Estimate Species-Specific Bionomic Traits for Anopheles Using a Hierarchical Bayesian Framework

This function estimates key bionomic traits of *Anopheles* mosquitoes using a set of hierarchical Bayesian models fitted independently for each trait across three taxonomic levels: genus, species complex, and species. The estimated traits include parous rate, endophagy, endophily, sac rate, indoor and outdoor human blood indices, and resting duration.

Usage

Bionomics_For_AnopholesModel()

Value

A data.frame containing bionomic estimates for each species, species complex, or genus, with the following columns:

species_name

Name of the species, complex, or genus (e.g., "Anopheles gambiae", "Gambiae complex", "GENUS").

M, M.sd

Parous rate and its standard deviation.

endophagy, endophagy.sd

Endophagy level and its standard deviation.

endophily, endophily.sd

Endophily level and its standard deviation.

A0, A0.sd

Sac rate and its standard deviation.

Chi

Overall human blood index (HBI), derived from indoor and outdoor components.

tau, tau.sd

Resting duration and its standard deviation.

Details

For human blood feeding behaviour, indoor and outdoor human blood indices are first estimated separately. The overall human blood index (HBI, denoted Chi) is then derived a posteriori as a deterministic function of endophagy: $$ Chi = indoor\_HBI \times endophagy + outdoor\_HBI \times (1 - endophagy) $$ Indoor and outdoor HBI estimates are not returned in the final output.

Resting duration is estimated by the model and returned as the parameter tau, preserving compatibility with downstream transmission models.

Internally, the function relies on creation_df() to format input data for each trait and run_stan() to perform Bayesian inference using Stan. Posterior summaries are aggregated across taxonomic levels using an internal helper function, and missing species or complexes are imputed using information from higher taxonomic levels when necessary.

Missing species-level estimates are imputed using available information at the species-complex or genus level, following a predefined taxonomic compatibility table. Species and complex names are normalised (e.g., mapping "Anopheles gambiae s.s. / Colluzi" to "Anopheles gambiae", and genus-level estimates are labelled as "GENUS"). A synthetic "Jamesii complex" row is added based on genus-level estimates to ensure completeness of the output.

Note

This function assumes that creation_df() and run_stan() are available in the environment and return appropriately formatted data and fitted Stan model objects.