Sites included in analysis (aggregated labels from master file in parentheses):


T = Tutakoke (Tutakoke, Camp)
K = Kashtut (Kashtut)
B = Bend Slough (Bend Slough, Lensink Pt, Lensink)
H = Hock Slough (Hock Slough, Village Slough)
E = Emperor (Emperor)


State transition matrix:
- \(\psi\) = transition probability, \(\phi\) = survival probability
- subscripts depict sites
- rows: time = t, columns: time = t+1
- last row and column represent the “dead” state
- some notational goofiness on the main diagnal depicting the sum of transitions


\(\left[\begin{array}{ccc} (1-\Sigma\psi)\phi_T & \psi_{TK}\phi_T & \psi_{TB}\phi_T & \psi_{TH}\phi_T & \psi_{TE}\phi_T & 1-\phi_T\\ \psi_{KT}\phi_K & (1-\Sigma\psi)\phi_K & \psi_{KB}\phi_K & \psi_{KH}\phi_K & \psi_{KE}\phi_K & 1-\phi_K\\ \psi_{BT}\phi_B & \psi_{BK}\phi_B & (1-\Sigma\psi)\phi_B & \psi_{BH}\phi_B & \psi_{BE}\phi_B & 1-\phi_B\\ \psi_{HT}\phi_H & \psi_{HK}\phi_H & \psi_{HB}\phi_H & (1-\Sigma\psi)\phi_H & \psi_{HE}\phi_H & 1-\phi_H\\ \psi_{ET}\phi_E & \psi_{EK}\phi_E & \psi_{EB}\phi_E & \psi_{EB}\phi_E & (1-\Sigma\psi)\phi_E & 1-\phi_E\\ 0 & 0 & 0 & 0 & 0 & 1\\ \end{array}\right]\)



Observation matrix:
- \(p\) = recapture probability
- subscripts depict sites
- rows: state at time = t, columns: observation at time = t
- last row represents “dead” state
- last column represents “not observed”


\(\left[\begin{array}{ccc} p_T & 0 & 0 & 0 & 0 & 1-p_T\\ 0 & p_K & 0 & 0 & 0 & 1-p_K\\ 0 & 0 & p_B & 0 & 0 & 1-p_B\\ 0 & 0 & 0 & p_H & 0 & 1-p_H\\ 0 & 0 & 0 & 0 & p_E & 1-p_E\\ 0 & 0 & 0 & 0 & 0 & 1\\ \end{array}\right]\)