Summary

1. Spatially clustered populations create unique challenges for conservation monitoring programmes. Advances in methodology typically are focused on either the design or the modelling stage of the study but do not involve integration of both.

2. We integrate adaptive cluster sampling and spatial occupancy modelling by developing two models to handle the dependence induced by cluster sampling. We compare these models to scenarios using simple random sampling and traditional occupancy models via simulation and data collected on a rare plant species, Tamarix ramosissima, found in China.

3. Our simulations show a marked improvement in confidence interval coverage for the new models combined with cluster sampling compared to simple random sampling and traditional occupancy models, with greatest improvement in the presence of low detection probability and spatial correlation in occupancy.

4. Accounting for the design using the simple cluster random-effects model reduces bias considerably, and full spatial modelling reduces bias further, especially for large n when the spatial covariance parameters can be estimated reliably. Both new models build on the strength of occupancy modelling and adaptive sampling and perform at least as well, and often better, than occupancy modelling alone.

5. We believe our approach is unique and potentially useful for a variety of studies directed at patchily distributed, clustered or rare species exhibiting spatial variation.