Format Species-Level Data for Hierarchical Stan Model — prepare_stan

Prepares 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.

prepare_stan_data(data.req, varname)

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.