{
  "_id": "6a1e95721d7bb097a0a6ba5e",
  "Package": "eDNAfuns",
  "Type": "Package",
  "Title": "Working with Metabarcoding Data in a Tidy Format",
  "Version": "0.1.0",
  "Authors@R": "person(given = \"Ramón\",\nfamily= c(\"Gallego Simón\"),\nrole= c(\"aut\",\"cre\"),\nemail= \"ramongallego@gmail.com\")",
  "Description": "A series of R functions that come in handy while working\nwith metabarcoding data. The reasoning of doing this is to have\nthe same functions we use all the time stored in a curated,\nreproducible way. In a way it is all about putting together the\ngrammar of the 'tidyverse' from Wickham et al.(2019)\n<doi:10.21105/joss.01686> with the functions we have used in\ncommunity ecology compiled in packages like 'vegan' from Dixon\n(2003) <doi:10.1111/j.1654-1103.2003.tb02228.x> and 'phyloseq'\nMcMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>.\nThe package includes functions to read sequences from FAST(A/Q)\ninto a tibble ('fasta_reader' and 'fastq_reader'), to process\n'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file'\noutput. When it comes to sequence counts across samples, the\npackage works with the long format in mind (a three column\n'tibble' with Sample, Sequence and counts ), with functions to\nmove from there to the wider format.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:26:43 UTC",
    "User": "root"
  },
  "Author": "Ramón Gallego Simón [aut, cre]",
  "Maintainer": "Ramón Gallego Simón <ramongallego@gmail.com>",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://ramongallego.r-universe.dev",
  "Date/Publication": "2025-10-01 07:00:09 UTC",
  "RemoteUrl": "https://github.com/cran/eDNAfuns",
  "RemoteRef": "HEAD",
  "RemoteSha": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
  "MD5sum": "ab78f7453f551f22990791df6ffd0be1",
  "_user": "ramongallego",
  "_type": "src",
  "_file": "eDNAfuns_0.1.0.tar.gz",
  "_fileid": "06226312d445853c7de3d66ea71f1999d92f807795b1e00b573f4e7d40e40154",
  "_filesize": 239687,
  "_sha256": "06226312d445853c7de3d66ea71f1999d92f807795b1e00b573f4e7d40e40154",
  "_created": "2026-06-02T08:26:43.000Z",
  "_published": "2026-06-02T08:33:54.943Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79030058234,
      "time": 259,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7352758356"
    },
    {
      "job": 79030058082,
      "time": 322,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352779426"
    },
    {
      "job": 79030058204,
      "time": 302,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7352767338"
    },
    {
      "job": 79030058187,
      "time": 294,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352784525"
    },
    {
      "job": 79029468930,
      "time": 212,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352670442"
    },
    {
      "job": 79030058101,
      "time": 147,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352719731"
    },
    {
      "job": 79030058191,
      "time": 186,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7352732028"
    },
    {
      "job": 79030058216,
      "time": 182,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7352730960"
    },
    {
      "job": 79030058124,
      "time": 199,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352736668"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/eDNAfuns",
  "_commit": {
    "id": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
    "author": "Ramón Gallego Simón <ramongallego@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.0\n",
    "time": 1759302009
  },
  "_maintainer": {
    "name": "Ramón Gallego Simón",
    "email": "ramongallego@gmail.com",
    "login": "ramongallego",
    "twitter": "@pollicipes",
    "description": "I am a marine biologist turned bioinformatician. I work with #metabarcoding data from #eDNA in marine systems. Currently a #CesarNombela fellow at UAM",
    "uuid": 15640943
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "googlesheets4",
      "role": "Imports"
    },
    {
      "package": "phyloseq",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "vroom",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "insect",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-40",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.1.0",
      "date": "2025-10-01"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ramongallego",
      "count": 1,
      "uuid": 15640943
    }
  ],
  "_userbio": {
    "uuid": 15640943,
    "type": "user",
    "name": "ramongallego",
    "description": "I am a marine biologist turned bioinformatician. I work with #metabarcoding data from #eDNA in marine systems. Currently a #CesarNombela fellow at UAM"
  },
  "_downloads": {
    "count": 134,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/eDNAfuns"
  },
  "_searchresults": 21,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/eDNAfuns.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "ramongallego",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2025-10-03"
    }
  ],
  "_exports": [
    "count_stop_codons",
    "eDNAindex",
    "fasta_reader",
    "fasta_writer",
    "fastq_reader",
    "fastq_writer",
    "mutation",
    "ng2nM",
    "nM2ng",
    "phyloseq2tidy",
    "plot_seq_len_hist",
    "read_indexing_PCR",
    "read_info_file",
    "read_step1_PCR",
    "tally_wide",
    "tibble_to_comm",
    "tibble_to_dist",
    "tibble_to_env",
    "tidy2phyloseq",
    "write_indexing_PCR"
  ],
  "_datasets": [
    {
      "name": "AMPURE",
      "title": "AMPURE",
      "object": "AMPURE",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Position",
        "Sample",
        "PCR_of_Origin",
        "Well_of_Origin",
        "Keepers",
        "n",
        "Well",
        "Row",
        "Column"
      ],
      "rows": 64,
      "table": true,
      "tojson": true
    },
    {
      "name": "ASV_table",
      "title": "ASV_table",
      "object": "ASV_table",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sample_name",
        "Hash",
        "nReads"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_hashes",
      "title": "example_hashes",
      "object": "example_hashes",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "header",
        "seq",
        "seq_len"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    },
    {
      "name": "Index_PCR",
      "title": "Index_PCR",
      "object": "Index_PCR",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "metadata",
      "title": "metadata",
      "object": "metadata",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "sample_name",
        "Treatment",
        "Day"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "molarity.data",
      "title": "molarity.data",
      "object": "molarity.data",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Sample",
        "Molarity",
        "Amp_len",
        "mass"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "OTU_taxonomy",
      "title": "OTU_taxonomy",
      "object": "OTU_taxonomy",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Hash",
        "Kingdom",
        "Phylum",
        "Class",
        "Order",
        "Family",
        "Genus"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "ps",
      "title": "ps",
      "object": "ps",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "template_PCR",
      "title": "template_PCR",
      "object": "template_PCR",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "test_seqs",
      "title": "test_seqs",
      "object": "test_seqs",
      "class": [
        "DNAbin"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "training.ASV.table",
      "title": "training.ASV.table",
      "object": "training.ASV.table",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Sample_name",
        "Locus",
        "Hash",
        "nReads"
      ],
      "rows": 1909,
      "table": true,
      "tojson": true
    },
    {
      "name": "training.metadata",
      "title": "training.metadata",
      "object": "training.metadata",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Sample_name",
        "eDNA.sample",
        "rep",
        "Transect",
        "position",
        "depth",
        "lat",
        "lon"
      ],
      "rows": 95,
      "table": true,
      "tojson": true
    },
    {
      "name": "tree",
      "title": "tree",
      "object": "tree",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "UDI_Indices",
      "title": "UDI_Indices",
      "object": "UDI_Indices",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Index",
        "Bases_in_Adapter_i7",
        "Bases_for_Sample_Sheet_i7",
        "Bases_for_Sample_Sheet_i5",
        "Bases_for_Sample_Sheet_i5_B",
        "Set"
      ],
      "rows": 384,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AMPURE",
      "title": "AMPURE",
      "topics": [
        "AMPURE"
      ]
    },
    {
      "page": "ASV_table",
      "title": "ASV_table",
      "topics": [
        "ASV_table"
      ]
    },
    {
      "page": "count_stop_codons",
      "title": "Count stop codons or return translated sequence",
      "topics": [
        "count_stop_codons"
      ]
    },
    {
      "page": "eDNAindex",
      "title": "Create scaled relative proportions of the number of reads of taxa in different samples",
      "topics": [
        "eDNAindex"
      ]
    },
    {
      "page": "example_hashes",
      "title": "example_hashes",
      "topics": [
        "example_hashes"
      ]
    },
    {
      "page": "fasta_reader",
      "title": "Read FASTA or FASTQ files into a tibble",
      "topics": [
        "fasta_reader",
        "fastq_reader"
      ]
    },
    {
      "page": "fasta_writer",
      "title": "Read FASTA or FASTQ files into a tibble",
      "topics": [
        "fasta_writer",
        "fastq_writer"
      ]
    },
    {
      "page": "Index_PCR",
      "title": "Index_PCR",
      "topics": [
        "Index_PCR"
      ]
    },
    {
      "page": "metadata",
      "title": "metadata",
      "topics": [
        "metadata"
      ]
    },
    {
      "page": "molarity.data",
      "title": "molarity.data",
      "topics": [
        "molarity.data"
      ]
    },
    {
      "page": "mutation",
      "title": "Generate mutated DNA sequences",
      "topics": [
        "mutation"
      ]
    },
    {
      "page": "ng2nM",
      "title": "functions to translate mass into molarity and vice versa, given we are talking about double stranded DNA it requires two inputs, the mass (or molarity) and the length of the DNA fragment It works with the two most common concentrations used in Molecular Ecology labs ng/mul for mass nM for molarity",
      "topics": [
        "ng2nM",
        "nM2ng"
      ]
    },
    {
      "page": "OTU_taxonomy",
      "title": "OTU_taxonomy",
      "topics": [
        "OTU_taxonomy"
      ]
    },
    {
      "page": "plot_seq_len_hist",
      "title": "Plot sequence length distribution",
      "topics": [
        "plot_seq_len_hist"
      ]
    },
    {
      "page": "ps",
      "title": "ps",
      "topics": [
        "ps"
      ]
    },
    {
      "page": "read_PCR",
      "title": "Read Indexing PCR Spreadsheet",
      "topics": [
        "read_indexing_PCR",
        "read_step1_PCR"
      ]
    },
    {
      "page": "read_info_file",
      "title": "Read cutadapt info files",
      "topics": [
        "read_info_file"
      ]
    },
    {
      "page": "tally_wide",
      "title": "Create contingency tables with two variables",
      "topics": [
        "tally_wide"
      ]
    },
    {
      "page": "template_PCR",
      "title": "template_PCR",
      "topics": [
        "template_PCR"
      ]
    },
    {
      "page": "test_seqs",
      "title": "test_seqs",
      "topics": [
        "test_seqs"
      ]
    },
    {
      "page": "tibble_to_vegan",
      "title": "Convert a long tibble to a community matrix",
      "topics": [
        "tibble_to_comm",
        "tibble_to_dist",
        "tibble_to_env"
      ]
    },
    {
      "page": "phyloseq_tidy",
      "title": "Convert a tidy ASV table to a phyloseq object",
      "topics": [
        "phyloseq2tidy",
        "tidy2phyloseq"
      ]
    },
    {
      "page": "training.ASV.table",
      "title": "training.ASV.table",
      "topics": [
        "training.ASV.table"
      ]
    },
    {
      "page": "training.metadata",
      "title": "training.metadata",
      "topics": [
        "training.metadata"
      ]
    },
    {
      "page": "tree",
      "title": "tree",
      "topics": [
        "tree"
      ]
    },
    {
      "page": "UDI_Indices",
      "title": "UDI_Indices",
      "topics": [
        "UDI_Indices"
      ]
    },
    {
      "page": "write_indexing_PCR",
      "title": "Write Indexing PCR Spreadsheet",
      "topics": [
        "write_indexing_PCR"
      ]
    }
  ],
  "_readme": "https://github.com/cran/eDNAfuns/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "ape",
    "askpass",
    "Biobase",
    "BiocGenerics",
    "biomformat",
    "Biostrings",
    "bit",
    "bit64",
    "cellranger",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "digest",
    "dplyr",
    "farver",
    "foreach",
    "fs",
    "gargle",
    "generics",
    "ggplot2",
    "glue",
    "googledrive",
    "googlesheets4",
    "gtable",
    "hms",
    "httr",
    "ids",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "mgcv",
    "mime",
    "multtest",
    "nlme",
    "openssl",
    "permute",
    "phyloseq",
    "pillar",
    "pixmap",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "readr",
    "rematch",
    "rematch2",
    "reshape2",
    "rlang",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "sp",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "uuid",
    "vctrs",
    "vegan",
    "viridisLite",
    "vroom",
    "withr",
    "XVector"
  ],
  "_score": 2.0211892990699383,
  "_indexed": true,
  "_nocasepkg": "ednafuns",
  "_universes": [
    "ramongallego"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-02T08:29:36.000Z",
      "distro": "noble",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "8a17f389c0c75e67ac0fe83760a87170b3d74b7a2813be114b7d22c1ff8854d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-02T08:30:20.000Z",
      "distro": "noble",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "4e9cb81c506b1cc9c0ab7a8885b497f0bd0e7514ed4a5eee22b30d34640fdb4c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-02T08:29:57.000Z",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "f1b81b2dd86765e7166630ca8f8d4b42494c69d67a7eeffe3df9ff65353e4268",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-02T08:30:48.000Z",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "3b401fb169a36a53935b1c6137bc649027f9af68c7315a5a1c70169bcf0850e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-06-02T08:29:36.000Z",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "403d223b5c549ac377d590b52aee5d9bb51809452fc4d71f7bd6d148e8394e27",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-02T08:28:18.000Z",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "7cd47b508e31aa17db7776e3ced35d6597094eba43d41fd01e6c11bba76c46ce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-02T08:28:17.000Z",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "ccfc91711c8329d70251da7ea159fa91d98969cf962596462e5f4f868d63f6f3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-02T08:28:13.000Z",
      "commit": "d56354ab3cb233850f64f9ff5cb3b81bbede0f73",
      "fileid": "1ce2f54aee21652e7151211535f35ce185dd2d47c60ed7c31bafcfb08df0a627",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ramongallego/actions/runs/26807719427"
    }
  ]
}