Data analysis:
We considered Bd to have been detected in a sample if ≥1 PCR technical
replicated tested positive for frog skin swabs. For eDNA samples, we
considered Bd to have been detected at the site if ≥1 technical
replicate was positive in ≥1 eDNA sample collected at the site. We
considered a technical replicate to be positive if an exponential
increase occurred at any point during the qPCR cycles (as described in
Goldberg et al., 2013, see also Ellison et al., 2006).
To model Bd DNA detection probability, we used a multi-scale occupancy
models in in R (version 3.6.0; R Project for Statistical Computing,
Vienna, Austria) and package eDNAoccupancy (as described in Sepulveda et
al., 2018; see also Dorazio & Erickson, 2017). We compared a null model
to models fitted with covariates that affected the occurrence of Bd DNA
in the sample (θ; sample type [swab vs. eDNA]), and covariates that
affected the detection of Bd DNA in the technical replicate or subsample
(p; analysis approach [field vs. lab]). We assessed the models using
posterior-predictive loss criterion (PPLC) and widely acceptable
information criteria (WAIC). We calculated detection probability and
their standard errors using a Markov chain containing 11,000 iterations
(1,000 burn-in).