Help File/Determining Occasions With Habitat Differences

[Julia.Page]

Hi there,
I'm very new to the program DENSITY as well as R and SECR, and am having some trouble with the bare basics of starting with data input in DENSITY. I am not able to use the Help file, which even after reading the alternative method for fixing this, our IT specialist for our government network still couldn't fix the security block on using the file. So, my first question is wondering if it would be possible to have the Help tab files downloaded into a PDF or Word document and emailed? Or if anyone has found an alternative solution to this issue?
My second question is regarding formatting my data into the correct input file for DENSITY. Our project is using small mammal trapping to determine population and community structure fluctuations within restored and not restored habitats within a larger area. We have 4 habitat types, with 1 of each in a restored/not restored area = 8 distinct sites. Within each site are 3 grids of 36 traps = 108 traps per site. We have trapped each site 3 times over the course of 9 months. In the first month we trapped 3 sites during the first week (with 4 trap nights), 2 during the second, and 3 during the third = 12 total trap nights. The next trapping session 3 months later, we trapped 3 different sites first, then 3 different sites next, and ended with 2 different sites. So in other words, we changed the formation of which sites were trapped during each of the three weeks. For numbering the 12 days, or occasions, in which animals were trapped over 3 sessions throughout the different habitat sites animals were technically only supposed to be trapped within that site for 4 of the 12 days in each session. However, we did have a couple animals move to a different habitat site through sessions. I originally labeled each day we trapped 1:36, but this is obviously wrong.
Session, ID, Occasion, Detector
1, 605, 2, PiUnC32
3, 605, 30, PiUnC28
Please excuse my inexperience with what is probably a very basic capture data format. Any help would be greatly appreciated!

Julia

[murray.efford]

Hi Julia

I have found a way to convert the density5.chm file to pdf and posted it at http://www.otago.ac.nz/density/pdfs/Density5.pdf. The result is clunky, but better than nothing. I suspect your problem is specific to using chm files over a network - if you can install on a local machine so much the better.

Regarding data formats - I think this is an issue of how you want to carve the data for analysis. There are different ways of defining 'sessions', with consequences for how you model between-grid or between-habitat effects. At a glance, you could treat each of the 8 habitat/treatment combinations as a 'session', each with its own trap layout file. For each of the 108 trap locations within a layout file you could identify the particular days active with 12 daily 0/1 'usage' fields out to the right of the coordinates (4 1's, 8 0's per row). Another way would be to split each 'session' further into grids. That might relieve you of the need to define a separate layout file for each session if each grid was trapped for 4 nights in each session and the same trap configuration was used on each of the 8 x 3 grids, but would discard the occasional between-grid recaptures.

I'm afraid there may need to be some trial and error. You will certainly want to consider between-session models, possibly with multiple session covariates, and for this the R package 'secr' is recommended over Density.

Regards
Murray

[Julia.Page]

Thank you for the pdf- that will be a huge help!

I will start with your suggestion of splitting sessions into the 8 habitat types- I think that will break down the data much better for analysis. One question with the detector usage format with 0/1 I have is if you need to also include traps which never caught anything (12 0's per row)?

Thank you,
Julia

[murray.efford]

My earlier post ignored that you repeated the design 3 times through the year, so you may need 24 sessions all-up. But maybe start with just one of the 3-monthly trials (8 'sessions') and master that...

One question with the detector usage format with 0/1 I have is if you need to also include traps which never caught anything (12 0's per row)?

'Usage' records whether you used the traps, not whether an animal used the traps! Traps that never caught were 'used' in this sense. (Maybe you started thinking of this as a trap occupancy problem - forget it!)

Murray