occs_queryDb: occs_queryDb Query online database for species occurrence...

In wallaceEcoMod/wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

occs_queryDb Query online database for species occurrence records.

Description

Queries 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

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.

Value

list of lists one list per species with occurrence records. Each individual species list with appropriate fields for analysis

Author(s)

Jamie Kass <[e-mail]>

Gonzalo E. Pinilla-Buitrago <[e-mail]>

Hannah Owens

Andrea Paz <[e-mail]>

Examples

## Not run: 
occs_queryDb(spName = "Bassaricyon alleni", occDb = "gbif", occNum = 10)

## End(Not run)

wallaceEcoMod/wallace documentation built on March 24, 2024, 5:15 p.m.