My gf collected mouse dropping (max 10 sometimes less) from different nestboxes in different area's on different times. Within those dropping she noted if some items where precent or not present. she did this per dropping.

so eg: in february she collected dropping 1 and in dropping 1 of nestbox 21 in area "ploegsteert" she found the precence of seeds bramble, seed unknown and snail parts. those are marked with a "1" for present, while the other factors like skeleton, hairs ,... are marked with 0 (because she didn't found them in those droppings.

Now we want to make a model on how to see this frequecy of items in the droppings because we want to know if there is an effect of area and period . I was thinking about a generalised mixed model but that would not include the binary system that she implemented.

Is there a way to include all areas, nestboxes within those area's, droppings withing tose nestboxes and item precence within those droppings?
we're just a bit trown of by the binary part.

we work in R and R studio.