Description Usage Arguments Details Value Note Author(s) References See Also
Read a database which follows the Darwin Core Standard [1].
1 2 3 |
data |
Vector of characters. Name of the input file. |
path.data |
Vector of characters. Path to the input file. |
cut.col |
Numeric vector. Columns number to read into database. By default, the columns c(1,78,79,200,218,219) are read. These correspond to headers of the Darwin Core satandard [1] : gbifID, decimalLongitude, decimalLatitude, elevation, speciesKey and species. See details. |
delt.undeterm |
Logical vector. If it is |
save.name |
Vector of characters. Name of the output file. |
wrt.frmt |
Vector of characters. Format to save output file. By default it will be written as a R object using the |
save.in |
Vector od characters. Path to the output file. |
We recommend to use this function when the database has more than one hundred
thousand occurrences and / or the computer has low memory.
readDbBash
uses the cut function from BASH programming
language and can be functional on Linux or Mac operative systems.
If this is not the case, we recomended to use the readDbR
which runs into the R platform and can be used on any operative
system (Linux, Mac, or Windows). However, the readDbBash
function always will be faster than readDbR
(up to four
times faster).
Databases downloaded from the Global Biodiversity Information Facility (GBIF) [2]
are exported with DarwinCore headers and the separator columns is TAB,
and hence all databases read using this functions must be able TAB as
separator. See readAndWrite
function.
For cut.col parameter, the numbers columns to split must be sorted sequentially. For databases downloaded from GBIF [2], the number for each header can be seem using data('ID_DarwinCore) command on console.
For more details about the formats to read and/or write, see
readAndWrite
function
writing a data table in Data.frame class and as vector return a table with descriptive quantities.
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.
[2] Global Biodiversity Information Facility. Available online at http://www.gbif.org/.
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