www.phidot.org

I would like to duplicate the models used below from a older paper and run them on an updated data set. I'm not sure of the best way to do this in RMark since the last time around it was done using MARK. The input file is ready to go in RMark I just need help setting up these models correctly. If anyone can help it would be greatly appreciated.

Thanks-

phi(t), p(t) - year specific survival and recapture
phi(a2-c/c), p(t) - survival= two age classes (a; age-1 and age-2+); both constant across years, recapture= year specific
phi(a2-t/c), p(t) - survival= age-1 year specific and age-2 constant, recapture= year specific
phi(a2-t/t), p(t) - survival= both ages year specific, recapture= year specific
phi(a3-t/c/c), p(t) - survival= three age classes (a; age-1, age-2 and age-3+); age-1 year specific, age-2 and age-3+ constant, recapture= year specific
phi(a3-t/t/c), p(t) - survival= age-1 and age-2 year specific, age-3+ constant, recapture= year specific
phi(a3-t/t/t), p(t) - survival= all three age classes year specific, recapture= year specific
phi(a3-t/t/c), p(a2-t/t) - survival= age-1 and age-2 year specific, age-3+ constant, recapture= both ages year specific
phi(a3-t/t/t), p(a2-t/t) - survival= all three age classes year specific, recapture= both ages year specific

Jay-

I'd be glad to help but I'd like to see some more effort on your part. There are some examples similar to what you want to do in Appendix C and in the workshop notes which are both available on the RMark page of phidot. I put a fair amount of effort in writing the documentation. Please read the documentation and if you are still having trouble then post what you have put together and I'll help.

--jeff

Thanks Jeff-
I have both of those documents on my desk as we speak. I'm currently reading through app c but am having some trouble getting the code that I've adapted from the examples to run on my input file. I appreciate the time that you have invested in writing these help manuals but it's not always easy to translate the examples, which work perfectly, into code that will work for my particular application. I'm still a relative beginner with R and MARK so combining the two has been tough.

I'll try to formulate some more specific questions but in the meantime if you know of certain sections in either of the two documents that would be particularly helpful please point them out.

Also, if anyone else has any help they'd like to offer or suggestions on how to get started I'd really appreciate it-

As with anything new there is a learning curve and it can be steep with both R and MARK. There are a number of examples and templates to use in RMark. See for example ?dipper -- although I need to update this to use mark.wrapper but at the very least it shows how to construct the first model on your list. You need to work through the first 8-10 sections in C at the very least. C6 and then C15 should be the most helpful for what you want to do. Any help you want to get with RMark would need far more detail about your problem and preferably your code and a snippet of the data. For example, with regard to time-age interactions it is important to know whether all of your marked animals are young or a mix of ages. What mr model are you using (CJS?), etc. I don't want to know these now. Go take several days to read the documentation and most importantly try the examples and make sure you understand them. Unless you understand what RMark is doing you could go awry. If you don't have time to learn RMark now you can always go back to MARK for the time being. regards --jeff