Phi{.} Psi{t} p{.}
The multistate model has 3 states, and I would like to allow exclusively the next transitions:
A -> B
B -> C
C -> B
In MARK, I specify a new Mlogit() parameter for each combination time step and transition because the Psi parameter is time varying. For example in the case that I would have 4 sampling occasions, the parameters would be:
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PsiAB <- Mlogit(1) # Sampling occasion 2
PsiAB <- Mlogit(2) # Sampling occasion 3
PsiAB <- Mlogit(3) # Sampling occasion 4
PsiBC <- Mlogit(4) # Sampling occasion 2
PsiBC <- Mlogit(5) # Sampling occasion 3
PsiBC <- Mlogit(6) # Sampling occasion 4
PsiCB <- Mlogit(7) # Sampling occasion 2
PsiCB <- Mlogit(8) # Sampling occasion 3
PsiCB <- Mlogit(9) # Sampling occasion 4
When I read the MARK book, I understood that I should specify a new parameter "Mlogit()" for each parameter I want to estimate. I assumed I should create a new Mlogit for each combination of transition and time because the transitions probabilities are time varying. Furthermore, I put as constant and fixed as 0 the rest of the transitions (A->C / B->A / C->A). Is it right?
RMark
I would like to run the same model in MARK, however I am not sure how to specify correctly the transitions. So first I did:
(1) Process data, specifying regular time periods between sampling occassions.
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model_process <- process.data (input, model="Multistrata", time.intervals = rep(1, 3))
(2) Make design data
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model_make=make.design.data(model_process)
(3) Fix as 0 the impossible transitions
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model_make$Psi$fix=NA
model_make$Psi$fix[model_make$Psi$A & model_make$Psi$toC] <- 0
model_make$Psi$fix[model_make$Psi$B & model_make$Psi$toA] <- 0
model_make$Psi$fix[model_make$Psi$C & model_make$Psi$toA] <- 0
(4) Estimate a p and Phi constant estimates per state, and a time-varying estimates for Psi per state
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p.dot <- list(formula=~1+stratum)
Phi.dot=list(formula=~1+stratum)
Psi.time=list(formula=~1+time+stratum)
(5) Run the model
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model_mark <- mark (model_process, model_make, model.parameters = list(S=Phi.dot, p=p.dot, Psi=Psi.time))
The problem is that I got totally different estimates between MARK and RMark, and it should be because I am not specifying properly the Mlogit in RMark.
Could you tell me, how is the code for estimating time-varying estimates of the Psi parameters?
Thanks in advance,