Occupancy Analysis
Using the observed percentage agreement of the two methods of 0.84 (1 = 100%) and the probability of random agreement of 0.64, Cohen’s kappa coefficient was calculated as 0.56 for manual survey-positive ponds versus their qPCR analysis results i.e. moderate agreement.
Site occupancy modelling was used to calculate the occupancy estimate and the probability of detection of S. nitida. Using the combined manual survey and qPCR assay results the occupancy estimate was calculated to be 0.35 (95% CRI 0.19, 0.56) with a probability of detection of 0.67 (Table 2).