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Site-varying alpha and gamma with trait-dependent beta

Source: R/site_varying_alpha_beta_gamma.R
site_varying_alpha_beta_gamma.Rd

Constructs site-by-invader crowding penalties and density-dependence scalars by combining trait-derived slopes with site-level random effects.

Site-level random slopes for \(C_z\) and \(r_z\) are added to the trait-dependent systems to produce site-varying crowding penalties \(\alpha_{is}\) and density-dependence scalars \(\Gamma_{is}\). Saturation effects \(\beta_i\) are trait-varying only; no site-varying \(\beta_{is}\) is constructed because \(S_z\) is site-only.

The function also exposes signed slopes and clamping diagnostics returned by derive_sensitivities().

Usage

site_varying_alpha_beta_gamma(
  fit_coeffs,
  Q_inv,
  sites,
  inv_ids,
  lrt = TRUE,
  quiet = FALSE
)

Arguments

fit_coeffs

Fitted residents-only GLMM (e.g. glmmTMB) used to extract fixed effects and site-level random slopes.

Q_inv

Data frame of invader trait scores with columns tr1 and tr2; row names must correspond to inv_ids.

sites

Character vector of site identifiers (rows of the output matrices).

inv_ids

Character vector of invader identifiers (columns of the output matrices).

lrt

Logical; passed to derive_sensitivities() to control likelihood-ratio testing for trait effects.

quiet

Logical; if TRUE, suppress warnings about missing or negligible site-level random effects.

Value

A list with the following elements:

  • alpha_is: matrix of site-by-invader crowding penalties

  • Gamma_is: matrix of site-by-invader density-dependence scalars

  • beta_i, beta_signed_i: invader-level saturation effects

  • alpha_signed_i: signed crowding slopes prior to clamping

  • theta_i, gamma_i: invader-level abiotic sensitivities

  • slope_C_i: trait-derived crowding slopes

  • delta_C_s, delta_r_s: site-level random effects

  • notes: character vector of diagnostics

  • df: tidy long-format data frame