Overview of the overlap package

Camera traps – cameras linked to detectors so that they fire when an animal is present – are a major source of information on the abundance and habitat preferences of rare or shy forest animals. Modern cameras record the time of the photo, and the use of this to investigate diel 1 activity patterns was immediately recognised (Griffiths and van Schaik, 1993). Initially this resulted in broad classification of taxa as diurnal, nocturnal, crepuscular, or cathemeral (van Schaik and Griffiths, 1996). More recently, researchers have compared activity patterns among species to see how overlapping patterns may relate to competition or predation (Linkie and Ridout, 2011; Carver et al., 2011; Ramesh et al., 2012; Carter et al., 2012; Kamler et al., 2012; Ross et al., 2013). Ridout and Linkie (2009) presented methods to fit kernel density functions to times of observations of animals and to estimate the coefficient of overlapping, a quantitative measure ranging from 0 (no overlap) to 1 (identical activity patterns). The code they used forms the basis of the overlap package. Although motivated by the analysis of camera trap data, overlap could be applied to data from other sources such as data loggers, provided data collection is carried out around the clock. Nor is it limited to diel cycles: tidal cycles or seasonal cycles, such as plant flowering or fruiting or animal breeding seasons could also be investigated.