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Collection and Extraction of Occupational Air Samples for Analysis of Fungal DNA

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Efficient Bayesian analysis of occupancy models with logit link functions.

Allan E Clark^1,2, Res Altwegg^1,2

¹Department of Statistical Sciences University of Cape Town Cape Town South Africa.

Ecology and Evolution

|February 16, 2019

Summary

This summary is machine-generated.

A new Gibbs sampler for occupancy models offers faster analysis and easier interpretation using logit link functions. This method, implemented in the R package Rcppocc, provides accurate results comparable to existing Bayesian software.

Keywords:

Bayesian spatial occupancy model Rcppocc imperfect detection occupancy model restricted spatial regression

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Area of Science:

Ecology
Computational Biology
Statistical Modeling

Background:

Occupancy models estimate species' site presence probability.
Current Bayesian software (WinBUGS, JAGS, Stan) can be slow for occupancy models.
The R package stocc uses probit link functions, limiting interpretation.

Purpose of the Study:

To develop a Gibbs sampler for fitting nonspatial and spatial occupancy models using logit link functions.
To enable easier interpretation of model coefficients via odds ratios.
To improve computational efficiency compared to existing methods.

Main Methods:

Developed a Gibbs sampler for Bayesian analysis of occupancy models with logit link functions.
Applied the method to the 2nd Southern African Bird Atlas Project data.
Implemented the algorithms in the R package Rcppocc.

Main Results:

The Gibbs sampler produced posterior samples identical to JAGS and Stan.
The new algorithm demonstrated faster posterior chain mixing in certain cases.
Species distribution maps for Cape weaver and helmeted guineafowl were generated.

Conclusions:

The developed Gibbs sampler provides an efficient and interpretable alternative for occupancy modeling.
The Rcppocc package offers a valuable tool for ecological and biodiversity research.
The logit link function enhances the practical application of occupancy models.