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Functionality for geographic and environmental thinning

Source: R/utils-spatial.R
thin_observations.Rd

For most species distribution modelling approaches it is assumed that occurrence records are unbiased, which is rarely the case. While model-based control can alleviate some of the effects of sampling bias, it can often be desirable to account for some sampling biases through spatial thinning (Aiello‐Lammens et al. 2015). This is an approach based on the assumption that over-sampled grid cells contribute little more than bias, rather than strengthening any environmental responses. This function provides some methods to apply spatial thinning approaches. Note that this effectively removes data prior to any estimation and its use should be considered with care (see also Steen et al. 2021).

Usage

thin_observations(
  data,
  background,
  env = NULL,
  method = "random",
  remainpoints = 10,
  mindistance = NULL,
  zones = NULL,
  probs = 0.75,
  global = TRUE,
  centers = NULL,
  verbose = TRUE
)

Arguments

data

A sf object with observed occurrence points. All methods threat presence-only and presence-absence occurrence points equally.

background

A SpatRaster object with the background of the study region. Use for assessing point density.

env

A SpatRaster object with environmental covariates. Needed when method is set to "environmental" or "bias" (Default: NULL).

method

A character of the method to be applied (Default: "random").

remainpoints

A numeric giving the number of data points at minimum to remain (Default: 10).

mindistance

A numeric for the minimum distance of neighbouring observations (Default: NULL).

zones

A SpatRaster to be supplied when option "zones" is chosen (Default: NULL).

probs

A numeric used as quantile threshold in "bias" method. (Default: 0.75).

global

A logical if during "bias" method global (entire env raster) or local (extracted at point locations) bias values are used as for quantile threshold. (Default: TRUE).

centers

A numeric used as number of centers for "environmental" method. (Default: NULL). If not set, automatically set to three or nlayers - 1 (whatever is bigger).

verbose

logical of whether to print some statistics about the thinning outcome (Default: TRUE).

Details

All methods only remove points from "over-sampled" grid cells/areas. These are defined as all cells/areas which either have more points than remainpoints or more points than the global minimum point count per cell/area (whichever is larger).

Currently implemented thinning methods:

  • "random": Samples at random across all over-sampled grid cells returning only "remainpoints" from over-sampled cells. Does not account for any spatial or environmental distance between observations.

  • "bias": This option removes explicitly points that are considered biased only (based on "env"). Points are only thinned from grid cells which are above the bias quantile (larger values equals greater bias). Thins the observations returning "remainpoints" from each over-sampled and biased cell.

  • "zones": Thins observations from each zone that is above the over-sampled threshold and returns "remainpoints" for each zone. Careful: If the zones are relatively wide this can remove quite a few observations.

  • "environmental": This approach creates an observation-wide clustering (k-means) under the assumption that the full environmental niche has been comprehensively sampled and is covered by the provided covariates env. For each over-sampled cluster, we then obtain ("remainpoints") by thinning points.

  • "spatial": Calculates the spatial distance between all observations. Then points are removed iteratively until the minimum distance between points is crossed. The "mindistance" parameter has to be set for this function to work.

References

  • Aiello‐Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B., & Anderson, R. P. (2015). spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography, 38(5), 541-545.

  • Steen, V. A., Tingley, M. W., Paton, P. W., & Elphick, C. S. (2021). Spatial thinning and class balancing: Key choices lead to variation in the performance of species distribution models with citizen science data. Methods in Ecology and Evolution, 12(2), 216-226.

Examples

if (FALSE) { # \dontrun{
 # Thin a certain number of observations
 # At random
 thin_points <- thin_observations(points, background, method = "random")
 # using a bias layer
 thin_points <- thin_observations(points, background, method = "bias", env = bias)
} # }