A step-by-step analysis of a simulated data set with S=100 sites, M=3 water samples from each site and K=12 qPCRs for each samples and associated covariates can be found here. Recently, when you download a spreadsheet, the associated file tends to be saved as a .xlsx file; please make sure before you use the data set that it is a .csv file.

A recording of a step-by-step analysis of a simulated data set with S=200, sites, M=2 water samples from each site, K=10 qPCRs for each sample,  with some occupied sites having an associated confirmed species presence record and two covariates for the probability of site occupancy can be found here.

There is also an online version of the app, RShiny App