Build standardized invader predictors r_is_z, C_is_z, S_is_z (expects env/traits frames already projected to model columns)

Usage

build_invader_predictors(
  fit_r,
  env_df_model,
  traits_inv_model,
  sites,
  inv_ids,
  r_mu_s,
  r_sd_s,
  W_site,
  gower_all,
  res_ids,
  sigma_alpha,
  C_mu_s,
  C_sd_s,
  S_s_z,
  verbose = TRUE
)

Arguments

fit_r: Fitted residents-only glmmTMB model.
env_df_model: Data frame of environment predictors used by the model (rows = sites). Either ENV_PC* (if PCA was used) or standardized env_df_z.
traits_inv_model: Data frame of invader traits used by the model (rows = invaders). Includes TR_PC* (if PCA was used) and any raw factor traits present in the model formula.
sites: Character vector of site identifiers (must match row names of env_df_model and W_site).
inv_ids: Character vector of invader identifiers (must match row names of traits_inv_model).
r_mu_s: Numeric vector of site-wise means used to standardize abiotic suitability (r_js).
r_sd_s: Numeric vector of site-wise standard deviations used to standardize abiotic suitability (r_js).
W_site: Site × resident weighting matrix (e.g. relative abundance or presence–absence weights).
gower_all: Square matrix or dist object of Gower distances among all residents and invaders.
res_ids: Character vector of resident species identifiers.
sigma_alpha: Numeric kernel bandwidth for crowding effects. If NULL or non-positive, a data-driven default is used.
C_mu_s: Numeric vector of site-wise means used to standardize crowding (C_is).
C_sd_s: Numeric vector of site-wise standard deviations used to standardize crowding (C_is).
S_s_z: Numeric vector of standardized site saturation values.
verbose: Logical; if TRUE, emit diagnostic messages.