Multiseason occupancy - how to enter yearly site covariates

[tds]

I want to run multiseason occupancy models in MARK. However, I can't figure out how to enter the yearly site covariates into the design matrix. For example, I have a different measure of cone crop per site per year. I want to see if colonization and extinction are influenced by the annual cone crop.

Could I set up the DM as:
psi 1 cc09 0 0 0 0 0 0 0 0 0
E 0 0 1 cc11 0 0 0 0 0 0 0
E 0 0 0 0 1 cc13 0 0 0 0 0
G 0 0 0 0 0 0 1 cc11 0 0 0
G 0 0 0 0 0 0 0 0 1 cc13 0
p 0 0 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 0 0 1
where cc09, cc11 and cc13 are each individual columns in the .inp, in which each site's cone crop for that year is listed.

(Also, is there a better way to illustrate the DM in phidot? More visual examples could help some beginning users.)

Thank you

[darryl]

You've got a good start, and your current design matrix is modelling an interaction between year and cone crop effects for each of the colonization and extinction probabilities (ie yr x cc).

A yr + cc model would look like
psi 1 cc09 0 0 0 0 0 0 0
E 0 0 1 cc11 0 0 0 0 0
E 0 0 1 cc13 1 0 0 0 0
G 0 0 0 0 0 1 cc11 0 0
G 0 0 0 0 0 1 cc13 1 0
p 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 1

And a cc model would look like
psi 1 cc09 0 0 0 0 0
E 0 0 1 cc11 0 0 0
E 0 0 1 cc13 0 0 0
G 0 0 0 0 1 cc11 0
G 0 0 0 0 1 cc13 0
p 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 1

Note that extinction and colonization are between season events therefore you might also want to think about whether it the amount of cone crop at the beginning or end of the period that is driving the changes. The above DMs are using the cone crop at the end of the period. If you think it's the value at the start, then your DM might look like (for yr +cc model):

psi 1 cc09 0 0 0 0 0 0 0
E 0 0 1 cc09 0 0 0 0 0
E 0 0 1 cc11 1 0 0 0 0
G 0 0 0 0 0 1 cc09 0 0
G 0 0 0 0 0 1 cc11 1 0
p 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 1
p 0 0 0 0 0 0 0 0 1

You don't need to do the same thing for both colonization and extinction.

Cheers
Darryl

[egc]

(Also, is there a better way to illustrate the DM in phidot? More visual examples could help some beginning users.)

Use the [code] tag. See items (2) and (4) in the forum FAQ

It is worth playing around with the various tags (bold, italic, quote, etc), to see what they do. It gives you a lot more flexibility and control over what you can post, and how it will look, which occasionally makes a difference.