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.