by jhines » Mon Aug 27, 2018 1:33 pm
Gavin,
Thanks for sending the data. The naive estimates don't make sense because the
multi-season model estimates yearly occupancy where occupancy in year t+1
depends on occupancy in year t. You have occupancy different for each site and
constant over years, but extinction is constant among all sites and years, so
the occupancy estimate for each site is affected by the extinction and
colonization parameters.
To obtain the quantity you're interested in (proportion of years occupied), I
think you need to either run a model where colonization equals 1 - extinction,
or re-structure the data where you treat each site/year combination as a
different site (row in detection history matrix) and run a single-season model
with site as a covariate.
If you run the colonization=1 - extinction model, you'll need to check the 4th
parameterization option in the run window and you'll see that the 1st design
matrix contains psi and all gamma's. Before doing that, you can copy the
design matrix from the model you ran by retrieving the previous model, click
on the 1st cell in the occupancy design matrix, then right-click and select
"Copy". Then paste it to Excel, then paste all but the 1st column back into
the design matrix for psi/gamma. You should end up with a design matrix like this:
-,a1,a2,a3,a4,a5,a6,a7,a8,
psi1 C1 C2 C3 C4 C5 C6 C7 C8 ... C74
gam(1) C1 C2 C3 C4 C5 C6 C7 C8 ... C74
gam(2) C1 C2 C3 C4 C5 C6 C7 C8 ... C74
gam(3) C1 C2 C3 C4 C5 C6 C7 C8 ... C74
gam(4) C1 C2 C3 C4 C5 C6 C7 C8 ... C74
gam(5) C1 C2 C3 C4 C5 C6 C7 C8 ... C74
gam(6) C1 C2 C3 C4 C5 C6 C7 C8 ... C74
:
:
Cheers,
Jim