Fit a current climatic niche reference — fit_climniche

Estimates the preprocessing, standardisation, current niche centre, climatic weighting matrix and empirical radial boundary once. The resulting object can be reused with project_climniche() for several future periods or climate models.

Usage

fit_climniche_reference(
  current,
  occupied = NULL,
  occupied_threshold = NULL,
  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
)

Arguments

current: Numeric matrix or data frame of current climatic conditions. Rows are cells or sites and columns are climatic variables.
occupied: Reference cells or weights, following the rules used by fit_climniche().
occupied_threshold: Optional cutoff for numeric reference weights.
cnfa: Optional compatible CENFA object.
center: Optional current niche centre in the fitted climatic space.
sensitivity: Optional non-negative climatic metric weights.
A: Optional climatic weighting matrix.
metric: Method used to build A when it is not supplied.
boundary: Weighted quantile defining the empirical radial boundary.
scale: If TRUE, standardise retained variables using current-climate means and standard deviations.
preprocess: If TRUE, remove near-zero variance and highly correlated variables before fitting.
preprocess_correlation: Maximum absolute correlation retained during preprocessing.
preprocess_min_sd: Minimum current-climate standard deviation as a fraction of the largest finite current standard deviation.
global_mean, global_sd: Optional centring and scaling values.

Value

A climniche_reference object.

Details

The reference object fixes the climatic space used for all subsequent projections. Future conditions do not alter the centre, weighting matrix, standardisation or empirical radial boundary.

Examples

sim <- simulate_climniche(n = 200, p = 6, seed = 4)
reference <- fit_climniche_reference(
  sim$current,
  occupied = sim$occupied,
  sensitivity = sim$sensitivity
)
reference