Trouble with multi-state, multi-season parameterization

questions concerning analysis/theory using program PRESENCE

Trouble with multi-state, multi-season parameterization

Postby dtsimpson » Sun Mar 26, 2017 12:04 pm

Hi all,

I am using the multi-season, multi-state model in Presence 11.8 to model occupancy and turnover in a series of metapopulations. States 1 and 2 describe differences in abundance. While I am having no trouble running the models with in the second, Psi, R, p, delta parameterization, I find interpretation of these parameters less intuitive than the default Psi(r,s), p(o,t) model. However, I cannot get the default model to work. I have run it with multiple designs and for multiple species, and I always get the same result: only psi_0 receives an actual estimate. Everything else receives a point estimate of 0, with SE = 10.

I have tried with the default design matrix [Psi(t), p(.)], as well as a custom design in which each transition probability is unique within but not between seasons, and detection varies between, but not within seasons. My design matrices look like this:

Psi0(0-1) 1 0 0 0 0 0 0 0
Psi0(0-2) 0 1 0 0 0 0 0 0
psi1(0-1) 0 0 1 0 0 0 0 0
psi1(0-2) 0 0 0 1 0 0 0 0
psi1(1-1) 0 0 0 0 1 0 0 0
psi1(1-2) 0 0 0 0 0 1 0 0
psi1(2-1) 0 0 0 0 0 0 1 0
psi1(2-2) 0 0 0 0 0 0 0 1
psi2(0-1) 0 0 1 0 0 0 0 0
psi2(0-2) 0 0 0 1 0 0 0 0
psi2(1-1) 0 0 0 0 1 0 0 0
psi2(1-2) 0 0 0 0 0 1 0 0
psi2(2-1) 0 0 0 0 0 0 1 0
psi2(2-2) 0 0 0 0 0 0 0 1
psi3(0-1) 0 0 1 0 0 0 0 0
psi3(0-2) 0 0 0 1 0 0 0 0
psi3(1-1) 0 0 0 0 1 0 0 0
psi3(1-2) 0 0 0 0 0 1 0 0
psi3(2-1) 0 0 0 0 0 0 1 0
psi3(2-2) 0 0 0 0 0 0 0 1
psi4(0-1) 0 0 1 0 0 0 0 0
psi4(0-2) 0 0 0 1 0 0 0 0
psi4(1-1) 0 0 0 0 1 0 0 0
psi4(1-2) 0 0 0 0 0 1 0 0
psi4(2-1) 0 0 0 0 0 0 1 0
psi4(2-2) 0 0 0 0 0 0 0 1

~~~

p11 (1) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (2) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (3) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (4) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (5) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (6) 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (7) 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (8) 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
p11 (9) 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
p11(10) 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
p11(11) 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
p11(12) 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
p11(13) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
p11(14) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
p11(15) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
p11(16) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
p11(17) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
p11(18) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
p11(19) 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
p11(20) 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
p11(21) 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
p11(22) 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
p11(23) 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
p11(24) 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
p11(25) 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
p11(26) 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
p11(27) 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
p11(28) 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
p11(29) 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
p11(30) 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
p21 (1) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (2) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (3) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (4) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (5) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (6) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (7) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (8) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21 (9) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(10) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(11) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(12) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(13) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(14) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(15) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(16) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(17) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(18) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(19) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(20) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(21) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(22) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(23) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(24) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(25) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(26) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(27) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(28) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(29) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p21(30) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
p12 (1) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
p12 (2) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
p12 (3) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
p12 (4) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
p12 (5) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
p12 (6) 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
p12 (7) 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
p12 (8) 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
p12 (9) 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
p12(10) 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
p12(11) 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
p12(12) 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
p12(13) 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
p12(14) 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
p12(15) 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
p12(16) 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
p12(17) 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
p12(18) 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
p12(19) 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
p12(20) 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
p12(21) 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
p12(22) 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
p12(23) 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
p12(24) 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
p12(25) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
p12(26) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
p12(27) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
p12(28) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
p12(29) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
p12(30) 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
p22 (1) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
p22 (2) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
p22 (3) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
p22 (4) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
p22 (5) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
p22 (6) 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
p22 (7) 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
p22 (8) 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
p22 (9) 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
p22(10) 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
p22(11) 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
p22(12) 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
p22(13) 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
p22(14) 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
p22(15) 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
p22(16) 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
p22(17) 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
p22(18) 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
p22(19) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
p22(20) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
p22(21) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
p22(22) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
p22(23) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
p22(24) 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
p22(25) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
p22(26) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
p22(27) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
p22(28) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
p22(29) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
p22(30) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

My output looks like this:
A1 Psi0(0-1) : 1.178655 0.330113
A2 Psi0(0-2) : 0.000000 10.000000
A3 psi1(0-1) : 0.000000 10.000000
A4 psi1(0-2) : 0.000000 10.000000
A5 psi1(1-1) : 0.000000 10.000000
A6 psi1(1-2) : 0.000000 10.000000
A7 psi1(2-1) : 0.000000 10.000000
A8 psi1(2-2) : 0.000000 10.000000
E1 p11(1) : 0.000000 10.000000
E2 p11(7) : 0.000000 10.000000
E3 p11(13) : 0.000000 10.000000
E4 p11(19) : 0.000000 10.000000

It goes on for all parameters except Psi0(0-1).

I cannot figure out what I'm doing wrong; this same design works fine when translated into the Psi, R, p, delta parameterization. The only problem is that I typically have to fix CR0(i) to 0, because there are no incidences in my dataset of these species going from unoccupied to high abundance during a single transitional period.

Is there something I am doing wrong in the design matrices, or is there something else I am missing?

Thanks for your help!
dtsimpson
 
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Joined: Thu Mar 23, 2017 5:31 pm

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