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  "Package": "taxify",
  "Title": "Offline Taxonomic Name Matching Against Local Darwin Core\nSnapshots",
  "Version": "0.2.12",
  "Authors@R": "person(\"Gilles\", \"Colling\", , \"gilles.colling051@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-3070-6066\"))",
  "Description": "Match taxonomic names against locally stored Darwin Core\nbackbone databases ('WFO', 'COL', 'GBIF', 'ITIS', 'NCBI\nTaxonomy', 'Open Tree of Life', 'WoRMS', 'Species Fungorum',\n'AlgaeBase'). Provides offline fuzzy and exact matching with\nsynonym resolution, hybrid name detection, and a unified output\nschema across all sources. All heavy computation runs in the\n'vectra' C11 columnar engine.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/gcol33/taxify",
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  "Author": "Gilles Colling [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-3070-6066>)",
  "Maintainer": "Gilles Colling <gilles.colling051@gmail.com>",
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    "add_anage",
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    "taxify_example_data",
    "taxify_load_register",
    "taxify_long",
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      "title": "Add macroalgal functional traits (AlgaeTraits)",
      "topics": [
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      ]
    },
    {
      "page": "add_alien_first_records",
      "title": "Add alien species first record years",
      "topics": [
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      ]
    },
    {
      "page": "add_amphibio",
      "title": "Add amphibian life-history traits (AmphiBIO)",
      "topics": [
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      ]
    },
    {
      "page": "add_anage",
      "title": "Add longevity and life-history traits (AnAge)",
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    },
    {
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      "title": "Add cross-taxon body mass and metabolic rate (AnimalTraits)",
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    },
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      "title": "Add bird morphology and migration (AVONET)",
      "topics": [
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      ]
    },
    {
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      "title": "Add plant traits from Baseflor (Catminat / Julve)",
      "topics": [
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    },
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      "page": "add_col_info",
      "title": "Add COL-specific columns",
      "topics": [
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    },
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      "page": "add_common_names",
      "title": "Add common (vernacular) names",
      "topics": [
        "add_common_names"
      ]
    },
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      "title": "Add conservation status",
      "topics": [
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    },
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      "title": "Add custom data by taxonomic matching",
      "topics": [
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      ]
    },
    {
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      "title": "Add seed mass and plant height (Diaz et al. 2022)",
      "topics": [
        "add_diaz_traits"
      ]
    },
    {
      "page": "add_ecoflora",
      "title": "Add British plant traits from Ecoflora",
      "topics": [
        "add_ecoflora"
      ]
    },
    {
      "page": "add_eive",
      "title": "Add EIVE ecological indicator values",
      "topics": [
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      "title": "Add fish traits (FishBase)",
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    },
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      "title": "Add German plant traits from FloraWeb",
      "topics": [
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    },
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      "title": "Add fungal lifestyle and trait data (FungalTraits)",
      "topics": [
        "add_fungal_traits"
      ]
    },
    {
      "page": "add_funguild",
      "title": "Add fungal functional guild data (FUNGuild)",
      "topics": [
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    },
    {
      "page": "add_gbif_info",
      "title": "Add GBIF-specific columns",
      "topics": [
        "add_gbif_info"
      ]
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    {
      "page": "add_glonaf",
      "title": "Add naturalized alien flora status (GloNAF)",
      "topics": [
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    {
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      "title": "Add hybrid parent and type information",
      "topics": [
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      ]
    },
    {
      "page": "add_invasive_status",
      "title": "Add invasive species status",
      "topics": [
        "add_invasive_status"
      ]
    },
    {
      "page": "add_leda",
      "title": "Add plant traits from LEDA Traitbase",
      "topics": [
        "add_leda"
      ]
    },
    {
      "page": "add_leptraits",
      "title": "Add butterfly traits (LepTraits)",
      "topics": [
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      ]
    },
    {
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      "title": "Add lizard life-history and ecological traits (Meiri 2018)",
      "topics": [
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      ]
    },
    {
      "page": "add_pantheria",
      "title": "Add mammal life-history traits (PanTHERIA)",
      "topics": [
        "add_pantheria"
      ]
    },
    {
      "page": "add_pignatti",
      "title": "Add Italian plant traits from Pignatti (on demand, via TR8)",
      "topics": [
        "add_pignatti"
      ]
    },
    {
      "page": "add_qualifier_info",
      "title": "Add qualifier information",
      "topics": [
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      ]
    },
    {
      "page": "add_wcvp",
      "title": "Add WCVP native range status",
      "topics": [
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      ]
    },
    {
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      "title": "Add WFO-specific columns",
      "topics": [
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      ]
    },
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      "title": "Add woodiness classification",
      "topics": [
        "add_woodiness"
      ]
    },
    {
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      "title": "Cite data sources used in a taxify result",
      "topics": [
        "cite"
      ]
    },
    {
      "page": "export_data",
      "title": "Export a taxify result to file",
      "topics": [
        "export_data"
      ]
    },
    {
      "page": "list_enrichments",
      "title": "List available enrichments",
      "topics": [
        "list_enrichments"
      ]
    },
    {
      "page": "lookup_genus",
      "title": "Look up a genus in the register",
      "topics": [
        "lookup_genus"
      ]
    },
    {
      "page": "print.taxify_result",
      "title": "Print a taxify_result",
      "topics": [
        "print.taxify_result"
      ]
    },
    {
      "page": "summary.taxify_result",
      "title": "Summarise a taxify_result",
      "topics": [
        "summary.taxify_result"
      ]
    },
    {
      "page": "taxify",
      "title": "Match taxonomic names against local backbone databases",
      "topics": [
        "taxify"
      ]
    },
    {
      "page": "taxify_clear_cache",
      "title": "Clear all cached backbones",
      "topics": [
        "taxify_clear_cache"
      ]
    },
    {
      "page": "taxify_data_dir",
      "title": "Get the taxify data directory",
      "topics": [
        "taxify_data_dir"
      ]
    },
    {
      "page": "taxify_download",
      "title": "Download a backbone database",
      "topics": [
        "taxify_download"
      ]
    },
    {
      "page": "taxify_download_enrichment",
      "title": "Download one or more enrichment .vtr files",
      "topics": [
        "taxify_download_enrichment"
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    },
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      "title": "Download a taxify backbone",
      "topics": [
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    {
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      "title": "Path to the bundled example database",
      "topics": [
        "taxify_example_data"
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    },
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      "page": "taxify_load_register",
      "title": "Load the unified genus register into memory",
      "topics": [
        "taxify_load_register"
      ]
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    {
      "page": "taxify_long",
      "title": "Reshape grouped enrichment columns to long format",
      "topics": [
        "taxify_long"
      ]
    },
    {
      "page": "taxify_refresh_manifest",
      "title": "Invalidate the session manifest cache",
      "topics": [
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      ]
    },
    {
      "page": "taxify_register_coverage",
      "title": "Show backend coverage for a genus",
      "topics": [
        "taxify_register_coverage"
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        "Downloading backbones",
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        "### The enrichment data directory",
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        "Arthropods (NW European)",
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        "Macroalgae (European)",
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      "title": "Fuzzy matching: methods, thresholds, and tuning",
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        "The three distance methods",
        "Damerau-Levenshtein (default, fuzzy_method = \"dl\")",
        "Levenshtein (fuzzy_method = \"levenshtein\")",
        "Jaro-Winkler (fuzzy_method = \"jw\")",
        "How thresholds work",
        "Fractional mode (0 < threshold < 1)",
        "Integer mode (threshold >= 1)",
        "What happens before fuzzy matching",
        "Worked example 1: clean names that need no fuzzy matching",
        "Worked example 2: OCR-degraded and hand-typed names",
        "Worked example 3: threshold too loose",
        "Worked example 4: comparing all three methods",
        "The fuzzy_dist column",
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        "When to loosen the threshold",
        "When to switch methods",
        "Using integer thresholds for uniform error budgets",
        "A two-pass workflow for messy data",
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        "Installing a backbone",
        "Basic matching",
        "Understanding the output",
        "Name cleaning",
        "Synonym resolution",
        "Match types",
        "The summary method",
        "Multi-backend fallback",
        "Enrichments",
        "Conservation status",
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        "Woodiness",
        "Custom data",
        "From a data.frame",
        "From a CSV file",
        "Supported file formats",
        "Hybrid names",
        "Genus register",
        "Cache management",
        "The full pipeline"
      ],
      "created": "2026-06-30 11:30:07",
      "modified": "2026-06-30 11:30:07",
      "commits": 1
    },
    {
      "source": "hybrid-names.Rmd",
      "filename": "hybrid-names.html",
      "title": "Hybrid name detection and parsing",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Hybrid names in taxonomy",
        "How taxify detects hybrids",
        "Worked example: matching a mixed species list",
        "Extracting hybrid details with add_hybrid_info()",
        "Worked example: parsing hybrid formulas",
        "What matches and what does not",
        "The multiplication sign and its substitutes",
        "Practical notes"
      ],
      "created": "2026-06-30 11:30:07",
      "modified": "2026-06-30 11:30:07",
      "commits": 1
    },
    {
      "source": "custom-data.Rmd",
      "filename": "custom-data.html",
      "title": "Joining custom data with add_data()",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The problem",
        "Joining a data.frame",
        "Joining from a CSV file",
        "Joining from an Excel file",
        "SQLite databases",
        "vectra native format",
        "Joining from a TSV file",
        "Other file formats",
        "Species column auto-detection",
        "Selecting columns with cols",
        "Column name collisions",
        "Duplicate species handling",
        "How the join works",
        "Controlling fuzzy matching",
        "Combining add_data() with enrichments"
      ],
      "created": "2026-06-30 11:30:07",
      "modified": "2026-06-30 11:30:07",
      "commits": 1
    },
    {
      "source": "migration.Rmd",
      "filename": "migration.html",
      "title": "Migrating from taxize, WorldFlora, and related tools",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The taxonomic-resolution landscape in R",
        "Function mapping: taxize to taxify",
        "Function mapping: WorldFlora to taxify",
        "Function mapping: lcvplants to taxify",
        "Function mapping: rWCVP to taxify",
        "Function mapping: taxadb to taxify",
        "Function mapping: Taxonstand to taxify",
        "Example 1: Basic name resolution",
        "Example 2: WFO matching with fuzzy + synonyms",
        "Example 3: Multi-backend fallback with enrichments",
        "Key differences at a glance",
        "What taxify does not do",
        "When the other packages are the better choice",
        "Discovering available enrichments",
        "Summary"
      ],
      "created": "2026-06-30 11:30:07",
      "modified": "2026-06-30 11:30:07",
      "commits": 1
    },
    {
      "source": "large-scale.Rmd",
      "filename": "large-scale.html",
      "title": "Working with large species lists",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How taxify scales",
        "The .vtr columnar format",
        "Exact matching: hash-indexed lookups",
        "Fuzzy matching: genus-blocked string distance",
        "Backbone loading and the session cache",
        "Worked example: exact vs. fuzzy matching",
        "Worked example: multi-backend fallback ordering",
        "Backbone sizes on disk",
        "Memory footprint",
        "Worked example: batch processing a very large list",
        "Cache management",
        "Disk storage and sharing across projects",
        "Worked example: pre-downloading resources",
        "Practical scaling guidance",
        "The fuzzy_threshold parameter",
        "Summary of performance-relevant functions"
      ],
      "created": "2026-06-30 11:30:07",
      "modified": "2026-06-30 11:30:07",
      "commits": 1
    }
  ],
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