As with the one-age analysis, we can perform recovery analysis in RMark (Seber or Brownie parameterization), but first the data must be re-formatted to LDLD format. Now though "groups" has a special meaning, in that HY birds transition to AHY but AHY stay put. As you recall from CJS analysis, we do this by adding a column to the design data (ddl) that reflects "age now". The attached code reads from the previous 2-age mallard data in MARK format, converts the data to form compatible with RMark, runs a series of 25 models, summarized the models, performs model averaging, and plots the model-averaged estimates of AHY and HY survival. Note that I picked off the first 8 years of survival estimates. Since there are 9 years of banding there are really only 8 intervals over which survival is meaningful (note that the last year CI is basically 0-1, indicating that the parameter cannot be identified).
Also note that in this script I manually created 25 models that represent the combinations of 5 types of variation in each of the 2 real parameters (S and r). However, I could have avoided all that by using the create.model.list() function in RMark to take the 5 S and 5 r formulas and automatically create the 25 models.
>mod.list<-create.model.list("Recovery")
The resulting model list would then be used as input in the mark.wrapper function
>mall.results<-mark.wrapper(model.list=mod.list,data=mall,ddl=mall.ddl)