I am not sure how do you store the data, but if you have a way to do it in excell, I would say do the modifications inside R.
The data structure for occupancy models is the same used in capture recapture, but rather than individuals, each row represents a station, location etc... so it should looks something like
site_1 00010010011 + categorical covs
site_2 10000010000 + ...
site_3 00000000000 + ...
Data <- data.frame(site = c('site_1', 'site_2'),
occu = c('00011000', '10000000'),
bankside = c('none','occasional'),
stringsAsFactors = FALSE)
So the detection histories are in the same variable pooled (pasted), each 0-1 means detection-non detection for a given site in a given sampling period. I am not sure if unmarked has any function to manage formats, but package marked certainly has (or had). The exact format will probably depend on the model to be fitted.
I think you can get friendly details (and examples of fitted models using excel) at Terry Donovan's companion website to the occupancy book http://www.uvm.edu/rsenr/vtcfwru/spreadsheets/?Page=occupancy/occupancy.htm
I am curious, you DNA analyze the scats for getting the species id or just pool all shrew scats? I spent some years monitoring small mammal communities (voles, lemmings and shrews) using multi-method occupancy modelling, that's why I am curious
cheers (feel free to ask anything, I may be of help)
BTW, edit to add that you mentioned you found one paper... This is the link for the first paper developing these family of methods (there was a similar paper around that time by Drew Tyre dealing with imperfect detection, a cool one, but didn't get the attention it deserved at that time):
Great advance from the guys of Patuxent (I reckon Darryl was there at that time). There are hundreds of papers about this topic, and approaches to expand them (I hope soon will get published one regarding non random distribution of false positives as part of my old work with the "arctic mice").
I have check the MARK book, and there is chapters regarding occupancy. I have not read them, but a lot of other chapters of the book, and I reckon it could be also the best introduction regarding occupancy modelling. It refers to software MARK, that fit capture-recapture but also occupancy models. You can use MARK as standalone software (in windows or under wine), or rather, call it from R with package RMark.
that's the link for the MARK book:
Just select chapter 21 from the smallish menu