occs_queryDb Query online database for species occurrence records.
occs_queryDb.RdQueries a given database for occurrence data on the provided species
Usage
occs_queryDb(
spNames,
occDb,
occNum = NULL,
doCitations = FALSE,
gbifUser = NULL,
gbifEmail = NULL,
gbifPW = NULL,
RmUncertain = FALSE,
logger = NULL
)Arguments
- spNames
character. Species Latin name, with format "Genus species".
- occDb
character. Biodiversity database to query; current choices are "gbif", "vertnet", and "BIEN"
- occNum
numeric. Maximum number of occurrence records to return
- doCitations
logical. Set TRUE to use `occCite` to get a complete list of original data sources in a citable format
- gbifUser
specify only if using `occCite` with GBIF to get a complete list of original data sources in a citable format. This, as well as `gbifEmail` and `gbifPW` are constraints imposed by GBIF to obtain the complete set of metadata associated with occurrence records and is not stored or used by `wallace` for any other purposes.
- gbifEmail
specify only if using `occCite` with GBIF to get a complete list of original data sources in a citable format.
- gbifPW
specify only if using `occCite` with GBIF to get a complete list of original data sources in a citable format.
- RmUncertain
specify if occurrences without uncertainty information should be removed (default is FALSE)
- logger
Stores all notification messages to be displayed in the Log Window of Wallace GUI. Insert the logger reactive list here for running in shiny, otherwise leave the default NULL
Value
list of lists one list per species with occurrence records. Each individual species list with appropriate fields for analysis
Details
This function is called by the module occs_queryDb to query a database for species occurrence records, subset to only those records with coordinates, remove records with duplicate coordinates, and select some columns with fields appropriate to studies in biogeography.