Hi Tessa,
Your input pao file is OK. The problem you are having is due to the large number of secondary
surveys in the data. When I wrote the multi-season model, I assumed that > 200 secondary
surveys per season must be an input error. PRESENCE prints the message in the output file and
stops.
Thinking about it now, I don't see a need for this restriction, so I removed the limitation.
However, the reason that it seemed unreasonable for there to be so many surveys per season is
that it seems unlikely that occupancy doesn't change over such a long period. What do the 233
surveys per season represent in your data? Days? Are you sure occupancy doesn't change over
this period? You might want to define your 'seasons' differently if that's not the case.
For many people, detection probabilities are nuisance parameters, and they are only interested
in occupancy, colonization and extinction. So, you could combine days into weeks, reducing the
number of surveys per season and get the same occupancy, colonizatin and extinction estimates, but
with weekly detection probabilities instead of daily probabilities. This would also reduce the
number of zeros in the data and make building models simpler. What you would lose by this is
the ability to estimate daily detection probabilites, or to model daily detection probabilities
as a function of some daily covariate.
If you download the latest version of PRESENCE, your pao file should work. Unfortunately, the
Patuxent webserver is having technical difficulties at the moment. I put a copy of PRESENCE at
the following link until the webserver is back online:
ftp://ftpext.usgs.gov/pub/er/md/laurel/ ... esence.exeOne other thing: If you are going to read a csv file into the input data form, the csv file
must contain a header line (eg., site,1-1,1-2,1-3,...1-233,2-1,2-2,...2-233)
Cheers,
Jim