Test Georeferenced Data

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

Calculate the mean propinquity[1] and some descriptors of the distribution.

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meanPropinquity(coord.table = NULL, calculatedBy = "species",
  wrt.frmt = "saveTXT", save.info.in = NULL, plot.dist = FALSE,
  plot.onMap = FALSE, save.plot.in = NULL)

`coord.table`	data frame class. Table with coordinates (decimalLongitude, decimalLatitude). If the process will be calculated by species, the table must include the species column.
`calculatedBy`	Vector of characters. If the argument is `'species'`, the mean propinquity will be calculated for each species. If it is `'whole'` the propinquity will be calculated as a whole.
`wrt.frmt`	Vector of characters. Format to save the 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.info.in`	Vector of characters. Path to the output file with information about Mean propinquity, median, mode, minimal spanning tree; by species or as a whole.
`plot.dist`	Logical vector. If `'TRUE'` a density plot for the distance between occurrences will be plotted and saved, by species or as a whole. If `'FALSE'` there will be no plot.
`plot.onMap`	Logical vector. If `'TRUE'` a map of occurences will be plotted and saved, by species or as a whole. If `'FALSE'` there will be no plot.
`save.plot.in`	Vector of characters. Path to the output file for each plot by species or as a whole.

If the process uses the parameters plot.dist and plot.onMap as 'TRUE', the process will be slow. The headers of the input file must follow the Darwin Core standard [2]. The user can see the guide using data('ID_DarwinCore) command. For more details about the formats to write, see readAndWrite function.

The output file will be saved with all species concatenated.

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] Rapoport. E.H. 1975 Areografia: Estrategias Geograficas de las Especies. Mexico, Fondo de Cultura Economica

[2] 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.