invasiveSp: Separate invasive species

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

View source: R/invasiveSp.R

Description

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

Usage

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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)

Arguments

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.

Details

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.

Value

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

Note

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

Author(s)

R-Alarcon Viviana and Miranda-Esquivel Daniel R.

References

[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.

See Also

readAndWrite


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