Autocorrelation between sites. What is a site?

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Autocorrelation between sites. What is a site?

Postby bgerber » Sat Dec 15, 2007 6:16 pm

What is a site?

I am in the design phase of a remote camera-trap/occupancy study for mesocarnivores of the eastern rainforests of Madagascar. The largest endemic Malagasy carnivore (Cryptoprocta ferox) has very uniform pelage; making it very unlikely to identify individuals from photographs (thus can’t use mark-recapture). Very little ecological information is known for this species. There is one estimate of density, but in a completely different habitat. What I am concerned about is spacing cameras appropriately. Is it important to space cameras so a single camera station is present in one potential home-range to avoid autocorrelation between sites (one potential individual for one site)? Am I correct in this assumption? If I decided to set the camera spacing based on body weight, which may be very far from accurate, then I have the potential of detecting multiple individuals at some sites. Is this a problem? Is it a problem if these highly mobile animals are in fact non-territorial? Is autocorrelation between sites an issue?

One more question: What would occupancy mean if camera stations were deployed randomly in a non-grid scenario (distance between camera sites varied from 100m to 2000m); leaving some potential homeranges with multiple cameras and some only one camera? What does 75% occupancy mean then?

Any thoughts of what a site is to a large mobile animal would be greatly appreciated.

Sincerely, Brian
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Postby darryl » Sun Dec 16, 2007 5:03 pm

Brian,
In your case I don't think you need to get too concerned about spatial autocorrelation, particularly if the animals are not territorial. You have to keep in mind that this is all at the species level, not the individual.

In terms of what you should define as a 'site' it seem the options are either something fairly small around the camera station (ie an effective detection range), or it would have to be something larger but would probably then want to have multiple stations within a site because detection now has 2 components to it; you locate the camera within the site where there's some chance an animal will walk past (if it's going to be using that site), then given it walks past, you get a photo of that.

How you interpret occupancy depends entirely on what you define as a 'site', and how you do your sampling. Often it helps to start with focusing on exactly what it is your trying to measure, then figure out the field methods that will get you there.

Are you only using cameras or can you do sign surveys also?

Darryl
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A site as the detection zone of a camera

Postby bgerber » Mon Dec 17, 2007 1:26 pm

We are only able to detect these carnivores with cameras. Due to the high turn over rate in the rainforest, detecting scat or sign is very difficult.

At this point we are uncertain whether these carnivores are territorial.

To me, a site in my case would be the camera detection zone located in a specific microhabitat. What I would like to determine for the largest carnivore is if they are occupying much of the National Park and if micro/macro habitat characteristics influence occupancy.

Do you see an issue in which cameras vary from 200m apart to 1500m apart? If I want to make an inference about the occupancy of a carnivore for the entire national park and place cameras randomly in such a way that some cameras are clumped and some are very far from another camera, is there not a bias towards the clumped cameras? Thus, I would bias my occupancy estimate high or low depending on if the clumped site was occupied or not occupied.

I have pilot data that was collected in this way. I have a total of 43 camera sites, but I keep thinking that I need to analyze a subset of the sites, based on a potential homerange. If I use all 43 sites, I can't seem to adequately reconcile how the spatial autocorrelation doesn't bias my inference for the entire park.

Thank you for you comments.
Sincerely, Brian Gerber
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Re: A site as the detection zone of a camera

Postby darryl » Mon Dec 17, 2007 4:47 pm

Brian

bgerber wrote:To me, a site in my case would be the camera detection zone located in a specific microhabitat. What I would like to determine for the largest carnivore is if they are occupying much of the National Park and if micro/macro habitat characteristics influence occupancy.


That's fine if you want to do it that way, although you'd have to interpret your psi estimate as 'use' (ie the species was within this point at some time during the sampling, but not necessarily all the time) so keep that in mind when you start thinking about microhabitat covariates. Plus, unless you're planning on having 100's of camera stations, you'll probably only be able to pull out large-scale effects. Finally, are your cameras going to be placed truly randomly, or only on game trails? This could also influence the biological interpretation of any apparently important covariates.

bgerber wrote:Do you see an issue in which cameras vary from 200m apart to 1500m apart? If I want to make an inference about the occupancy of a carnivore for the entire national park and place cameras randomly in such a way that some cameras are clumped and some are very far from another camera, is there not a bias towards the clumped cameras? Thus, I would bias my occupancy estimate high or low depending on if the clumped site was occupied or not occupied.


Presuming those distances are relatively large compared to the detection range of a camera, then no. As you're defining your site as the detection range of the camera, then if there's some clustering due to random chance then so be it, that arrangement is as equally likely as any other. How do you know that any cluster will either be all occupied, or none? Couldn't the boundary occur somewhere within the cluster?

bgerber wrote:I have pilot data that was collected in this way. I have a total of 43 camera sites, but I keep thinking that I need to analyze a subset of the sites, based on a potential homerange. If I use all 43 sites, I can't seem to adequately reconcile how the spatial autocorrelation doesn't bias my inference for the entire park.


If you have random placement then I don't think it's too much of an issue, here's my logic. No claims it's not flawed. Forgetting about detectability for a moment, if you knew whether or not each site on the landscape was occupied (potentially with spatial correlation), then through them all in a hat and randomly drew out 1 site at a time and noted whether it was occupied, then you should get an unbiased estimate of the fraction of sites that are in the hat that are occupied. If you knew the degree of spatial correlation, then perhaps you could come up with a more efficient sampling scheme than simple random sampling, but that may then be sensitive to the assumed level of correlation. As for detectability, provided that the outcome of a survey at any site does not depend upon whether the species was detected or not at another site, I think you're fine. About the only way I can imagine spatial correlation would be a problem here (off the top of my head) would be for a highly territorial species such if you have 2 sites within an individuals home range, there's no way you could get a detection (of the species remember, not necessarily the same individual) at both sites in the same night. With camera traps though a simple fix would be define your 'survey' as longer period such that there is some chance of getting a detection at both places, ie make it long enough for the animals to move around a bit, eg a 5-day period perhaps.

Sorry for the lengthy reply.

Cheers
Darryl
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