Hi Murray,
I’m analyzing some data that seems to be appropriate for a mark-resight analysis, but I have a few clarifying questions about the input files. The goal is to estimate the density of badgers using camera traps at water tanks with individual ID based on variation in dorsal head stripes. The cameras were stationed at a tank for 21 consecutive days, which will be split into sampling occasions. Looking at the mark-resign vignette, the data best fits model 1a, which is a mark-resight model with incomplete identification of marked animals.
In relation to markocc, can there be multiple mark occasions? If so, can marking occasions be mixed throughout the sighting occasions or only at the beginning? For example, let's say there are 6 total sampling occasions. With a mixed design, occasion 1 and 3 are coded as marking, and with an un-mixed design only occasion 1 and 2 are marking. If the marking occasions are unmixed, i.e., adjacent to each other, should they be truncated into 1 large occasion? A truncated session doesn’t seem appropriate because you would lose information on the initial detection of marked individuals. However, I want to double check that assumption. Last, when creating the Tu and Tm files, the vignette describes the format as, “session”, “marking”, “sighting(s)” with “marking” coded as binary and “sighting” coded as a count. Yet, I don’t see any mention for a Trap ID. Should there be a Trap ID or does secr assume that the order of the rows is identical to the order of the rows in the trap file?
Thanks for the clarification,
Matt