Jolly Seber; Incomplete sampling; structural zeroes; MCMC

[giovarossi73]

Hi,
we am working on toads by using mark recapture sampling method with chips and transponder and this research is being done for 10 years. Animals were caught almost every day for the period of two months during their reproductive movements to and from a small lake with the drift fancing technique. Virtually none of them could pass through the barrier without being seen. We have always marked all of them (almost a thousand animals per year) with the same tag, but we used different colours for every animal each year. In the first years we have taken only a small number of animals that we have marked with an individual tag. The budget for the study increased over the years, so in the last two years we were able to individually mark all the two new cohorts.

I have a few questions.

Are we going to have some false resoults by using a Jolly Seber formulation as Link Barker for the years in which the tagging was incomplete (when only a small portion of the animals was individuallt tagged)? I mean: rates of "phi", "p" and "f" parameters for the marked animals should be the same for non-marked ones?!

The natural pattern of the reproductive phenomenon deals with structual zeroes when no animals are caugth and that could be in the first or the last days of the sampling and more important also in some days in the middle of the sampling period due to the sudden lowering of the temperature. This structural zeros are very informative for the understanding of the effects of the environmental variables on toad ethology, but the frequentist approach in Mark is badly afflicted by zeroes (and also values one and two) as they are associated with very low deviance residuals.
So we tried the MCMC calculation and to test it's reliability we've used (for only the cohorts completely marked) the POPAN formulation; we've used the gibbsit procedure and we increase the values it gives by 10. The result is that the superpopulation parameter "N" is smaller than the observed number of animals. Could you please tell me why we have this problem and what do you suggest to do to avoid it?
Thank you.