Climatch SDM model building method

The model building component of an implementation of the ABARES Climatch species distribution modelling (SDM) method (ABARES, 2020).

Usage

climatch(
  x,
  p,
  algorithm = c("euclidean", "closest_standard_score"),
  d_max = 50,
  sd_data = NULL,
  as_score = TRUE,
  ...
)

# S3 method for class 'Raster'
climatch(
  x,
  p,
  algorithm = c("euclidean", "closest_standard_score"),
  d_max = 50,
  sd_data = NULL,
  as_score = TRUE,
  ...
)

# S3 method for class 'SpatRaster'
climatch(
  x,
  p,
  algorithm = c("euclidean", "closest_standard_score"),
  d_max = 50,
  sd_data = NULL,
  as_score = TRUE,
  ...
)

# S3 method for class 'SpatVector'
climatch(
  x,
  p,
  algorithm = c("euclidean", "closest_standard_score"),
  d_max = 50,
  sd_data = NULL,
  as_score = TRUE,
  ...
)

# S3 method for class 'data.frame'
climatch(
  x,
  p,
  algorithm = c("euclidean", "closest_standard_score"),
  d_max = 50,
  sd_data = NULL,
  as_score = TRUE,
  ...
)

Arguments

x: Climate (or environmental) data as a terra::SpatRaster, terra::SpatVector, or raster::Raster* (with any CRS), or a data.frame with WGS84 lon and lat columns.
p: Species occurrence data as a data.frame (or matrix) with WGS84 lon and lat columns.
algorithm: Climatch method algorithm selected from "euclidean" (default) or "closest_standard_score".
d_max: Maximum range distance, in kilometres, used when matching occurrence points to nearest climate data points/cells (default = 50).
sd_data: Optional data.frame for calculating the standard deviation for climate variable, or a vector of pre-calculated values.
as_score: Logical to indicate whether to generate a score 0-10 (default = TRUE) or values 0-1 (FALSE).
...: Additional parameters.

Value

A "Climatch" model S4 object containing slots:

method: SDM method: "climatch".
algorithm: Algorithm: "euclidean" or "closest_standard_score").
variables: List of climate (or environmental) variable names.
sd: The standard deviation of each variable calculated via the climate data (x) or the sd_data when provided.
presence: The selected (nearest within range) climate data for each occurrence point.
coordinates: The coordinates for the selected climate data.
as_score: Indication of whether to generate a score 0-10 or values 0-1.

References

ABARES (2020). Climatch v2.0 User Manual. Canberra. https://climatch.cp1.agriculture.gov.au/ Accessed: November 2021.