocViews": "metaboliteAnnotation, chemotaxonomy, scoringSystem,\nnaturalProducts, computationalMetabolomics, taxonomicDistance,\nspecializedMetabolome",
  "Config/pak/sysreqs": "cmake libglpk-dev make libarchive-dev libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev python3",
  "Repository": "https://taxonomicallyinformedannotation.r-universe.dev",
  "Date/Publication": "2026-06-04 15:10:38 UTC",
  "RemoteUrl": "https://github.com/taxonomicallyinformedannotation/tima",
  "RemoteRef": "HEAD",
  "RemoteSha": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-04 17:00:15 UTC",
    "User": "root"
  },
  "Author": "Adriano Rutz [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0443-9902>),\nPierre-Marie Allard [ctb] (ORCID:\n<https://orcid.org/0000-0003-3389-2191>)",
  "MD5sum": "3e7fdb8a93f2eeea58554e0dc19ca2ce",
  "_user": "taxonomicallyinformedannotation",
  "_type": "src",
  "_file": "tima_2.13.0.9000.tar.gz",
  "_fileid": "b10ad48db3d09e0087c512115602e4dfe6bcc7dc51ebd65600fc9a9d07f30f3d",
  "_filesize": 15163413,
  "_sha256": "b10ad48db3d09e0087c512115602e4dfe6bcc7dc51ebd65600fc9a9d07f30f3d",
  "_created": "2026-06-04T17:00:15.000Z",
  "_published": "2026-06-04T17:14:11.037Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79571595268,
      "time": 163,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7417892055"
    },
    {
      "job": 79571595282,
      "time": 180,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7417897577"
    },
    {
      "job": 79571595289,
      "time": 216,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7417913136"
    },
    {
      "job": 79571595314,
      "time": 218,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7417912805"
    },
    {
      "job": 79571595378,
      "time": 189,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7418087871"
    },
    {
      "job": 79571595310,
      "time": 473,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7418082354"
    },
    {
      "job": 79571595324,
      "time": 175,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7417985810"
    },
    {
      "job": 79571595334,
      "time": 432,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7418127180"
    },
    {
      "job": 79570806417,
      "time": 255,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7417827472"
    },
    {
      "job": 79571595267,
      "time": 193,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7417902805"
    },
    {
      "job": 79571595319,
      "time": 242,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7417922455"
    },
    {
      "job": 79571595283,
      "time": 179,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7417897602"
    },
    {
      "job": 79571595256,
      "time": 257,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7417928311"
    }
  ],
  "_buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/taxonomicallyinformedannotation/tima",
  "_commit": {
    "id": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
    "author": "Adriano Rutz <adriano.rutz@hotmail.com>",
    "committer": "Adriano Rutz <adriano.rutz@hotmail.com>",
    "message": "Fix: update tests\n",
    "time": 1780585838
  },
  "_maintainer": {
    "name": "Adriano Rutz",
    "email": "adafede@gmail.com",
    "login": "adafede",
    "mastodon": "@adafede@mastodon.online",
    "linkedin": "in/adrianorutz",
    "orcid": "0000-0003-0443-9902",
    "description": "Pharmaceutical Scientist | Computational Metabolomics",
    "uuid": 44283913
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "archive",
      "version": ">= 1.1.13",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "version": ">= 1.44.0",
      "role": "Imports"
    },
    {
      "package": "cli",
      "version": ">= 3.6.6",
      "role": "Imports"
    },
    {
      "package": "docopt",
      "version": ">= 0.7.2",
      "role": "Imports"
    },
    {
      "package": "fs",
      "version": ">= 2.1.0",
      "role": "Imports"
    },
    {
      "package": "httr",
      "version": ">= 1.4.8",
      "role": "Imports"
    },
    {
      "package": "httr2",
      "version": ">= 1.2.2",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "version": ">= 2.3.1",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "version": ">= 2.0.0",
      "role": "Imports"
    },
    {
      "package": "lgr",
      "version": ">= 0.5.2",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "version": ">= 1.0.5",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "MetaboCoreUtils",
      "version": ">= 1.18.1",
      "role": "Imports"
    },
    {
      "package": "MsBackendMgf",
      "version": ">= 1.18.0",
      "role": "Imports"
    },
    {
      "package": "MsBackendMsp",
      "version": ">= 1.14.0",
      "role": "Imports"
    },
    {
      "package": "MsCoreUtils",
      "version": ">= 1.22.1",
      "role": "Imports"
    },
    {
      "package": "msentropy",
      "version": ">= 0.1.4",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "version": ">= 1.2.2",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "version": ">= 2.13.0",
      "role": "Imports"
    },
    {
      "package": "reticulate",
      "version": ">= 1.46.0",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "version": ">= 1.2.0",
      "role": "Imports"
    },
    {
      "package": "rotl",
      "version": ">= 3.1.1",
      "role": "Imports"
    },
    {
      "package": "Spectra",
      "version": ">= 1.20.1",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "version": ">= 1.8.7",
      "role": "Imports"
    },
    {
      "package": "targets",
      "version": ">= 1.12.0",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "version": ">= 1.2.1",
      "role": "Imports"
    },
    {
      "package": "tidytable",
      "version": ">= 0.11.2",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "yaml",
      "version": ">= 2.3.12",
      "role": "Imports"
    },
    {
      "package": "altdoc",
      "version": ">= 0.7.2",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "version": ">= 1.30.27",
      "role": "Suggests"
    },
    {
      "package": "BiocVersion",
      "version": ">= 3.22.0",
      "role": "Suggests"
    },
    {
      "package": "grateful",
      "version": ">= 0.3.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "version": ">= 1.51",
      "role": "Suggests"
    },
    {
      "package": "pkgload",
      "version": ">= 1.5.2",
      "role": "Suggests"
    },
    {
      "package": "quarto",
      "version": ">= 1.5.1",
      "role": "Suggests"
    },
    {
      "package": "shiny",
      "version": ">= 1.13.0",
      "role": "Suggests"
    },
    {
      "package": "shinyhelper",
      "version": ">= 0.3.2",
      "role": "Suggests"
    },
    {
      "package": "shinyjs",
      "version": ">= 2.1.1",
      "role": "Suggests"
    },
    {
      "package": "shinytest2",
      "version": ">= 0.5.1",
      "role": "Suggests"
    },
    {
      "package": "shinyvalidate",
      "version": ">= 0.1.3",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.3.2",
      "role": "Suggests"
    },
    {
      "package": "visNetwork",
      "version": ">= 2.1.4",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "version": ">= 3.0.2",
      "role": "Suggests"
    }
  ],
  "_owner": "taxonomicallyinformedannotation",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-23",
      "n": 3
    },
    {
      "week": "2025-24",
      "n": 2
    },
    {
      "week": "2025-25",
      "n": 2
    },
    {
      "week": "2025-26",
      "n": 5
    },
    {
      "week": "2025-27",
      "n": 19
    },
    {
      "week": "2025-28",
      "n": 16
    },
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-31",
      "n": 8
    },
    {
      "week": "2025-32",
      "n": 3
    },
    {
      "week": "2025-33",
      "n": 2
    },
    {
      "week": "2025-34",
      "n": 9
    },
    {
      "week": "2025-36",
      "n": 1
    },
    {
      "week": "2025-38",
      "n": 1
    },
    {
      "week": "2025-39",
      "n": 4
    },
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 50
    },
    {
      "week": "2025-46",
      "n": 91
    },
    {
      "week": "2025-47",
      "n": 100
    },
    {
      "week": "2025-48",
      "n": 69
    },
    {
      "week": "2025-49",
      "n": 63
    },
    {
      "week": "2025-50",
      "n": 36
    },
    {
      "week": "2025-51",
      "n": 15
    },
    {
      "week": "2025-52",
      "n": 14
    },
    {
      "week": "2026-01",
      "n": 2
    },
    {
      "week": "2026-08",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 18
    },
    {
      "week": "2026-10",
      "n": 25
    },
    {
      "week": "2026-11",
      "n": 64
    },
    {
      "week": "2026-12",
      "n": 30
    },
    {
      "week": "2026-13",
      "n": 5
    },
    {
      "week": "2026-15",
      "n": 13
    },
    {
      "week": "2026-16",
      "n": 48
    },
    {
      "week": "2026-17",
      "n": 19
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 16
    },
    {
      "week": "2026-20",
      "n": 13
    },
    {
      "week": "2026-21",
      "n": 15
    },
    {
      "week": "2026-22",
      "n": 89
    },
    {
      "week": "2026-23",
      "n": 30
    }
  ],
  "_tags": [
    {
      "name": "2.12.0",
      "date": "2025-12-05"
    },
    {
      "name": "2.13.0",
      "date": "2026-05-22"
    }
  ],
  "_topics": [
    "metaboliteannotation",
    "chemotaxonomy",
    "scoringsystem",
    "naturalproducts",
    "computationalmetabolomics",
    "taxonomicdistance",
    "specializedmetabolome",
    "lc-msms",
    "metabolite-annotation",
    "metabolomics",
    "natural-products",
    "scoring-system",
    "specialized-metabolome",
    "taxonomy",
    "quarto"
  ],
  "_stars": 16,
  "_contributors": [
    {
      "user": "adafede",
      "count": 2428,
      "uuid": 44283913
    },
    {
      "user": "imgbotapp",
      "count": 4,
      "uuid": 31427850
    }
  ],
  "_userbio": {
    "uuid": 91277421,
    "type": "organization",
    "name": "taxonomicallyinformedannotation"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tima"
  },
  "_devurl": "https://github.com/taxonomicallyinformedannotation/tima",
  "_pkgdown": "https://taxonomicallyinformedannotation.github.io/tima",
  "_searchresults": 33,
  "_quarto": true,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/tima.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "adduct_to_string",
    "annotate_masses",
    "annotate_spectra",
    "calculate_mass_of_m",
    "calculate_mz_from_mass",
    "calculate_similarity",
    "change_params_small",
    "create_components",
    "create_edges",
    "create_edges_spectra",
    "filter_annotations",
    "get_compounds_xrefs",
    "get_example_files",
    "get_file",
    "get_gnps_tables",
    "get_last_version_from_zenodo",
    "get_organism_taxonomy_ott",
    "go_to_cache",
    "harmonize_adducts",
    "import_spectra",
    "install",
    "install_tima",
    "parse_adduct",
    "prepare_annotations_gnps",
    "prepare_annotations_mzmine",
    "prepare_annotations_mztab",
    "prepare_annotations_sirius",
    "prepare_annotations_spectra",
    "prepare_features_components",
    "prepare_features_edges",
    "prepare_features_tables",
    "prepare_libraries_rt",
    "prepare_libraries_sop_bigg",
    "prepare_libraries_sop_closed",
    "prepare_libraries_sop_ecmdb",
    "prepare_libraries_sop_hmdb",
    "prepare_libraries_sop_lotus",
    "prepare_libraries_sop_merged",
    "prepare_libraries_sop_pubchemlite",
    "prepare_libraries_spectra",
    "prepare_params",
    "prepare_taxa",
    "process_smiles",
    "read_mztab",
    "run_app",
    "run_tima",
    "tima_full",
    "validate_inputs",
    "weight_annotations",
    "write_mztab"
  ],
  "_help": [
    {
      "page": "adduct_to_string",
      "title": "Build the canonical adduct string from typed components.",
      "topics": [
        "adduct_to_string"
      ]
    },
    {
      "page": "annotate_masses",
      "title": "Annotate masses",
      "concept": [
        "annotation"
      ],
      "topics": [
        "annotate_masses"
      ]
    },
    {
      "page": "annotate_spectra",
      "title": "Annotate spectra",
      "concept": [
        "annotation"
      ],
      "topics": [
        "annotate_spectra"
      ]
    },
    {
      "page": "calculate_mass_of_m",
      "title": "Calculate mass of M",
      "concept": [
        "mass-spectrometry"
      ],
      "topics": [
        "calculate_mass_of_m"
      ]
    },
    {
      "page": "calculate_mz_from_mass",
      "title": "Calculate m/z from neutral mass (inverse operation)",
      "concept": [
        "mass-spectrometry"
      ],
      "topics": [
        "calculate_mz_from_mass"
      ]
    },
    {
      "page": "calculate_similarity",
      "title": "Calculate similarity between spectra",
      "concept": [
        "mass-spectrometry"
      ],
      "topics": [
        "calculate_similarity"
      ]
    },
    {
      "page": "change_params_small",
      "title": "Change Parameters (Convenience Function)",
      "concept": [
        "workflow"
      ],
      "topics": [
        "change_params_small"
      ]
    },
    {
      "page": "clean_chemo",
      "title": "Clean Chemical Annotations",
      "topics": [
        "clean_chemo"
      ]
    },
    {
      "page": "copy_backbone",
      "title": "Copy backbone",
      "topics": [
        "copy_backbone"
      ]
    },
    {
      "page": "create_components",
      "title": "Create components",
      "concept": [
        "workflow"
      ],
      "topics": [
        "create_components"
      ]
    },
    {
      "page": "create_edges",
      "title": "Create spectral similarity network edges",
      "concept": [
        "workflow"
      ],
      "topics": [
        "create_edges"
      ]
    },
    {
      "page": "create_edges_spectra",
      "title": "Create edges spectra",
      "concept": [
        "workflow"
      ],
      "topics": [
        "create_edges_spectra"
      ]
    },
    {
      "page": "filter_annotations",
      "title": "Filter annotations",
      "concept": [
        "annotation"
      ],
      "topics": [
        "filter_annotations"
      ]
    },
    {
      "page": "get_compounds_xrefs",
      "title": "Retrieve external database identifiers for compounds by InChIKey via Wikidata",
      "concept": [
        "data-retrieval"
      ],
      "topics": [
        "get_compounds_xrefs"
      ]
    },
    {
      "page": "get_example_files",
      "title": "Get example files",
      "concept": [
        "data-retrieval"
      ],
      "topics": [
        "get_example_files"
      ]
    },
    {
      "page": "get_example_sirius",
      "title": "Get example sirius",
      "topics": [
        "get_example_sirius"
      ]
    },
    {
      "page": "get_file",
      "title": "Download file from URL",
      "concept": [
        "data-retrieval"
      ],
      "topics": [
        "get_file"
      ]
    },
    {
      "page": "get_gnps_tables",
      "title": "Get GNPS Tables",
      "concept": [
        "data-retrieval"
      ],
      "topics": [
        "get_gnps_tables"
      ]
    },
    {
      "page": "get_last_version_from_zenodo",
      "title": "Get Latest Version from Zenodo",
      "concept": [
        "data-retrieval"
      ],
      "topics": [
        "get_last_version_from_zenodo"
      ]
    },
    {
      "page": "get_organism_taxonomy_ott",
      "title": "Get organism taxonomy (Open Tree of Life Taxonomy)",
      "concept": [
        "data-retrieval"
      ],
      "topics": [
        "get_organism_taxonomy_ott"
      ]
    },
    {
      "page": "go_to_cache",
      "title": "Navigate to cache directory",
      "concept": [
        "workflow"
      ],
      "topics": [
        "go_to_cache"
      ]
    },
    {
      "page": "harmonize_adducts",
      "title": "Harmonize adduct notations",
      "concept": [
        "mass-spectrometry"
      ],
      "topics": [
        "harmonize_adducts"
      ]
    },
    {
      "page": "import_spectra",
      "title": "Import spectra",
      "concept": [
        "mass-spectrometry"
      ],
      "topics": [
        "import_spectra"
      ]
    },
    {
      "page": "install",
      "title": "Install TIMA Package and Dependencies (DEPRECATED)",
      "concept": [
        "workflow"
      ],
      "topics": [
        "install"
      ]
    },
    {
      "page": "install_tima",
      "title": "Install TIMA Package and Dependencies",
      "concept": [
        "workflow"
      ],
      "topics": [
        "install_tima"
      ]
    },
    {
      "page": "parse_adduct",
      "title": "Parse adduct",
      "concept": [
        "mass-spectrometry"
      ],
      "topics": [
        "parse_adduct"
      ]
    },
    {
      "page": "prepare_annotations_gnps",
      "title": "Prepare annotations GNPS",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_annotations_gnps"
      ]
    },
    {
      "page": "prepare_annotations_mzmine",
      "title": "Prepare annotations mzmine",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_annotations_mzmine"
      ]
    },
    {
      "page": "prepare_annotations_mztab",
      "title": "Prepare annotations from mzTab-M",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_annotations_mztab"
      ]
    },
    {
      "page": "prepare_annotations_sirius",
      "title": "Prepare annotations SIRIUS",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_annotations_sirius"
      ]
    },
    {
      "page": "prepare_annotations_spectra",
      "title": "Prepare annotations MS2",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_annotations_spectra"
      ]
    },
    {
      "page": "prepare_features_components",
      "title": "Prepare features components",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_features_components"
      ]
    },
    {
      "page": "prepare_features_edges",
      "title": "Prepare features edges",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_features_edges"
      ]
    },
    {
      "page": "prepare_features_tables",
      "title": "Prepare features table",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_features_tables"
      ]
    },
    {
      "page": "prepare_libraries_rt",
      "title": "Prepare libraries of retention times",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_rt"
      ]
    },
    {
      "page": "prepare_libraries_sop_bigg",
      "title": "Prepare libraries of structure organism pairs BiGG",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_bigg"
      ]
    },
    {
      "page": "prepare_libraries_sop_closed",
      "title": "Prepare libraries of structure organism pairs CLOSED",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_closed"
      ]
    },
    {
      "page": "prepare_libraries_sop_ecmdb",
      "title": "Prepare libraries of structure organism pairs ECMDB",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_ecmdb"
      ]
    },
    {
      "page": "prepare_libraries_sop_hmdb",
      "title": "Prepare libraries of structure organism pairs HMDB",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_hmdb"
      ]
    },
    {
      "page": "prepare_libraries_sop_lotus",
      "title": "Prepare libraries of structure organism pairs LOTUS",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_lotus"
      ]
    },
    {
      "page": "prepare_libraries_sop_merged",
      "title": "Prepare merged structure organism pairs libraries",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_merged"
      ]
    },
    {
      "page": "prepare_libraries_sop_pubchemlite",
      "title": "Prepare libraries of structure organism pairs PubChem Lite",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_sop_pubchemlite"
      ]
    },
    {
      "page": "prepare_libraries_spectra",
      "title": "Prepare libraries of spectra",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_libraries_spectra"
      ]
    },
    {
      "page": "prepare_params",
      "title": "Prepare workflow parameters",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_params"
      ]
    },
    {
      "page": "prepare_taxa",
      "title": "Prepare taxa",
      "concept": [
        "preparation"
      ],
      "topics": [
        "prepare_taxa"
      ]
    },
    {
      "page": "process_smiles",
      "title": "Process SMILES strings",
      "concept": [
        "chemical-classification"
      ],
      "topics": [
        "process_smiles"
      ]
    },
    {
      "page": "read_mztab",
      "title": "Read mzTab-M and export TIMA-compatible files",
      "concept": [
        "preparation"
      ],
      "topics": [
        "read_mztab"
      ]
    },
    {
      "page": "run_app",
      "title": "Run TIMA Shiny app",
      "concept": [
        "workflow"
      ],
      "topics": [
        "run_app"
      ]
    },
    {
      "page": "run_tima",
      "title": "Run Complete TIMA Workflow",
      "concept": [
        "workflow"
      ],
      "topics": [
        "run_tima"
      ]
    },
    {
      "page": "tima_full",
      "title": "Run Complete TIMA Workflow (DEPRECATED)",
      "concept": [
        "workflow"
      ],
      "topics": [
        "tima_full"
      ]
    },
    {
      "page": "transform_score_sirius_csi",
      "title": "Transform SIRIUS CSI score",
      "topics": [
        "transform_score_sirius_csi"
      ]
    },
    {
      "page": "validate_inputs",
      "title": "Validate Input Data",
      "concept": [
        "workflow"
      ],
      "topics": [
        "validate_inputs"
      ]
    },
    {
      "page": "weight_annotations",
      "title": "Weight annotations",
      "concept": [
        "annotation"
      ],
      "topics": [
        "weight_annotations"
      ]
    },
    {
      "page": "write_mztab",
      "title": "Write TIMA results as mzTab-M",
      "concept": [
        "annotation"
      ],
      "topics": [
        "write_mztab"
      ]
    }
  ],
  "_pkglogo": "https://github.com/taxonomicallyinformedannotation/tima/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/taxonomicallyinformedannotation/tima/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "archive",
    "askpass",
    "backports",
    "base64url",
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "callr",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "digest",
    "docopt",
    "evaluate",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "glue",
    "here",
    "highr",
    "hms",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "jsonlite",
    "knitr",
    "lambda.r",
    "lattice",
    "lgr",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MetaboCoreUtils",
    "mime",
    "MsBackendMgf",
    "MsBackendMsp",
    "MsCoreUtils",
    "msentropy",
    "nlme",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "prettyunits",
    "processx",
    "progress",
    "ProtGenerics",
    "ps",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "Rcpp",
    "RcppTOML",
    "rentrez",
    "reticulate",
    "rlang",
    "rncl",
    "rotl",
    "rprojroot",
    "S4Vectors",
    "secretbase",
    "snow",
    "Spectra",
    "stringi",
    "sys",
    "targets",
    "tibble",
    "tidyselect",
    "tidytable",
    "utf8",
    "vctrs",
    "withr",
    "xfun",
    "XML",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "tima.qmd",
      "filename": "tima.html",
      "title": "General comments about the infrastructure",
      "engine": "quarto::html",
      "headings": [],
      "created": "2025-07-02 11:39:51",
      "modified": "2026-06-03 15:42:44",
      "commits": 30
    }
  ],
  "_score": 6.790819784279975,
  "_indexed": true,
  "_nocasepkg": "tima",
  "_universes": [
    "taxonomicallyinformedannotation",
    "adafede"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:03:31.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "c3a9d4502470cd8ef0324f49bab8d8a7ddd659872f974f7e514cd9da9138b313",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:03:43.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "795bc017fbcd62b840aa845b22e3622784be9074f50117d5ef895dbcb1e6088b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:03:47.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "5d53c6dc19f01a4c54bf53da3e947757fe3d8129f1f9dd702caf9a6eea46717f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:03:41.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "6e3cd4051c9a66a62d8e0560558382c6ebf0ae2aa4577da5f6631089a2878923",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:11:06.000Z",
      "arch": "aarch64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "a2c246e372f211c1fc2ce4544b1e2aef7b203a174d2ee7603ababb3ad5146ba9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:08:28.000Z",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "6f6a19447fe1b6c9e8d244fc2830e269f4039e86854bbefd368792b4191adadc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:07:05.000Z",
      "arch": "aarch64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "6e5d54a7e2fae76456b85dbb45ca1cfbc17c370bde8d60bc6f4835d3232d314f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:11:09.000Z",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "ec0069d4e0f7dc32afa7be6fef2728c157d6be15a5c214b21812078d4a94d987",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:04:10.000Z",
      "arch": "emscripten",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "b1665074d42a53cff950a1cfdd4ee2366c3cedc318b2f49be48c4fd20e01f3c4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:03:19.000Z",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "fa9f654c5cbaa72ae15f605e50f4f9ab07c13d661fb9b95a8af7b92a86b196d8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:02:33.000Z",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "b16e91c535723be0e6ba9aea2e1f18153e6d0e1109b880344219e6c47457c08b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.13.0.9000",
      "date": "2026-06-04T17:03:39.000Z",
      "arch": "x86_64",
      "commit": "6c183952ab5c26b6121f1b466e3b00776b14a1ed",
      "fileid": "3acb1ef0f8aa9b7455f2b2c39db04d9cc8b8b905c5a6120dc0c0e8b893902544",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/taxonomicallyinformedannotation/actions/runs/26966604005"
    }
  ]
}