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 tl_import for details.
- db
a connection to the taxadb database. See details.
Examples
# \donttest{
# \dontshow{
## All examples use a temporary directory
Sys.setenv(TAXADB_HOME=file.path(tempdir(), "taxadb"))
options("taxadb_default_provider"="itis_test")
# }
## default schema is the dwc table
taxa_tbl()
#> # Source: table<"v22.12_dwc_itis_test"> [?? x 15]
#> # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1017-azure:R 4.3.3/:memory:]
#> taxonID scientificName taxonRank acceptedNameUsageID taxonomicStatus
#> <chr> <chr> <chr> <chr> <chr>
#> 1 ITIS:1025094 Leontopithecus fu… species ITIS:1025093 synonym
#> 2 ITIS:1025099 Midas tripartitus species ITIS:1025098 synonym
#> 3 ITIS:1025101 Hapale nigrifrons species ITIS:1025100 synonym
#> 4 ITIS:1025103 Midas bicolor species ITIS:572923 synonym
#> 5 ITIS:1025108 Simia lugens species ITIS:1025104 synonym
#> 6 ITIS:1025109 Callitrix torquat… species ITIS:1025106 synonym
#> 7 ITIS:1025118 Callithrix donaco… species ITIS:1025112 synonym
#> 8 ITIS:1025123 Callithrix cinera… species ITIS:1025122 synonym
#> 9 ITIS:1025135 Plecturocebus dub… species ITIS:1025134 synonym
#> 10 ITIS:1025136 Callithrix caliga… species ITIS:1025134 synonym
#> # ℹ more rows
#> # ℹ 10 more variables: update_date <lgl>, kingdom <chr>, phylum <chr>,
#> # class <chr>, order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> # vernacularName <chr>, infraspecificEpithet <lgl>
## common names table
taxa_tbl(schema = "common")
#> # Source: table<"v22.12_common_itis_test"> [?? x 16]
#> # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1017-azure:R 4.3.3/:memory:]
#> vernacularName language update_date acceptedNameUsageID taxonID
#> <chr> <chr> <date> <chr> <chr>
#> 1 man English 2002-07-30 ITIS:180092 ITIS:944513
#> 2 man English 2002-07-30 ITIS:180092 ITIS:944514
#> 3 man English 2002-07-30 ITIS:180092 ITIS:944515
#> 4 man English 2002-07-30 ITIS:180092 ITIS:944516
#> 5 man English 2002-07-30 ITIS:180092 ITIS:944517
#> 6 man English 2002-07-30 ITIS:180092 ITIS:944518
#> 7 man English 2002-07-30 ITIS:180092 ITIS:944519
#> 8 man English 2002-07-30 ITIS:180092 ITIS:944520
#> 9 man English 2002-07-30 ITIS:180092 ITIS:944521
#> 10 man English 2002-07-30 ITIS:180092 ITIS:944522
#> # ℹ more rows
#> # ℹ 11 more variables: scientificName <chr>, taxonRank <chr>,
#> # taxonomicStatus <chr>, kingdom <chr>, phylum <chr>, class <chr>,
#> # order <chr>, family <chr>, genus <chr>, specificEpithet <chr>,
#> # infraspecificEpithet <lgl>
# }