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N1 , N 2 ,..., N k -1 , N k
Survival Rates
1 , 2 ,..., k -2 , k -1
Capture Probabilities
p1 , p 2 ,..., p k -1 , p k
Recruitment Numbers
B1 , B 2 ,..., Bk -2 , B k -1
M1 , M 2 ,..., M k -1 , M k
PARAMETER ESTIMATION
JOLLY-SEBER MODEL
This model makes the following assumptions:
1. Every animal present in the population at the time of i th sample (i = 1,
2, , k) has the same probability of capture (pi).
2. Every marked animal present in the population immediately after the i
th sample has the same probability of survival (i ) until the (i + 1)th
sampling time (i = 1, 2, , k-1).
3. Marks are not lost or overlooked.
4. All samples are instantaneous and each release is made immediately
after the sample.
5. All emigration is permanent.
6. Fates of animals are independent
Parameter Estimation
Jolly-Seber Model
First will cover intuitive approach. This is an open
population version of M(t).
Later I will break up into components for more
formal inference
[= n / N
]
pi = m i / M
i
i
i
Note: Only p2, p3, , pk-1 are estimable.
p1 and pk are not estimable.
(4.4)
m i / n i M i /N i
Similar to the Lincoln-Petersen model solve the equation and obtain:
i = ni M
i /m i
N
= n /p
N
i
i i
will be estimated later.
Note: M
i
Note: Only N2, N3, , Nk-1 are estimable. Not N1 nor Nk.
(4.1)
/( M
m +R )
i = M
i +1
i
i
i
(4.2)
and M
have to be estimated and that equation will be
Note: M
i +1
i
given later.
Note: 1, 2, , 2 are estimable.
1 is not estimable.
i = Si Fi
i apparent survival
Si true survival
Fi fidelity (prob did not emigrate)
Note- We cannot get true survival from capture-recapture data alone.
Add telemetry to estimate F or assume that F=1 in particular
applications.
=N
- ( N
-n +R )
B
i
i +1
i
i
i
i
(4.3)
= m + (R Z /r )
M
i
i
i i i
Note: M2,
The
M
i
M3, , M k-1
are estimable.
intuitive approach.
M1 = 0
(4.5)
N1 is not estimable.
Mk is not estimable.
Zi/(Mi-mi)
ri/Ri
Zi/(Mi-mi) ri/Ri
which gives
= m + (R Z /r )
M
i
i
i i i
Note- I wont expect you to use these equations, I just want you to
understand roughly why the method works.
,..., N
,N
N1 , N
2
k -1
k
Survival Rates
1 , 2 ,..., k -2 , k -1
Capture Probabilities
p1 , p 2 ,..., p k -1 , p k
,..., M
,M
M1 , M
2
k -1
k
,..., B
,B
B1 , B
2
k -2
k -1
Assumptions (continued)
Mark Induced Mortality
Positive bias on population size estimators especially when
capture probability is small
EXAMPLE
Data Table 4.3, Estimators Table 4.4. Old approachnow we would use
MARK so we can fit a variety of sub models but it still illustrates the key
points
High capture probabilities except for August 1973 to December 1973.
Therefore the precision of estimators is generally very good.
Population Sizes - Slight negative bias possible due to heterogeneity and trap
happy response.
Survival Rates - Should be very accurate and precise. Values are very close
to one, except the last one. This may be due to losses of
young animals, but it is difficult to tell because the study
ends here.
Recruitment Numbers -
,..., N
,N
N1 , N
2
k -1
k
Survival Rates
1 , 2 ,..., k -2 , k -1
Capture Probabilities
p1 , p 2 ,..., p k -1 , p k
,..., M
,M
M1 , M
2
k -1
k
,..., B
,B
B1 , B
2
k -2
k -1
MODEL RESTRICTIONS
Model A - Full Model
1 , 2 ,..., k 1
p1 , p 2 ,..., p k
Model B - Constant Survival
1 = 2 ,..., = k 1 =
Model C Constant Capture
p1 = p 2 ,..., = p k = p
Model D - Constant Survival, Constant Capture
1 = 2 ,..., = k 1 =
p1 = p 2 ,..., = p k = p
1 , 2 ,..., k -2 , k -1
Capture Probabilities
p1 , p 2 ,..., p k -1 , p k
Cormack-Jolly-Seber Model
Motivation of Model Structure and Estimation
Expected Values of Cells
X 111
R 11p 2 2 p3
X 11 0
R 11p 2 (1 2 p3 )
X1 0 1
R 11 (1 - p 2 ) 2 p3
X1 0 0
R 1[1 1p 2 2 p3 1p 2 (1 2 p3 ) 1 (1 - p 2 ) 2 p3 ]
X 0 11
R 2 2 p3
X 010
R 2 (1 2 p3 )
X 0 01
Cormack-Jolly-Seber Model
Motivation of Model Structure and Estimation
Intuitive Estimation
Can we separately estimate the components of
2p3?
Cormack-Jolly-Seber Model
Motivation of Model Structure and Estimation
X 0 11 R 2 2 p3
( p ) = X / R
2
0 11
Cormack-Jolly-Seber Model
Motivation of Model Structure and Estimation
Expected Values of Cells
X 111 R 11p 2 2 p3
X 1 0 1 R 11 (1 - p 2 ) 2 p3
X 111 + X 1 0 1 R 11 2 p3
X 111 /(X 111 + X 1 0 1 ) p 2
p 2 = X 111 /(X 111 + X 1 0 1 )
Cormack-Jolly-Seber Model
Motivation of Model Structure and Estimation
Expected Values of Cells
X 111 R 11p 2 2 p3
1 = X 111 /R 1p 2 ( 2 p 3 )
Therefore using previous results we can
estimate the first survival rate.
MARK does it better (MLEs) (: -)))!!
Generalisations of the
Cormack-Jolly-Seber Model using MARK
Multiple age classes
Model selection
Minimize AIC = -2 log L + 2(#pars)
There is penalty for over parameterization
logit (i ) = ln (i / 1 i )i
logit is most common link function used.
It keeps survival rates between 0,1.
log (i ) = + X i
would not!
Model
AICc
Delta
AICc
AICc
Weight
#Par
666.160
0.00*
0.89445
670.866
4.71
0.08505
673.998
7.84
0.01776
678.748
12.59
0.00165
679.588
13.43
0.00109
11
*Best Model
----------------------------------------------------------------------------------------
Model Details
First we will look at the full CJS Model
Next Look at the Best Model where survival
differs between flood and nonflood years and
where p is constant over years.
Standard Error
Lower
Upper
1:Phi
0.7181818
0.1555470
0.3610409
0.9199575
2:Phi
0.4346708
0.0688290
0.3075047
0.5710588
3:Phi
0.4781705
0.0597091
0.3643839
0.5942685
4:Phi
0.6261177
0.0592656
0.5048461
0.7333741
5:Phi
0.5985335
0.0560517
0.4855434
0.7019412
6:Phi *0.7284299
0.0000000
0.7284299
0.7284299
7:p
0.6962027
0.1657637
0.3302969
0.9141508
8:p
0.9230769
0.0728778
0.6161497
0.9889758
9:p
0.9130435
0.0581758
0.7140650
0.9778505
10:p
0.9007892
0.0538330
0.7360176
0.9672856
11:p
0.9324138
0.0458025
0.7684926
0.9828579
12:p
*0.7284328
0.0000000
0.7284328
0.7284328
FLOOD SURVIVAL
= 0.469 (0.043)
NONFLOOD SURVIVAL
= 0.607 (0.031)
CAPTURE PROBABILITY
= 0.90 (0.029)