colext() - Getting occupancy estimates and SE for categorical site covariates over seasons

[Louis H]

Hi all,

I'm relatively new to the unmarked package and I'm having trouble figuring out what seems to be a straightforward output of occupancy models. I'm using the colext() function as I have 4 years (i.e. seasons) of data for 9 areas with each several (though not an equal number of) sites.

I have added 'area', factor with 9 levels, as a Site-level covariate. I simply want to get an occupancy estimate ± SE for all areas over all years for plotting purposes, similarly to the output of smoothed() - though this gives you overall occupancy rates, no SE and no differentiation per covariate ( e.g. area).

I have considered using the initial occupancuy (psi) estimates and the colonization (gam) and extinction (eps) rates to calculate the occupancy rate over years like so: psi + psi*gam - psi*eps, but that does not take into account SE.

Thank you very much for any guidance!

Louis

Since I think this is more of a theoretical question, I'm uinsure as to how much extra info I shold share to help with answering my question. Below some gerenal info:

I have basically used following two models:

colext(~area, ~area, ~area, ~1, data = umf)

colext(~area, ~area*Year, ~area*Year, ~1, data = umf)

('Year' is a Yearly-site-level covariate with 4 levels)

My unmarked dataframe structure looks like this:

265 sites

Maximum number of observations per site: 28 

Mean number of observations per site: 22.7 

Number of primary survey periods: 4 

Number of secondary survey periods: 7 

Sites with at least one detection: 96 

Tabulation of y observations:

   0    1 <NA> 

5588  428 1404