Return a reference to a given table in the taxadb database

Return a reference to a given table in the taxadb database

Usage

taxa_tbl(
  provider = getOption("taxadb_default_provider", "itis"),
  schema = c("dwc", "common"),
  version = latest_version(),
  db = td_connect()
)

Arguments

provider

from which provider should the hierarchy be returned? Default is 'itis', which can also be configured using options(default_taxadb_provider=..."). See [td_create] for a list of recognized providers.

schema

One of "dwc" (for Darwin Core data) or "common" (for the Common names table.)

version

Which version of the taxadb provider database should we use? defaults to latest. See available_versions() for details.

db

a connection to the taxadb database. See details.

Value

a lazy dplyr table backed by the requested Parquet snapshot.

Details

The returned table is a duckdb view over Parquet, so it can be manipulated with any dplyr verb and is only ever read to the extent your query requires. Unless a local copy has been installed with td_download(), the data is streamed from remote storage on demand.

Examples

# \donttest{

  ## default schema is the Darwin Core table
  taxa_tbl()
#> # A query:  ?? x 15
#> # Database: DuckDB 1.5.5 [unknown@Linux 6.17.0-1022-azure:R 4.6.0/:memory:]
#>    taxonID  scientificName taxonRank acceptedNameUsageID taxonomicStatus kingdom
#>    <chr>    <chr>          <chr>     <chr>               <chr>           <chr>  
#>  1 ITIS:10… Leontopithecu… species   ITIS:1025093        synonym         Animal…
#>  2 ITIS:10… Midas tripart… species   ITIS:1025098        synonym         Animal…
#>  3 ITIS:10… Hapale nigrif… species   ITIS:1025100        synonym         Animal…
#>  4 ITIS:10… Midas bicolor  species   ITIS:572923         synonym         Animal…
#>  5 ITIS:10… Leontocebus m… subspeci… ITIS:1207742        synonym         Animal…
#>  6 ITIS:10… Saguinus fusc… subspeci… ITIS:1025157        synonym         Animal…
#>  7 ITIS:10… Leontocebus w… species   ITIS:1025102        accepted        Animal…
#>  8 ITIS:10… Leontocebus w… subspeci… ITIS:1025155        accepted        Animal…
#>  9 ITIS:10… Leontocebus w… subspeci… ITIS:1025156        accepted        Animal…
#> 10 ITIS:10… Leontocebus w… subspeci… ITIS:1025157        accepted        Animal…
#> # ℹ more rows
#> # ℹ 9 more variables: phylum <chr>, class <chr>, order <chr>, family <chr>,
#> #   genus <chr>, specificEpithet <chr>, infraspecificEpithet <chr>,
#> #   vernacularName <chr>, update_date <chr>

  ## common names table
  taxa_tbl(schema = "common")
#> # A query:  ?? x 15
#> # Database: DuckDB 1.5.5 [unknown@Linux 6.17.0-1022-azure:R 4.6.0/:memory:]
#>    taxonID  vernacularName language acceptedNameUsageID scientificName taxonRank
#>    <chr>    <chr>          <chr>    <chr>               <chr>          <chr>    
#>  1 ITIS:55… Tibetan Babax  english  ITIS:1282110        Babax koslowi  species  
#>  2 ITIS:55… Chinese Babax  english  ITIS:1282108        Babax lanceol… species  
#>  3 ITIS:55… Giant Babax    english  ITIS:1282109        Babax waddelli species  
#>  4 ITIS:55… Spotted Croci… english  ITIS:1282057        Crocias albon… species  
#>  5 ITIS:55… Grey-crowned … english  ITIS:1282056        Crocias langb… species  
#>  6 ITIS:56… Black-faced L… english  ITIS:916118         Garrulax affi… species  
#>  7 ITIS:56… White-throate… english  ITIS:1282111        Garrulax albo… species  
#>  8 ITIS:56… Brown-capped … english  ITIS:916113         Garrulax aust… species  
#>  9 ITIS:56… White-speckle… english  ITIS:1282091        Garrulax bieti species  
#> 10 ITIS:56… Nilgiri Laugh… english  ITIS:1282059        Garrulax cach… species  
#> # ℹ more rows
#> # ℹ 9 more variables: taxonomicStatus <chr>, kingdom <chr>, phylum <chr>,
#> #   class <chr>, order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> #   infraspecificEpithet <chr>

# }