Build residents-by-sites long table and fit the residents-only GLMM

Creates a long data set with one row per (site, resident) pair, attaches standardized environment and resident traits, then fits a GLMM for residents. Also returns fixed-effect predictions on the link scale as a site×resident matrix (r_js) and the response-scale mean (mu_js).

Usage

prep_resident_glmm(
  comm_res,
  env_df_z,
  traits_res_glmm,
  fml,
  family = glmmTMB::tweedie(link = "log"),
  seed = 123,
  fit_model = TRUE
)

Arguments

comm_res

Numeric matrix (sites × residents) of observed counts or abundance. Row names are site IDs; column names are resident species IDs.

env_df_z

Data frame of standardized site-level environment. Row names are site IDs and must match rownames(comm_res).

traits_res_glmm

Data frame of standardized resident traits used in the GLMM. Row names are resident IDs and must match colnames(comm_res).

fml

A model formula for glmmTMB::glmmTMB (e.g., from build_model_formula()).

family

A glmmTMB family object. Default is glmmTMB::tweedie(link="log").

seed

Integer. Random seed.

fit_model

logical; if FALSE, return dat_r/fml without fitting.

Value

list(dat_r, fit_r, grid_res, r_js, mu_js, sites, res_ids)