{
  "_id": "6a628589d3420cf5dfdb3e4a",
  "Package": "BOLDconnectR",
  "Title": "Retrieve, Transform and Analyze the Barcode of Life Data Systems\nData",
  "Version": "1.0.1",
  "Authors@R": "c(\nperson(\"Sameer\", \"Padhye\", , \"spadhye@uoguelph.ca\", role = c(\"aut\", \"cre\")),\nperson(\"Liliana\", \"Ballesteros-Mejia\", , \"cballest@uoguelph.ca\", role = \"aut\"),\nperson(\"Timothy\", \"Agda\", , \"tagda@uoguelph.ca\", role = \"aut\"),\nperson(\"Jireh\", \"Agda\", , \"agdaj@uoguelph.ca\", role = \"aut\"),\nperson(\"Sujeevan\", \"Ratnasingham\", , \"sratnasi@uoguelph.ca\", role = \"aut\")\n)",
  "Maintainer": "Sameer Padhye <spadhye@uoguelph.ca>",
  "Description": "Facilitates retrieval, transformation and analysis of the\ndata from the Barcode of Life Data Systems (BOLD) database\n<https://boldsystems.org/>. This package allows both public and\nprivate user data to be easily downloaded into the R\nenvironment using a variety of inputs such as: IDs (processid,\nsampleid), BINs, dataset codes, project codes, taxonomy,\ngeography etc. It provides frictionless data conversion into\nformats compatible with other R-packages and third-party tools,\nas well as functions for sequence alignment & clustering,\nbiodiversity analysis and spatial mapping.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "biocViews": "",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-23 21:14:00 UTC",
    "User": "root"
  },
  "Author": "Sameer Padhye [aut, cre], Liliana Ballesteros-Mejia [aut],\nTimothy Agda [aut], Jireh Agda [aut], Sujeevan Ratnasingham\n[aut]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-07-23 18:10:02 UTC",
  "RemoteUrl": "https://github.com/cran/BOLDconnectR",
  "RemoteRef": "HEAD",
  "RemoteSha": "b4510741cabcb775823de138fc59af31618da9f3",
  "_user": "cran",
  "_type": "src",
  "_file": "BOLDconnectR_1.0.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/906406cafb86e03c60e23149c1422d16edb06f702b475b36a3fd16ab434f4a68",
  "_filesize": 1347041,
  "_sha256": "906406cafb86e03c60e23149c1422d16edb06f702b475b36a3fd16ab434f4a68",
  "_expires": "2026-10-31T21:20:07.000Z",
  "_created": "2026-07-23T21:14:00.000Z",
  "_published": "2026-07-23T21:20:09.483Z",
  "_jobs": [
    {
      "job": 89335234852,
      "time": 284,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8579017808"
    },
    {
      "job": 89335234803,
      "time": 309,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8579028312"
    },
    {
      "job": 89334142340,
      "time": 301,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8578901448"
    },
    {
      "job": 89335234783,
      "time": 227,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8578993369"
    },
    {
      "job": 89335234759,
      "time": 248,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8579003254"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/30043265996",
  "_status": "failure",
  "_upstream": "https://github.com/cran/BOLDconnectR",
  "_commit": {
    "id": "b4510741cabcb775823de138fc59af31618da9f3",
    "author": "Sameer Padhye <spadhye@uoguelph.ca>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.1\n",
    "time": 1784830202
  },
  "_maintainer": {
    "name": "Sameer Padhye",
    "email": "spadhye@uoguelph.ca",
    "login": "sameerpadhye",
    "linkedin": "in/sameer-padhye-173910106",
    "description": "Analyst with 9 years of experience collecting, modeling, analyzing and interpreting scientific data. ",
    "uuid": 46449628
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 5.5",
      "role": "Imports"
    },
    {
      "package": "BAT",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.13",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.1",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.3.2",
      "role": "Imports"
    },
    {
      "package": "httr",
      "version": ">= 1.4.2",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "version": ">= 1.7",
      "role": "Imports"
    },
    {
      "package": "maps",
      "version": ">= 3.3",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "rnaturalearth",
      "role": "Imports"
    },
    {
      "package": "sf",
      "version": ">= 0.9.4",
      "role": "Imports"
    },
    {
      "package": "skimr",
      "version": ">= 2.1.2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.1.1",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "version": ">= 2.5.7",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "msa",
      "role": "Suggests"
    },
    {
      "package": "muscle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-38",
      "n": 1
    },
    {
      "week": "2026-30",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.0.0",
      "date": "2025-09-17"
    },
    {
      "name": "1.0.1",
      "date": "2026-07-23"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "sameerpadhye",
      "count": 2,
      "uuid": 46449628
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 623,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 259,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BOLDconnectR"
  },
  "_searchresults": 12,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BOLDconnectR.html",
    "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",
    "LICENSE",
    "manual.pdf"
  ],
  "_realowner": "sameerpadhye",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2025-09-17"
    },
    {
      "version": "1.0.1",
      "date": "2026-07-23"
    }
  ],
  "_exports": [
    "bold.analyze.align",
    "bold.analyze.diversity",
    "bold.analyze.map",
    "bold.analyze.tree",
    "bold.apikey",
    "bold.data.summarize",
    "bold.export",
    "bold.fetch",
    "bold.fields.info",
    "bold.full.search",
    "bold.public.search"
  ],
  "_datasets": [
    {
      "name": "test.data",
      "title": "Canadian spider data by Blagoev et al.(2015)",
      "object": "test.data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "processid",
        "sampleid"
      ],
      "rows": 1336,
      "table": true,
      "tojson": true
    },
    {
      "name": "test.data2",
      "title": "Example Barcode Core Data Model (BCDM) dataset",
      "object": "test.data2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "processid",
        "record_id",
        "insdc_acs",
        "sampleid",
        "specimenid",
        "taxid",
        "short_note",
        "identification_method",
        "museumid",
        "fieldid",
        "collection_code",
        "processid_minted_date",
        "inst",
        "funding_src",
        "sex",
        "life_stage",
        "reproduction",
        "habitat",
        "collectors",
        "site_code",
        "specimen_linkout",
        "collection_event_id",
        "sampling_protocol",
        "tissue_type",
        "collection_date_start",
        "collection_time",
        "associated_taxa",
        "associated_specimens",
        "voucher_type",
        "notes",
        "taxonomy_notes",
        "collection_notes",
        "geoid",
        "marker_code",
        "kingdom",
        "phylum",
        "class",
        "order",
        "family",
        "subfamily",
        "tribe",
        "genus",
        "species",
        "subspecies",
        "identification",
        "identification_rank",
        "species_reference",
        "identified_by",
        "sequence_run_site",
        "nuc",
        "nuc_basecount",
        "sequence_upload_date",
        "bin_uri",
        "bin_created_date",
        "elev",
        "depth",
        "coord",
        "coord_source",
        "coord_accuracy",
        "elev_accuracy",
        "depth_accuracy",
        "realm",
        "biome",
        "ecoregion",
        "region",
        "sector",
        "site",
        "country_iso",
        "country.ocean",
        "province.state",
        "bold_recordset_code_arr",
        "collection_date_end"
      ],
      "rows": 78,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bold.analyze.align",
      "title": "Transform and align the sequence data retrieved from BOLD",
      "topics": [
        "bold.analyze.align"
      ]
    },
    {
      "page": "bold.analyze.diversity",
      "title": "Create a biodiversity profile of the retrieved data",
      "topics": [
        "bold.analyze.diversity"
      ]
    },
    {
      "page": "bold.analyze.map",
      "title": "Visualize BIN occurrence data on maps",
      "topics": [
        "bold.analyze.map"
      ]
    },
    {
      "page": "bold.analyze.tree",
      "title": "Analyze and visualize the multiple sequence alignment",
      "topics": [
        "bold.analyze.tree"
      ]
    },
    {
      "page": "bold.apikey",
      "title": "Set the BOLD private data API key",
      "topics": [
        "bold.apikey"
      ]
    },
    {
      "page": "bold.data.summarize",
      "title": "Generate specific summaries from the downloaded BCDM data",
      "topics": [
        "bold.data.summarize"
      ]
    },
    {
      "page": "bold.export",
      "title": "Export files generated by BOLDconnectR",
      "topics": [
        "bold.export"
      ]
    },
    {
      "page": "bold.fetch",
      "title": "Retrieve data from the BOLD database",
      "topics": [
        "bold.fetch"
      ]
    },
    {
      "page": "bold.fields.info",
      "title": "Retrieve metadata of the BOLD data fields",
      "topics": [
        "bold.fields.info"
      ]
    },
    {
      "page": "bold.full.search",
      "title": "Search user based (private) and publicly available data on the BOLD database",
      "topics": [
        "bold.full.search"
      ]
    },
    {
      "page": "bold.public.search",
      "title": "Search publicly available data on the BOLD database",
      "topics": [
        "bold.public.search"
      ]
    },
    {
      "page": "test.data",
      "title": "Canadian spider data by Blagoev et al.(2015)",
      "topics": [
        "test.data"
      ]
    },
    {
      "page": "test.data2",
      "title": "Example Barcode Core Data Model (BCDM) dataset",
      "topics": [
        "test.data2"
      ]
    }
  ],
  "_readme": "https://github.com/cran/BOLDconnectR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ape",
    "askpass",
    "base64enc",
    "BAT",
    "bit",
    "bit64",
    "boot",
    "caret",
    "class",
    "classInt",
    "cli",
    "clock",
    "cluster",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DEoptim",
    "diagram",
    "digest",
    "doParallel",
    "dplyr",
    "e1071",
    "evaluate",
    "expm",
    "farver",
    "fastcluster",
    "fastmap",
    "fastmatch",
    "FNN",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "geometry",
    "ggplot2",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "highr",
    "hitandrun",
    "hms",
    "htmltools",
    "httr",
    "hypervolume",
    "igraph",
    "ipred",
    "isoband",
    "iterators",
    "jsonlite",
    "kernlab",
    "KernSmooth",
    "knitr",
    "ks",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "linprog",
    "listenv",
    "lpSolve",
    "lubridate",
    "magic",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mclust",
    "mgcv",
    "mime",
    "mnormt",
    "ModelMetrics",
    "multicool",
    "mvtnorm",
    "nlme",
    "nls2",
    "nnet",
    "numDeriv",
    "openssl",
    "optimParallel",
    "palmerpenguins",
    "parallelly",
    "pbapply",
    "pdist",
    "permute",
    "phangorn",
    "phytools",
    "pillar",
    "pkgconfig",
    "PlotTools",
    "plyr",
    "pracma",
    "prettyunits",
    "pROC",
    "prodlim",
    "progress",
    "progressr",
    "proto",
    "proxy",
    "purrr",
    "quadprog",
    "R6",
    "raster",
    "rbibutils",
    "rcdd",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppProgress",
    "Rdpack",
    "recipes",
    "repr",
    "reshape2",
    "rlang",
    "rnaturalearth",
    "rpart",
    "s2",
    "S7",
    "scales",
    "scatterplot3d",
    "sf",
    "shape",
    "skimr",
    "sp",
    "sparsevctrs",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "terra",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "TreeTools",
    "tzdb",
    "units",
    "utf8",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "wk",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "boldconnectr_workflow.Rmd",
      "filename": "boldconnectr_workflow.html",
      "title": "A simple workflow using BOLDconnectR",
      "author": "Padhye SM, Ballesteros-Mejia CL,Agda TJA, Agda JRA, Ratnasingham S",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A simple workflow using BOLDconnectR",
        "Retrieval and Analysis of BOLD Data for the Fairy Shrimp Genus Streptocephalus (Crustacea: Anostraca)",
        "Installation and Import",
        "Suggested packages",
        "API key",
        "Please note",
        "1. Searching and fetching",
        "2. Concise summary of the data",
        "3. Visualizing their occurrence distribution",
        "4. Alignment and visualization",
        "4a. Sequence alignment",
        "4b. Neighbor Joining Tree",
        "5. Calculating BIN richness estimates and multisite beta diversity measure between different countries",
        "5a. BIN richness",
        "5b. Beta diversity",
        "Export data",
        "Additional notes"
      ],
      "created": "2026-07-23 18:10:02",
      "modified": "2026-07-23 18:10:02",
      "commits": 1
    }
  ],
  "_score": 3.079181246047625,
  "_indexed": false,
  "_nocasepkg": "boldconnectr",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://sameerpadhye.r-universe.dev/BOLDconnectR",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-07-23T21:17:01.000Z",
      "distro": "resolute",
      "commit": "b4510741cabcb775823de138fc59af31618da9f3",
      "fileid": "https://r2.ropensci.org/c4db9655e17fcd2d709efa5bdd36ccabc510fbc7d20e4c282aef424e9910f4aa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/30043265996"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-07-23T21:17:15.000Z",
      "distro": "resolute",
      "commit": "b4510741cabcb775823de138fc59af31618da9f3",
      "fileid": "https://r2.ropensci.org/9d61b65c10cc459f5fd65c832f6df3b5f16d40adfc0e4181e4f4a772ee63b81a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/30043265996"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-07-23T21:18:17.000Z",
      "commit": "b4510741cabcb775823de138fc59af31618da9f3",
      "fileid": "https://r2.ropensci.org/c890cb49f94f876b2d375099e3e882d2eea89361c938d7c82983fa185f4c44b5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/30043265996"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-07-23T21:15:50.000Z",
      "commit": "b4510741cabcb775823de138fc59af31618da9f3",
      "fileid": "https://r2.ropensci.org/f8a2d2ebed51e28a1c77754d17b3c026950b596805be48b76b28745b9e7ab088",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/30043265996"
    }
  ]
}