A simple function to return information about a particular species, including name validity and country occurrences.
BeeBDCQuery(
beeName = NULL,
searchChecklist = TRUE,
printAllSynonyms = FALSE,
beesChecklist = NULL,
beesTaxonomy = NULL
)Character or character vector. A single or several bee species names to search for in the beesTaxonomy and beesChecklist tables.
Logical. If TRUE (default), search the country checklist for each species.
Logical. If TRUE, all synonyms will be printed out for each entered name. default = FALSE.
A tibble. The bee checklist file for BeeBDC. If is NULL then
beesChecklist() will be called internally to download the file. Default = NULL.
A tibble. The bee taxonomy file for BeeBDC. If is NULL then
beesTaxonomy() will be called internally to download the file. Default = NULL.
Returns a list with the elements 'taxonomyReport' and 'SynonymReport'. IF searchChecklist is TRUE, then 'checklistReport' will also be returned.
# For the sake of these examples, we will use the example taxonomy and checklist
system.file("extdata", "testTaxonomy.rda", package="BeeBDC") |> load()
system.file("extdata", "testChecklist.rda", package="BeeBDC") |> load()
# Single entry example
testQuery <- BeeBDCQuery(
beeName = "Lasioglossum bicingulatum",
searchChecklist = TRUE,
printAllSynonyms = TRUE,
beesTaxonomy = testTaxonomy,
beesChecklist = testChecklist)
#> Starting taxonomy report...
#> Lasioglossum bicingulatum is an accpeted name with the taxon id number 30809.
#> - 'Lasioglossum bicingulatum' has the synonyms:
#> Starting checklist report...
#> - Lasioglossum bicingulatum (Smith, 1853) is reportedly found in:
#> Australia
#> The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'.
#> These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
# Multiple entry example
testQuery <- BeeBDCQuery(
beeName = c("Lasioglossum bicingulatum", "Nomada flavopicta",
"Lasioglossum fijiense (Perkins and Cheesman, 1928)"),
searchChecklist = TRUE,
printAllSynonyms = TRUE,
beesTaxonomy = testTaxonomy,
beesChecklist = testChecklist)
#> Starting taxonomy report...
#> Lasioglossum bicingulatum is an accpeted name with the taxon id number 30809.
#> Nomada flavopicta is an accpeted name with the taxon id number 16654.
#> - 'Lasioglossum bicingulatum' has the synonyms:
#> - 'Nomada flavopicta' has the synonyms:
#> Starting checklist report...
#> - Lasioglossum bicingulatum (Smith, 1853) is reportedly found in:
#> Australia
#> - Nomada flavopicta (Kirby, 1802) is reportedly found in:
#> Austria, Azerbaijan, Belarus, Brussels, Bulgaria, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Greenland, Guernsey, Hungary, Iran, Italy, Jersey, Kazakhstan, Kyrgyzstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Netherlands, Norway, Poland, Romania, Russian Federation, Slovakia, Slovenia, Spain, Sweden, Switzerland, Tajikistan, Turkey, Ukraine, Uzbekistan, United Kingdom
#> The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'.
#> These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
# Example way to examine a report from the output list
testQuery$checklistReport
#> # A tibble: 42 × 24
#> validName DiscoverLife_name rNaturalEarth_name shortName continent
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Lasioglossum bicing… Australia Australia Australia Oceania
#> 2 Nomada flavopicta (… Austria Austria Austria Europe
#> 3 Nomada flavopicta (… Azerbaijan Azerbaijan Azerbaij… Asia
#> 4 Nomada flavopicta (… Belarus Belarus Belarus Europe
#> 5 Nomada flavopicta (… Belgium Brussels Belgium NA
#> 6 Nomada flavopicta (… Bulgaria Bulgaria Bulgaria Europe
#> 7 Nomada flavopicta (… Croatia Croatia Croatia Europe
#> 8 Nomada flavopicta (… Czechia Czech Republic Czechia Europe
#> 9 Nomada flavopicta (… Denmark Denmark Denmark Europe
#> 10 Nomada flavopicta (… Estonia Estonia Estonia Europe
#> # ℹ 32 more rows
#> # ℹ 19 more variables: DiscoverLife_ISO <chr>, `Alpha-2` <chr>,
#> # iso_a3_eh <chr>, official <chr>, Source <chr>, matchCertainty <chr>,
#> # canonical <chr>, canonical_withFlags <chr>, family <chr>, subfamily <chr>,
#> # genus <chr>, subgenus <lgl>, specificEpithet <chr>, species <chr>,
#> # infraspecies <chr>, scientificNameAuthorship <chr>, taxon_rank <chr>,
#> # Notes <chr>, name <chr>