load_occ: Load occurrence data

In sylvainschmitt/SSDM: Stacked Species Distribution Modelling

Load occurrence data

Description

Load occurrence data from CSV file to perform modelling, ensemble_modelling or stack_modelling.

Usage

load_occ(
  path = getwd(),
  Env,
  file = NULL,
  ...,
  Xcol = "Longitude",
  Ycol = "Latitude",
  Spcol = NULL,
  GeoRes = TRUE,
  reso = max(res(Env@layers[[1]])),
  verbose = TRUE,
  GUI = FALSE
)

Arguments

path	character. Path to the directory that contains the occurrence table.
Env	raster stack. Environmental variables in the form of a raster stack used to perform spatial thinning (can be the result of the load_var function).
file	character. File containing the occurrence table, if NULL (default) the .csv file located in the path will be loaded.
...	additional parameters given to read.csv.
Xcol	character. Name of the Latitude or X coordinate variable.
Ycol	character. Name of the Longitude or Y coordinate variable.
Spcol	character. Name of the column containing species names or IDs.
GeoRes	logical. If TRUE, performs geographical thinning on occurrences to limit geographical biases in the SDMs.
reso	numeric. Resolution used to perform the geographical thinning, default is the resolution of Env.
verbose	logical. If TRUE, allows the function to print text in the console.
GUI	logical. Parameter reserved for graphical interface.

Value

A data frame containing the occurrence dataset (spatially thinned or not).

See Also

load_var to load environmental variables.

Examples

## Not run: 
load_occ(path = system.file('extdata',  package = 'SSDM'), Env,
         Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
         file = 'Occurrences.csv', sep = ',')

## End(Not run)

sylvainschmitt/SSDM documentation built on April 13, 2025, 6:09 a.m.