Test Georeferenced Data

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

This function separates species with restricted distribution to a polygon or a defined area, following a series of conditions.

spOutPoly(data = NULL, rd.frmt = "readRDS", path = NULL,
  shp.poly = NULL, max.per.out = 5, max.occ.out = 3, execute = T,
  B1 = F, B2 = T, wrt.frmt = "saveRDS", save.inside.in = NULL,
  save.outside.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.
`shp.poly`	SpatialPolygonDataframe Class. Polygon of the referenced areas. The area where the species has to be distributed.
`max.per.out`	Numeric vector. Maximum percentege of occurrences that can be outside of polygon for the species to be considered as species with restricted distribution. See details.
`max.occ.out`	Numeric vector. Absolute maximum number of occurrences that can be outside of a polygon for the species to be considered as species with restricted distribution. See details.
`execute`	Logical vector. If `'TRUE'`, the process will be executed on species. If `'FALSE'` the species will only be classified and an information table will be saved.
`B1`	Logical vector. If `'TRUE'`, the condition B1T will be applied. If `'FALSE'` the condition B1F will be applied. See details.
`B2`	Logical vector. If `'TRUE'`, the condition B2T will be applied. If `'FALSE'` the condition B2F will be applied. See details.
`wrt.frmt`	Vector of characters. Format to save output file. By default it will be written as a R object using
`save.inside.in`	Vector of characters. Path to the output file for each species whose distribution was considered restricted to polygon.
`save.outside.in`	Vector of characters. Path to the output file for each species whose distribution was considered widespread.

#' To see the descriptions and details about conditions and parameters the user should check R-Alarcon V. and Miranda-Esquivel DR.(submitted) geocleaMT: An R package to cleaning geographical data from electronic biodatabases.

The condition A, B3 and C for species classification are executed by default, and these can not be modified.

The headers of the input file must follow the Darwin Core standard [1]. 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.

If execute is 'TRUE' a table data.frame class with information about how was the species classified and an output file by species with occurrences. If execute is FALSE, a table data.frame class will be saved, with information about how was the species classified.

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

readAndWrite

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