A simple function to return information about a particular species, including name validity and country occurrences.
Usage
BeeBDCQuery(
beeName = NULL,
searchChecklist = TRUE,
printAllSynonyms = FALSE,
beesChecklist = NULL,
beesTaxonomy = NULL
)Arguments
- beeName
Character or character vector. A single or several bee species names to search for in the beesTaxonomy and beesChecklist tables.
- searchChecklist
Logical. If TRUE (default), search the country checklist for each species.
- printAllSynonyms
Logical. If TRUE, all synonyms will be printed out for each entered name. default = FALSE.
- beesChecklist
A tibble. The bee checklist file for BeeBDC. If is NULL then
beesChecklist()will be called internally to download the file. Default = NULL.- beesTaxonomy
A tibble. The bee taxonomy file for BeeBDC. If is NULL then
beesTaxonomy()will be called internally to download the file. Default = NULL.
Value
Returns a list with the elements 'taxonomyReport' and 'SynonymReport'. IF searchChecklist is TRUE, then 'checklistReport' will also be returned.
Examples
# 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 31378.
#> - '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 31378.
#> Nomada flavopicta is an accpeted name with the taxon id number 17033.
#> - '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, 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: 41 × 23
#> validName DiscoverLife_name rNaturalEarth_name shortName DiscoverLife_ISO
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Lasioglossum… Australia Australia Australia AS
#> 2 Nomada flavo… Austria Austria Austria AU
#> 3 Nomada flavo… Azerbaijan Azerbaijan Azerbaij… AJ
#> 4 Nomada flavo… Belarus Belarus Belarus BO
#> 5 Nomada flavo… Belgium Brussels Belgium BE
#> 6 Nomada flavo… Bulgaria Bulgaria Bulgaria BU
#> 7 Nomada flavo… Croatia Croatia Croatia HR
#> 8 Nomada flavo… Czechia Czech Republic Czechia EZ
#> 9 Nomada flavo… Denmark Denmark Denmark DA
#> 10 Nomada flavo… Estonia Estonia Estonia EN
#> # ℹ 31 more rows
#> # ℹ 18 more variables: `Alpha-2` <chr>, `Alpha-3` <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>,
#> # infraspecificEpithet <chr>, Notes <chr>