Format Species-Level Data for Hierarchical Stan Model
prepare_stan_data.RdPrepares species-level binomial data for a hierarchical Bayesian model in Stan. Converts a dataset with species and complex identifiers and counts into a list formatted for Stan input. The model infers complex-level effects from species-level observations.
Arguments
- data.req
A data frame with species-level observations. Must include `speciesNb`, `complexNb`, and count columns `<varname>.num` (successes) and `<varname>.den` (trials).
- varname
Character. Name of the target variable (e.g., `"HBI"`, `"endophagy"`). Used to identify numerator and denominator columns.
Value
A named list with components:
- `N_species_obs`
Number of species-level observations (rows).
- `N_species`
Number of unique species.
- `N_complexes`
Number of unique complexes.
- `r_species`
Vector of observed counts of successes per observation.
- `N_species_`
Vector of total counts (trials) per observation.
- `species_id`
Integer vector mapping each observation to a species ID.
- `species_complex`
Integer vector mapping each species to a complex ID.