Test Georeferenced Data

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

Separate species categorized as invasive for The Global Invasive Species Information Network (ISSG) [1] and Island Biodiversity and Invasive Species (IBIS) [2].

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invasiveSp(data = NULL, rd.frmt = "readRDS", path = NULL, starts.in = 1,
  save.Sp.list = TRUE, wrt.frmt = "saveRDS", save.foreign.in = NULL,
  save.non.foreign.in = NULL, save.temp.in = NULL)

`data`	Vector of characters. Name of the input file.
`rd.frmt`	Vector of characters. The file format to read. By default it will be read as a R object using the `'readRDS'` argument, but it can be read as plain text using the `'readTXT'` argument. See details.
`path`	Vector of characters. Path to the input file.
`starts.in`	starts.in Numeric vector. Row number to start the process.
`save.Sp.list`	Logic. If `'TRUE'`, two files are saved, one has the list of invasive species and other has the list of non-invasive species, both have two columns genus and specific epithet and it will be used as input for the `gbifDownSp` function.
`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.foreign.in`	Vector of characters. Path to write the output file with species that are categorized as invasive.
`save.non.foreign.in`	Vector of characters. Path to write the output file with species that are not categorized as invasive.
`save.temp.in`	Vector of characters. Path to the temporal file as backup of the process. If the process is stopped, the user could reset it assigning the row number in `start.in` parameter and the process will start again using the temporal file.

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

If the argument in the save.Sp.list parameter is 'TRUE', the files will be saved in the path assigned in the path parameter.

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

A table data.frame class with a list of invasive species. A table data.frame class with a list of non-invasive species.

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

R-Alarcon Viviana and Miranda-Esquivel Daniel R.

[1] Lowe, S. et al. 2000. 100 of the world's worst invasive alien species: A selection from the global invasive species database. The Invasive Species Specialist Group (ISSG) a specialist group of the Species Survival Commission (SSC) of the World Conservation Union (IUCN).

[2] Kells, S. S. and Worswick, C. 1997. An introduction to the IBIS database. Melbourne Institute of Applied Economic and Social Research.

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

readAndWrite

alarconvv/geocleaMT documentation built on July 10, 2019, 12:50 a.m.