Fit climniche to raster data

Usage

fit_climniche_raster(
  current,
  future,
  occupied = NULL,
  occupied_threshold = NULL,
  domain = NULL,
  domain_threshold = 0,
  cnfa = NULL,
  center = NULL,
  sensitivity = NULL,
  A = NULL,
  metric = c("diag", "factor"),
  boundary = 0.95,
  scale = TRUE,
  preprocess = TRUE,
  preprocess_correlation = 0.95,
  preprocess_min_sd = 1e-08,
  global_mean = NULL,
  global_sd = NULL,
  tolerance = NULL,
  tolerance_quantile = 0.1,
  boundary_exceedance_tolerance = 0
)

Arguments

current: Raster* object of current climate layers.
future: Raster* object of future climate layers with the same geometry and layer order as current.
occupied: Optional RasterLayer with binary or continuous occurrence, range, or SDM suitability values.
occupied_threshold: Values at or below this threshold receive zero reference weight. Values above it keep their original value.
domain: Optional RasterLayer limiting cells where exposure is analysed.
domain_threshold: Values greater than this threshold define the domain.
cnfa: Optional CENFA cnfa object. Its marginality and sensitivity slots are used when center, sensitivity, or A are not supplied.
center: Optional realised niche centre in the climate space used by the fit. If omitted, the centre is the weighted mean of current reference rows.
sensitivity: Optional non-negative variable weights. Used to build a diagonal metric when A is not supplied.
A: Optional square metric matrix. When supplied, it overrides sensitivity, cnfa, and metric for distance calculations.
metric: Method used to build A when A is missing. "diag" uses variable-level sensitivity weights. "factor" uses the factor metric available from a compatible CENFA object.
boundary: Quantile used to define the empirical boundary of the current realised niche. Must be between 0 and 1.
scale: Logical. If TRUE, current and future values are centred and scaled with the current-layer mean and standard deviation before distances are calculated.
preprocess: Logical. If TRUE, remove near-zero variance variables and highly correlated variables before metric fitting.
preprocess_correlation: Maximum absolute pairwise correlation retained among current climate variables during preprocessing.
preprocess_min_sd: Minimum current-climate standard deviation retained during preprocessing.
global_mean: Optional means used for centering. If omitted, column means of current are used.
global_sd: Optional standard deviations used for scaling. If omitted, column standard deviations of current are used.
tolerance: Optional tolerance around zero for Niche Distance Shift. If NULL, the fitted object uses tolerance_quantile.
tolerance_quantile: Quantile of absolute Niche Distance Shift used to set tolerance when tolerance = NULL.
boundary_exceedance_tolerance: Tolerance used to label whether Niche Boundary Exceedance is greater than zero for descriptor summaries.

Value

An object of class climniche_fit with RasterLayer outputs stored in x$rasters.

Details

fit_climniche_raster() is the Raster* workflow for users working with the raster package. It extracts aligned cell values, applies domain and occupied rasters, calls the matrix workflow, and writes the fitted quantities back to RasterLayer outputs.