mscjs_phiSex_pGearEffort.jag

#data{
#  for(i in 1:nind) {  
#    sex12[i] <- ifelse(equals(Sex[i],0), 1, 2)
#  }
#}



model{

phi[1] ~ dunif(0,1) # Annual survival prob for females
phi[2] ~ dunif(0,1) # male survival

p0fyke ~ dunif(0,1)   # Capture prob in fyke when effort is 1
#p0seine ~ dunif(0,1)
p0pit ~ dunif(0,1)
p0seine ~ dunif(0,1)

# We don't have much effort info for seine
# Apparently no seining happened in years 4 and 5
pSeine[1] ~ dunif(0,1)
pSeine[2] <- p0seine #dunif(0,1)
pSeine[3] <- p0seine #dunif(0,1)
pSeine[4] <- 0
pSeine[5] <- 0

for(t in 1:5) {
  # Effective capture probability in fyke net in year t
  # fykeEffort should be the number of days of effort in each year
  pFyke[t] <-  1-(1-p0fyke)^fykeEffort[t]
  # pitEffort is the number of antanae run each year. (Time was constant among years)
  pPit[t]  <- 1-(1-p0pit)^pitEffort[t]
}

for(t in 1:n.occ){
  cap.probs[1,t,1] <- (1-pSeine[t])*(1-pFyke[t])*(1-pPit[t]) # Pr(not detected|alive)
  cap.probs[1,t,2] <- pSeine[t]*(1-pFyke[t])*(1-pPit[t]) # Pr(detected in seine, but not by other gear)
  cap.probs[1,t,3] <- pFyke[t]*(1-pSeine[t])*(1-pPit[t])
  cap.probs[1,t,4] <- pPit[t]*(1-pFyke[t])*(1-pSeine[t])
  cap.probs[1,t,5] <- pFyke[t]*pPit[t]*(1-pSeine[t])
  cap.probs[1,t,6] <- pSeine[t]*pFyke[t]*(1-pPit[t])
  cap.probs[1,t,7] <- pSeine[t]*pPit[t]*(1-pFyke[t])
  cap.probs[1,t,8] <- pSeine[t]*pFyke[t]*pPit[t]
  cap.probs[2,t,1] <- 1 # If dead, can't be detected
  cap.probs[2,t,2] <- 0
  cap.probs[2,t,3] <- 0
  cap.probs[2,t,4] <- 0
  cap.probs[2,t,5] <- 0
  cap.probs[2,t,6] <- 0
  cap.probs[2,t,7] <- 0
  cap.probs[2,t,8] <- 0
}

  for (i in 1:nind){
    z[i, f[i]] <- 1 # Known to be alive in first capture year
    for(t in 1:f[i]) {
      survivor[i,t] <- 0
    }
    for (t in (f[i]+1):n.occ){
      z[i,t] ~ dbern(z[i,t-1]*phi[sex12[i]]) # Actual alive/dead state (partially observed)
      state[i,t] <- ifelse(z[i,t]<1, 2, 1)
      y[i,t] ~ dcat(cap.probs[state[i,t],t,1:8])
      survivor[i,t] <- z[i,t]>0
    }
  }
    
  for(t in 2:n.occ){
    PrNewCap[t] <- 1 - (1-pFyke[t])*(1-pSeine[t])
    PrRecap[t] <- 1 - (1-pFyke[t])*(1-pSeine[t])*(1-pPit[t])
    Survivors[t] <- sum(survivor[,t])
#    N[t] <- NewCaps[t-1]/PrNewCap[t] + Recaps[t-1]/PrRecap[t]
    N[t] <- NewCaps[t-1]/PrNewCap[t] + Survivors[t]
  }


}