different number of secondary occasions per primary occasion--dynamic occupancy

[Asia Murphy]

**I apologize if this posts twice**

Hello, I'm trying to run dynamic occupancy models in unmarked. The problem is that I have different numbers of secondary survey occasions for each primary occasion (i.e., one year has 6 secondary occasions, another has 8). I see that in unmarkedMultFram you can define the number of primary occasions; is there an argument or workaround to define the number of secondary occasions per primary occasion? Appreciate any help that can be given.

[Jeffrey Royle]

hi Asia,

 varying numbers of secondary periods is accommodate implicitly by padding data with missing values.

 For example, if you look at this data file from the help file for colext:

# Fake data
R <- 4 # number of sites
J <- 3 # number of secondary sampling occasions
T <- 2 # number of primary periods

y <- matrix(c(
   1,1,0,  0,0,0,
   0,0,0,  0,0,0,
   1,1,1,  1,1,0,
   1,0,1,  0,0,1), nrow=R, ncol=J*T, byrow=TRUE)

this shows 2 primary periods with 3 secondary periods each.  If instead the 2nd primary period only had 2 secondary samples then you change one set of data to NA:

y <- matrix(c(
   1,1,0,  0,0,NA,
   0,0,0,  0,0,NA,
   1,1,1,  1,1,NA,
   1,0,1,  0,0,NA), nrow=R, ncol=J*T, byrow=TRUE)

In general, you make the data file have the highest value of J for all sites and then pad with NAs. 

regards

andy

On Thu, Aug 4, 2016 at 9:11 AM, Asia Murphy <asiaj...@gmail.com> wrote:

**I apologize if this posts twice**

Hello, I'm trying to run dynamic occupancy models in unmarked. The problem is that I have different numbers of secondary survey occasions for each primary occasion (i.e., one year has 6 secondary occasions, another has 8). I see that in unmarkedMultFram you can define the number of primary occasions; is there an argument or workaround to define the number of secondary occasions per primary occasion? Appreciate any help that can be given.

--
You received this message because you are subscribed to the Google Groups "unmarked" group.
To unsubscribe from this group and stop receiving emails from it, send an email to unmarked+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Asia Murphy]

Thank you so much!!

To unsubscribe from this group and stop receiving emails from it, send an email to unmarked+u...@googlegroups.com.