Climatch SDM predict method — predict.Climatch • bssdm

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

Usage

# S3 method for class 'Climatch'
predict(
  object,
  x,
  algorithm = NULL,
  sd_data = NULL,
  as_score = NULL,
  raw_output = NULL,
  filename = "",
  parallel_cores = NULL,
  debug = FALSE,
  ...
)

Arguments

object

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 (TRUE) or values 0-1 (FALSE).

x

Climate (or environmental) data with corresponding model variables as a terra::SpatRaster, raster::Raster*, data.frame, or matrix.

algorithm

Optional (overriding) Climatch method algorithm selected from "euclidean" or "closest_standard_score".

sd_data

Optional (overriding) data.frame for calculating the standard deviation for climate variable, or a vector of pre-calculated values.

as_score

Optional (overriding) logical to indicate whether to generate a score 0-10 (TRUE) or values 0-1 (FALSE).

raw_output

Logical to indicate whether to return raw predicted values (TRUE) or as an object (as per x: FALSE). Default is NULL, returning either raw values or a spatial raster (as per x).

filename

Optional filename for writing spatial raster output (only). Default is "".

parallel_cores

Optional number of cores available for parallel processing, thus enable parallel processing. Default is NULL (serial).

debug

Output additional debug information (memory block info, etc.). Default is FALSE.

...

Additional parameters.

Value

Predicted values as a raw vector or a terra::SpatRaster, raster::Raster*, data.frame, or matrix (as per x).

References

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