Statistical analysis
To measure the agreement between the two survey methods, that is, manual survey and eDNA analysis, Cohen’s kappa coefficient (Cohen 1960) was calculated as follows:
\begin{equation} k=\frac{\Pr\left(a\right)-Pr(e)}{1-Pr(e)}\nonumber \\ \end{equation}
where Pr(a) is the relative agreement among rates, and Pr(e) is the hypothetical probability of chance agreement, using the observed data to calculate the probabilities of each method randomly giving a positive detection. If the methods are in complete agreement, then j = 1. If there is no agreement other than what would be expected by chance, j = 0.
Once PCR analyses had been performed, the program PRESENCE version 13.12 [available from http://www.mbr-pwrc.usgs.gov/software/presence.html (Mackenzie et al. 2002)] was used for occupancy modelling of the data. A single-season model was used which assumes that species are never falsely detected at a site when absent, but that may or may not be detected when present; the detection of a species at an individual site is independent of the detection of the species at all other sites; and the probability of detecting the species across all sites is constant.