Test Georeferenced Data

Description Usage Arguments Details Value Note Author(s) References See Also

Download occurrences from the Global Biodiversity Information Facility (GBIF) [1]

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gbifDownSp(sp.name = NULL, taxon.key = NULL, genus = NULL,
  epithet = NULL, starts.in = 1, wrt.frmt = "saveRDS",
  save.download.in = NULL, ...)

`sp.name`	Vector of characters. A species list to download. See details.
`taxon.key`	Vector of characters. A codes list, these codes are assigned by GBIF [1] to each species. See details.
`genus`	Vector od Characters. A genera list to download.
`epithet`	Vector of characters. A epithet list to download.
`starts.in`	Numeric vector. Row number to start the process.
`wrt.frmt`	Vector of characters. Format to save output file. By default it will be written as a R object using `'saveRDS'` argument, but it can be saved as plain text using `'saveTXT'` argument. See details.
`save.download.in`	Character. Vector of characters. Path to the output file for each species downloaded.
`...`	All parameters that can parsed to `occ_search` function from `rgbif` package [2] as limit, basisOfRecord, country, publishingCountry, lastInterpreted, geometry, collectionCode, institutionCode and year.

Additional parameters (...) see occ_search function from rgbif package. The user can only use one parameter at a time: sp.name, taxon.key or genus and/or epithet.

For sp.name parameter, a list of species names could be assigned. The species names must have genus and epithet, separated by a single space.

For taxon.key parameter the list have to be the ID number that assigns GBIF to each taxonomical level.

The headers of the input file must follow the Darwin Core standard [3]. The user can see the guide using data('ID_DarwinCore) command.

For more details about the formats to read and/or write, see readAndWrite function.

Save one file by species. This file is a list of all occurrences recorded from GBIF.

See: R-Alarcon V, Miranda-Esquivel DR.(submitted) geocleaMT: An R package to cleaning geographical data from electronic biodatabases.

R-Alarcon Viviana and Miranda-Esquivel Daniel R.

[1] Global Biodiversity Information Facility. Available online at http://www.gbif.org/.

[2] Chamberlain, S. et al. 2015. rgbif: Interface to the Global Biodiversity Information Facility ‘API’. R package version 0.9.0. The Comprehensive R Archive Network (CRAN). Available online at http://cran.r-project.org/package=rgbif.

[3] Wieczorek, J. et al. 2012. Darwin core: An evolving community-developed biodiversity data standard. PloS One 7: e29715.

readAndWrite

occ_search

Dmirandae/geocleaMT-1 documentation built on Nov. 18, 2019, 6:26 p.m.