age-specific/cohort CJS model(corrected)

[williamMO]

Hello All,

Sorry my previous post didn't come out well.

I just got registered here. I wonder if someone can help me with questions listed below
regarding age-cohort CJS model (addressed in Chapter 7 in Mark manual book). Any help is greatly appreciated.

Suppose I have three age groups, say age-0, age-1 and age-2. In each year a certain number of animals were released from each age group and was recaptured for three occasions (an increment of 1 year between occasions). Now I want to use Mark program and estimate age-specific survival rate (i.e. survival rates for age-0, age-1, and age-2 groups). Here age-2 group includes animals of 2-years old or older. The hypothesized encounter history is given as below:

history age_group count
1111 0 20
1110 0 30
1100 0 10
1101 0 15
1000 0 5
1001 0 12
1010 0 16
1011 0 23
0111 0 30
0011 0 50
1111 1 40
1110 1 60
1100 1 70
1101 1 35
1000 1 25
1001 1 52
1010 1 66
1011 1 73
0111 1 40
0011 1 60
1111 2 90
1110 2 80
1100 2 70
1101 2 51
1000 2 53
1001 2 71
1010 2 37
1011 2 21
0111 2 50
0011 2 70


1. What should be the be input data format for me to run an age-cohort model in Mark? I assume I need 4 columns in the input data file like below:
history age-0 age-1 age-2
1111 20 40 90
1110 30 60 80
1100 10 70 70
1101 15 35 51
1000 5 25 53
1001 12 52 71
1010 16 66 37
1011 23 73 21
0111 30 40 50
0011 50 60 70
The first column is the encounter history, the last three columns being the count for that particular history for each age-group. Am I correct?


2. Assume phi[1], phi[2] and phi[3] are the survival rates for age-0, age-1 and age-2 groups. Also, for my PIM for survival rates, is it like the following?

Survival rate for age-0 group
--- j=1 j=2 j=3
i=1 1 2 3
i=2 - 1 2
i=3 - - 1

survival rate for age-1 group
--- j=1 j=2 j=3
i=1 2 3 3
i=2 - 2 3
i=3 - - 2

survival rate for age-1 group
---- j=1 j=2 j=3
i=1 3 3 3
i=2 - 3 3
i=3 - - 3

3. After I input the data in Mark, I can get the output summary, i.e. the commonly known m-array for each age-group? Are those summary data Mark used when running the analysis?

The summary data for age-0 is given below
----------------- j=1 j=2 j=3 total
i=1 (Ri=131) ----- 75 39 0 114
i=2 (Ri=30+75=105) - 80 0 80
i=3 (Ri=50+119=169) - - 150 150

I see this output summary problem is not correct. Since if we look at i=2, Ri=30+75, where 30 is newly released animal at occasion i=2, while 75(at age-1 now) the total number of animal released at occasion i=1 but re-captured at j=1. But, those 105 animal are of different ages. If this is the data Mark uses for analysis, how can we distinguish the age-difference among 105 animals? Do I misunderstand anything here?


Thanks for your help!