{
  "_id": "6acb6d37fe5cc25786e8fe8a",
  "Package": "avidaR",
  "Title": "A Computational Biologist’s Toolkit To Get Data From 'avidaDB'",
  "Version": "1.2.1",
  "Authors@R": "c(person(given = \"Miguel A.\",\nfamily = \"Fortuna\",\nemail = \"fortuna@ebd.csic.es\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-8374-1941\")),\nperson(given = \"Raúl\",\nfamily = \"Ortega\",\nrole = \"cre\",\nemail = \"raul.ortega@ebd.csic.es\",\ncomment = c(ORCID = \"0000-0002-1306-5378\")))",
  "Description": "Easy-to-use tools for performing complex queries on\n'avidaDB', a semantic database that stores genomic and\ntranscriptomic data of self-replicating computer programs\n(known as digital organisms) that mutate and evolve within a\nuser-defined computational environment.",
  "License": "MIT + file LICENSE",
  "URL": "https://gitlab.com/fortunalab/avidaR",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev libx11-dev",
  "Repository": "https://fortunalab.r-universe.dev",
  "Date/Publication": "2024-06-24 07:35:42 UTC",
  "RemoteUrl": "https://gitlab.com/fortunalab/avidar",
  "RemoteRef": "HEAD",
  "RemoteSha": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-11 10:59:41 UTC",
    "User": "root"
  },
  "Author": "Miguel A. Fortuna [aut] (ORCID:\n<https://orcid.org/0000-0002-8374-1941>),\nRaúl Ortega [cre] (ORCID: <https://orcid.org/0000-0002-1306-5378>)",
  "Maintainer": "Raúl Ortega <raul.ortega@ebd.csic.es>",
  "_user": "fortunalab",
  "_type": "src",
  "_file": "avidaR_1.2.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/001bbc94a94deaeeeeaeba517677b719f8c6955344a107f8ecb59097b0ebe0ca",
  "_filesize": 194508,
  "_sha256": "001bbc94a94deaeeeeaeba517677b719f8c6955344a107f8ecb59097b0ebe0ca",
  "_expires": "2027-01-19T11:04:21.000Z",
  "_created": "2026-10-11T10:59:41.000Z",
  "_published": "2026-10-11T11:04:23.322Z",
  "_buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114453845021,
      "time": 148,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11700510855"
    },
    {
      "job": 114453845039,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11700212341"
    },
    {
      "job": 114453845186,
      "time": 217,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11700501017"
    },
    {
      "job": 114453845069,
      "time": 154,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11700680468"
    },
    {
      "job": 114453399257,
      "time": 154,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11700800042"
    },
    {
      "job": 114453845020,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11699947854"
    },
    {
      "job": 114453845106,
      "time": 97,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11700102436"
    },
    {
      "job": 114453845065,
      "time": 101,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11699947835"
    },
    {
      "job": 114453845135,
      "time": 98,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11700312034"
    }
  ],
  "_upstream": "https://gitlab.com/fortunalab/avidar",
  "_commit": {
    "id": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
    "author": "Miguel A. Fortuna <mfortuna.lab@gmail.com>",
    "committer": "Miguel A. Fortuna <mfortuna.lab@gmail.com>",
    "message": "Merge branch 'development' into 'main'\n\nVersion 1.2.1 - minor update\n\nSee merge request fortunalab/avidaR!8",
    "time": 1719214542
  },
  "_maintainer": {
    "name": "Raúl Ortega",
    "email": "raul.ortega@ebd.csic.es",
    "orcid": "0000-0002-1306-5378"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "base64enc",
      "version": ">= 0.1-3",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "version": ">= 1.3.2",
      "role": "Imports"
    },
    {
      "package": "httr",
      "version": ">= 1.4.2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.6",
      "role": "Imports"
    },
    {
      "package": "readr",
      "version": ">= 1.4.0",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.1.2",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 3.0.6",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "version": ">= 0.4.11",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "curl",
      "version": ">= 5.0.2",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "gitlab-fortunalab",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_userbio": {
    "uuid": 57902298,
    "type": "organization",
    "name": "fortunalab",
    "followers": 0
  },
  "_downloads": {
    "count": 367,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/avidaR"
  },
  "_devurl": "https://gitlab.com/fortunalab/avidar",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/avidaR.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://gitlab.com/fortunalab/avidar",
  "_realowner": "fortunalab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2022-04-08"
    },
    {
      "version": "1.1.2",
      "date": "2022-05-30"
    },
    {
      "version": "1.1.3",
      "date": "2022-08-22"
    },
    {
      "version": "1.2.0",
      "date": "2023-09-14"
    },
    {
      "version": "1.2.1",
      "date": "2024-06-21"
    }
  ],
  "_exports": [
    "convert_org_into_seq",
    "convert_seq_into_org",
    "get_db_summary",
    "get_docker_image_from_experiment_id",
    "get_doi_from_experiment_id",
    "get_experiment_id_from_organism_id",
    "get_genome_id_from_genome_seq",
    "get_genome_id_from_logic_operation",
    "get_genome_id_from_phenotype_id",
    "get_genome_id_from_transcriptome_id",
    "get_genome_id_of_wild_type_organisms",
    "get_genome_seq_from_genome_id",
    "get_logic_operation_from_phenotype_id",
    "get_mutant_at_pos",
    "get_phenotype_id_from_genome_id",
    "get_phenotype_id_from_genome_seq",
    "get_phenotype_id_from_logic_operation",
    "get_phenotype_id_from_transcriptome_id",
    "get_tandem_id_from_genome_id",
    "get_tandem_id_from_genome_seq",
    "get_tandem_id_from_logic_operation",
    "get_tandem_id_from_phenotype_id",
    "get_tandem_seq_from_tandem_id",
    "get_transcriptome_id_from_genome_id",
    "get_transcriptome_id_from_genome_seq",
    "get_transcriptome_id_from_logic_operation",
    "get_transcriptome_id_from_phenotype_id",
    "get_transcriptome_seq_from_transcriptome_id",
    "instruction_set",
    "logic_operation",
    "plot_transcriptome",
    "triplestore_access"
  ],
  "_help": [
    {
      "page": "convert_org_into_seq",
      "title": "Converts a genome instruction sequence into a digital organism file",
      "topics": [
        "convert_org_into_seq"
      ]
    },
    {
      "page": "convert_seq_into_org",
      "title": "Converts a genome instruction sequence into a digital organism file",
      "topics": [
        "convert_seq_into_org"
      ]
    },
    {
      "page": "get_db_summary",
      "title": "Get database summary",
      "topics": [
        "get_db_summary"
      ]
    },
    {
      "page": "get_docker_image_from_experiment_id",
      "title": "Get docker image from experiment",
      "topics": [
        "get_docker_image_from_experiment_id"
      ]
    },
    {
      "page": "get_doi_from_experiment_id",
      "title": "Get doi from experiment",
      "topics": [
        "get_doi_from_experiment_id"
      ]
    },
    {
      "page": "get_experiment_id_from_organism_id",
      "title": "Get experiment from organism",
      "topics": [
        "get_experiment_id_from_organism_id"
      ]
    },
    {
      "page": "get_genome_id_from_genome_seq",
      "title": "Get genome from genome sequence",
      "topics": [
        "get_genome_id_from_genome_seq"
      ]
    },
    {
      "page": "get_genome_id_from_logic_operation",
      "title": "Get genome from logic operations",
      "topics": [
        "get_genome_id_from_logic_operation"
      ]
    },
    {
      "page": "get_genome_id_from_phenotype_id",
      "title": "Get genome from phenotype",
      "topics": [
        "get_genome_id_from_phenotype_id"
      ]
    },
    {
      "page": "get_genome_id_from_transcriptome_id",
      "title": "Get genome from transcriptome",
      "topics": [
        "get_genome_id_from_transcriptome_id"
      ]
    },
    {
      "page": "get_genome_id_of_wild_type_organisms",
      "title": "Get genomes of wild-type organisms",
      "topics": [
        "get_genome_id_of_wild_type_organisms"
      ]
    },
    {
      "page": "get_genome_seq_from_genome_id",
      "title": "Get genome sequence from genome",
      "topics": [
        "get_genome_seq_from_genome_id"
      ]
    },
    {
      "page": "get_logic_operation_from_phenotype_id",
      "title": "Get the logic operations computed by a digital organism whose genome encodes a specific phenotype",
      "topics": [
        "get_logic_operation_from_phenotype_id"
      ]
    },
    {
      "page": "get_mutant_at_pos",
      "title": "Get single-point mutants of wild-type organisms",
      "topics": [
        "get_mutant_at_pos"
      ]
    },
    {
      "page": "get_phenotype_id_from_genome_id",
      "title": "Get phenotype from genome",
      "topics": [
        "get_phenotype_id_from_genome_id"
      ]
    },
    {
      "page": "get_phenotype_id_from_genome_seq",
      "title": "Get phenotype from genome sequence",
      "topics": [
        "get_phenotype_id_from_genome_seq"
      ]
    },
    {
      "page": "get_phenotype_id_from_logic_operation",
      "title": "Get phenotype from logic operations",
      "topics": [
        "get_phenotype_id_from_logic_operation"
      ]
    },
    {
      "page": "get_phenotype_id_from_transcriptome_id",
      "title": "Get phenotype from transcriptome",
      "topics": [
        "get_phenotype_id_from_transcriptome_id"
      ]
    },
    {
      "page": "get_tandem_id_from_genome_id",
      "title": "Get tandem repeat from genome",
      "topics": [
        "get_tandem_id_from_genome_id"
      ]
    },
    {
      "page": "get_tandem_id_from_genome_seq",
      "title": "Get tandem repeat from genome sequence",
      "topics": [
        "get_tandem_id_from_genome_seq"
      ]
    },
    {
      "page": "get_tandem_id_from_logic_operation",
      "title": "Get tandem repeat from logic operations",
      "topics": [
        "get_tandem_id_from_logic_operation"
      ]
    },
    {
      "page": "get_tandem_id_from_phenotype_id",
      "title": "Get tandem repeat from phenotype",
      "topics": [
        "get_tandem_id_from_phenotype_id"
      ]
    },
    {
      "page": "get_tandem_seq_from_tandem_id",
      "title": "Get the tandem repeat sequence from tandem repeat",
      "topics": [
        "get_tandem_seq_from_tandem_id"
      ]
    },
    {
      "page": "get_transcriptome_id_from_genome_id",
      "title": "Get transcriptome from genome",
      "topics": [
        "get_transcriptome_id_from_genome_id"
      ]
    },
    {
      "page": "get_transcriptome_id_from_genome_seq",
      "title": "Get transcriptome from genome sequence",
      "topics": [
        "get_transcriptome_id_from_genome_seq"
      ]
    },
    {
      "page": "get_transcriptome_id_from_logic_operation",
      "title": "Get transcriptome from logic operations",
      "topics": [
        "get_transcriptome_id_from_logic_operation"
      ]
    },
    {
      "page": "get_transcriptome_id_from_phenotype_id",
      "title": "Get transcriptome from phenotype",
      "topics": [
        "get_transcriptome_id_from_phenotype_id"
      ]
    },
    {
      "page": "get_transcriptome_seq_from_transcriptome_id",
      "title": "Get transcriptome sequence from transcriptome",
      "topics": [
        "get_transcriptome_seq_from_transcriptome_id"
      ]
    },
    {
      "page": "instruction_set",
      "title": "Get the genetic language of Avida",
      "topics": [
        "instruction_set"
      ]
    },
    {
      "page": "logic_operation",
      "title": "Get the list of logic operations that a digital organism can compute",
      "topics": [
        "logic_operation"
      ]
    },
    {
      "page": "plot_transcriptome",
      "title": "Get a plot of the transcriptome as a chord diagram",
      "topics": [
        "plot_transcriptome"
      ]
    },
    {
      "page": "triplestore_access",
      "title": "Class to manage triplestore access options",
      "topics": [
        "triplestore_access"
      ]
    }
  ],
  "_readme": "https://gitlab.com/fortunalab/avidar/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "bit",
    "bit64",
    "circlize",
    "cli",
    "clipr",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "dplyr",
    "generics",
    "GlobalOptions",
    "glue",
    "hms",
    "httr",
    "jsonlite",
    "lifecycle",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "readr",
    "rlang",
    "shape",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "xml2"
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "avidar",
  "_universes": [
    "fortunalab",
    "gitlab-fortunalab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.1",
      "date": "2026-10-11T11:01:48.000Z",
      "distro": "resolute",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/636c45cf41199d24d318e33dceed26a174103f3a7a78d6b4390f5bb59de5dbb3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.2.1",
      "date": "2026-10-11T11:02:13.000Z",
      "distro": "resolute",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/59a1c53c9191bbb0dfbf56fe3b0c6fda40c5ac58b98e4b674bfd3d68a3626f0c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.1",
      "date": "2026-10-11T11:02:50.000Z",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/f959feb116fa5fd0841c1e51b146ea71131b75d499889cdf7b6c5b68741189f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.2.1",
      "date": "2026-10-11T11:01:45.000Z",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/e3ab3bee7f78e284e5c3c28b22ba82d71a09db1d765cd8ce8585584d3e106a0f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.1",
      "date": "2026-10-11T11:01:48.000Z",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/0d199ee4ddaadccbbc40c6c241e9364d0260757012a22d2ce51258ef85052396",
      "status": "success",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.1",
      "date": "2026-10-11T11:00:50.000Z",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/9e5d72c2be1b916b63bc9379131973afe8a897d3f8e42472a259a5b71b0f30f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.1",
      "date": "2026-10-11T11:00:49.000Z",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/c28eab193737c95a37d280d2f6a3ffffdda1746a2437c9ad259091bfc6c3390b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.2.1",
      "date": "2026-10-11T11:00:44.000Z",
      "commit": "041f05a21f5bd5cca148309b5f8106f76b2c11f0",
      "fileid": "https://r2.ropensci.org/859fc0b8bc8c8461f57f4719e4f371a5e69da7b53101d01e46dc31cc7f17ef3e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fortunalab/actions/runs/38133787111"
    }
  ]
}