Here's where I am so far:
I have been trying to create grouping indices for the U transitions (object name: PsiU), and for the nonsensical transitions (object name: Psi0), below is the code i've been trying to use to create Psi0:
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Psi0=as.numeric(row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="A"&crdms2.ddl$Psi$tostratum=="H",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="A"&crdms2.ddl$Psi$tostratum=="J",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="A"&crdms2.ddl$Psi$tostratum=="S",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="H"&crdms2.ddl$Psi$tostratum=="A",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="H"&crdms2.ddl$Psi$tostratum=="S",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="J"&crdms2.ddl$Psi$tostratum=="A",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="J"&crdms2.ddl$Psi$tostratum=="H",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="S"&crdms2.ddl$Psi$tostratum=="H",]), row.names(crdms2.ddl$Psi[crdms2.ddl$Psi$stratum=="S"&crdms2.ddl$Psi$tostratum=="J",]))
the code is taken from someone else's script (see https://github.com/jlaake/RMark/blob/master/RMark/R/RMark-package.R and scroll down to the part about mulitistrata models) and they only used it to index a single transition. when i add more transitions, the code still runs but it only actually includes the first transition listed in the grouping index. So if you have a fix for that, i'd love to see it. I suppose i could create a set of indices and just list them in the parameter definition statement below, but there must be a simpler way.
I am able to define Psi so that the Psi0 transitions (or at least the one of them that is actually included in Psi0) are set to zero while estimating all other transitions as follows:
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Psistos.specfix=list(formula=~1+stratum:tostratum,fixed=list(index=Psi0,value=0))
It seems like it shouldn't be possible to add in the PsiU transitions held constant, but I am hoping I'm wrong and someone else knows how to do this.
Thanks for any help you can give!