sample_pseudoabs_time: Sample pseudo-absence points for SDM analysis for points with...

In tidysdm: Species Distribution Models with Tidymodels

Sample pseudo-absence points for SDM analysis for points with a time point.

Description

This function samples pseudo-absence points from a raster given a set of presences. The locations returned as the center points of the sampled cells, which can not overlap with the presences (in contrast to background points, see sample_background_time). The following methods are implemented:

• 'random': pseudo-absences randomly sampled from the region covered by the raster (i.e. not NAs).

• 'dist_min': pseudo-absences randomly sampled from the region excluding a buffer of 'dist_min' from presences (distances in 'm' for lonlat rasters, and in map units for projected rasters).

• 'dist_max': pseudo-absences randomly sampled from the unioned buffers of 'dist_max' from presences (distances in 'm' for lonlat rasters, and in map units for projected rasters). Using the union of buffers means that areas that are in multiple buffers are not oversampled. This is also referred to as "thickening".

• 'dist_disc': pseudo-absences randomly sampled from the unioned discs around presences with the two values of 'dist_disc' defining the minimum and maximum distance from presences.

Usage

sample_pseudoabs_time(
  data,
  raster,
  n_per_presence,
  coords = NULL,
  time_col = "time",
  lubridate_fun = c,
  method = "random",
  class_label = "pseudoabs",
  return_pres = TRUE,
  time_buffer = 0
)

Arguments

data	An sf::sf data frame, or a data frame with coordinate variables. These can be defined in coords, unless they have standard names (see details below).
raster	the terra::SpatRaster, stars or terra::SpatRasterDataset from which cells will be sampled. If a terra::SpatRasterDataset, the first dataset will be used to define which cells are valid, and which are NAs.
n_per_presence	number of pseudoabsence points to sample for each presence
coords	a vector of length two giving the names of the "x" and "y" coordinates, as found in data. If left to NULL, the function will try to guess the columns based on standard names c("x", "y"), c("X","Y"), c("longitude", "latitude"), or c("lon", "lat")
time_col	The name of the column with time; if time is not a lubridate object, use lubridate_fun to provide a function that can be used to convert appropriately
lubridate_fun	function to convert the time column into a lubridate object
method	sampling method. One of 'random', 'dist_min', 'dist_max', or 'dist_disc'.
class_label	the label given to the sampled points. Defaults to pseudoabs
return_pres	return presences together with pseudoabsences in a single tibble
time_buffer	the buffer on the time axis around presences that defines their effect when sampling pseudoabsences. If set to zero, presences have an effect only on the time step to which they are assigned in raster; if a positive value, it defines the number of days before and after the date provided in the time column for which the presence should be considered (e.g. 20 days means that a presence is considered in all time steps equivalent to plus and minus twenty days from its date).

Details

#' @details Note that the time axis of the raster should be in POSIXct or Date format, or use ‘tstep="years"’. See terra::time() for details on how to set the time axis.

Value

An object of class tibble::tibble. If presences are returned, the presence level is set as the reference (to match the expectations in the yardstick package that considers the first level to be the event)

tidysdm documentation built on April 3, 2025, 9:56 p.m.