Occupancy modelling : study design and models for data collected along transects

Occupancy, defined as the proportion of sites occupied by a species, is a state variable of interest in ecology and conservation. When modelling species occupancy it is crucial to account for the detection process, as most species can remain undetected at sites where present. This is usually achieved by carrying out separate repeat visits to each sampling site but other methods are sometimes used, such as surveying spatial sub-units within each sampling site, or even collecting detection data continuously along a transect, during a single visit. This thesis deals with two aspects of occupancy modelling: (i) we explore issues related to the design of occupancy studies, including the trade-off in survey effort allocation between sites and repeat visits, sample size determination and the impact of sampling with replacement in studies based on spatial replication; and (ii) we develop and evaluate new models to estimate occupancy from species detection data collected along transects, motivated by the analysis of a data set from a Surnatran tiger Panthera tigris sumatrae survey which followed this type of sampling protocol. The models we propose, which describe the detection process as a continuous point process, can account for clustering and/or abundance-induced heterogeneity in the detection process and represent a step forward with respect to current modelling approaches which involve data discretisation and two-stage ad hoc procedures.