1) Creating a mask via shapefile.
My research is on an island and therefore I have a very defined area of study. I would like to import the shoreline shapefile as my mask for secr analysis and I've done this successfully using make.mask. My question is about the buffer that is in make.mask. I understand that make.mask can be used to create buffers around traps and then clip those buffers around a shapefile but I just want to use the shapefile itself as the mask. Is that possible and if so is it done just by removing the buffer argument in make.make? Here is my code:
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Traps <- read.traps ("Detection_File.txt", detector = "multi")
Capthist <- read.capthist(captfile="Capture_File.txt", trapfile="Detection_File.txt", detector = "multi", fmt="trapID", noccasions=6)
Polygon <- readShapePoly("Polygon2")
Mask <- make.mask(traps(Traps), spacing = 50, type = "polygon", poly = Polygon)
This seems to work fine, but I would appreciate clarification that it's correct
2) Creating groups. I would like to create separate groups for "sex" but I'm not sure how to input that information. Do I include M/F as an individual covariate in the Capthist and then just include g="sex" in secr.fit? I know that when you using individual covariates, you need to use the CL, so I wanted to make sure that if I enter the sex as an individual covariate in Capthist, I can still use the full likelihood if I specify them as groups.
Thanks