Data Input & Design Matrix for multi-method analysis

[jamesmort]

We are attempting to determine differences in detection probabilities of two bird count methods. Our study design has 93 sites (sample units), with 5 bird count stations (surveys) at each site (there are some missing surveys). A bird count using each method was completed at each count station.
Our query is in two parts: 1) design matrix set-up; 2) strange-looking theta values
Following available guidance, we have set up our data in the PRESENCE (v10.5) Data Input Form as follows:
Rows Cols #srvy/seasn #meth/srvy #site covs #sam covs
93 10 2 1 0 0

Data 1-1 1-2 2-1 2-2 3-1 3-2 4-1 4-2 5-1 5-2
Site1 0 0 0 0 - - 0 0 0 0
Site2 0 0 0 0 0 0 - - 0 0
Site2 0 0 0 0 0 0 - - 0 0
etc
We then ran a model - Run > Analysis: single-season > Multi-method, entered ‘2’ into the #Methods dialogue box, and set up our occupancy design matrix as follows:
a1 a2
Psi 1 0
theta1 0 1
theta2 0 1
theta3 0 1
theta4 0 1
theta5 0 1

At this stage, we would like to keep occupancy and thetas constant, as we are interested in the probability of detection. The problems start when we try setting up our probability design matrix. As we understand it, the matrix should look like this:
b1 b2
p[1-1] 1 0
p[1-2] 0 1
p[2-1] 1 0
p[2-2] 0 1
p[3-1] 1 0
p[3-2] 0 1
p[4-1] 1 0
p[4-2] 0 1
p[5-1] 1 0
p[5-2] 0 1

However, it actually looks like this:
b1 b2
p[1-1-1] 1 0
p[1-1-2] 0 1
p[1-2-1] 1 0
p[1-2-2] 0 1
p[2-1-1] 1 0
p[2-1-2] 0 1
p[2-2-1] 1 0
p[2-2-2] 0 1
p[3-1-1] 1 0
p[3-1-2] 0 1

For some reason unknown to us, the coding of p does not match the set up in our Data Input Form, and we seem to have no way of manually changing it.
When we run the analysis, we get a single estimate of psi, a single estimate of theta and estimates of p for each method. The theta value however is 0.000000 (with standard error of 10.000000), which does not seem right to us.
Can you please advise us on whether or not we have our Input Data Form and Design Matrix set up correctly, and if not what we can do to correct it? Alternatively, could you point us in the direction of a worked example of the input requirements of multi-method occupancy analysis?

Thanks,

James

[jamesmort]

After further experimentation and some input from colleagues, we believe we have resolved this query ourselves, as follows:

Data Input Form design:

Rows Cols #srvy/seasn #meth/srvy #site covs #sam covs
93 10 5 2 0 0

Occupancy design matrix:

a1 a2
Psi 1 0
theta1 0 1
theta2 0 1
theta3 0 1
theta4 0 1
theta5 0 1

Probability design matrix:

b1 b2
p[1-1-1] 1 0
p[1-1-2] 0 1
p[1-2-1] 1 0
p[1-2-2] 0 1
p[1-3-1] 1 0
p[1-3-2] 0 1
p[1-4-1] 1 0
p[1-4-2] 0 1
p[1-5-1] 1 0
p[1-5-2] 0 1

The probability design matrix coding now makes sense to us, and we get a value for theta.

James