seasonal site covariates

[ReneeLorica]

Hi All,

I'm new to PRESENCE so I hope you'll excuse my ignorance.

I am trying to analyze a 3-season, 3-observer data set, and I was wondering if anyone can help me with how to input a site covariate that changes between seasons in the Input Data Form. I have 6 site covariates and didn't have problem with 4 of them since they stay constant but 2 of them changes between seasons, and it seems the Input Data Form for site covariate will not accommodate my seasonal site covariates. I was wondering if anyone can help me with this. Your help will be greatly appreciated!

Cheers, Renee

[tajensen]

Hello Renee

At the top of the Data Input Form type in the number of site covariates next to 'No. Site Covar'. This value will likely be 10 since you have four covariates that are common to all seasons and six covariates that differ among seasons (i.e., 2 * 3 = 6).

When you build your models in the design matrix you can type in the season-specific site covariates to correspond with the parameter you want to estimate. This can be the trickiest part until you get the hang of it, so I recommend posting your design matrix here for additional help.

Regards,
Tim

[ReneeLorica]

Hi Tim,

Thanks very much for responding. I really appreciate it. Following your advice, this is now how my Input Data Form for Site covariates looks like for Site1:

sitecov cane althab habq dist age1 age2 age3 rain1 rain2 rain3
1 1 1 1 -0.911 2 1 1 0.005 -0.624 0.407

My first model is psi(.),gamma(.),eps(.),p(.) so my Design matrix looked like this:

Occupancy
a1
psi1 1

Colonization
b1
gam1 1
gam2 1

Extinction
c1
eps1 1
eps2 1

Detection
d1
P(1-1) 1
P(1-2) 1
P(1-3) 1
P(2-1) 1
P(2-2) 1
P(2-3) 1
P(3-1) 1
P(3-2) 1
P(3-3) 1

What I've tried so far are combinations of different covariates for psi,gamma,eps and p so for example, my Design matrix would look like this for psi(cane),gamma(.),eps(.),p(observer)

Occupancy
a1 a2
psi1 1 cane

Colonization
b1
gam1 1
gam2 1

Extinction
c1
eps1 1
eps2 1

Detection
d1 d2
P(1-1) 1 Observer
P(1-2) 1 Observer
P(1-3) 1 Observer
P(2-1) 1 Observer
P(2-2) 1 Observer
P(2-3) 1 Observer
P(3-1) 1 Observer
P(3-2) 1 Observer
P(3-3) 1 Observer

I take care not to put in too many covariates. What I don't know how to do is add psi2 and why do you add it in the first place. I saw it in one of the posts that seemingly had the same issue I have with seasonal site covariate.

I'm sorry if my questions seem very newbie but I'm just learning all these as I go along. Thanks again for your time. And sorry for the long post.

Renee

[tajensen]

Hi Renee,

I don't have much experience with the multi-season models but it sounds like you might want to try a different model parameterization. In the 'Setup Numerical Estimation Run' window there is a box called 'Model parameterization' where there are four options to choose from. The second and third options allow you to model psi1, psi2, and psi3 directly, which would allow you to model your seasonal site covariates like this, for example:

Code: Select all

            -,a1,a2,a3,a4,a5,a6,
psi1          1 0 0 rain1 0 0
psi2          0 1 0 0 rain2 0
psi3          0 0 1 0 0 rain3


Are you specifically interested in colonization and extinction rates, or just occupancy and detection among the seasons?

Tim

[ReneeLorica]

Hi Tim,

Thanks again. I'm just really interested in occupancy and detection but since I have a 3-season data, then I can't really get away with it, can I?

Renee

[tajensen]

A much simpler way to handle your data would be to split it into three separate projects in PRESENCE, with each project representing one season. Once the data are separated you can run each under the single-season analysis, which is far simpler to learn. I also have three seasons of data and chose to run each separately since I was not concerned with extinction/colonization rates.

Here is a link to an online book that has some *very* useful examples: http://www.uvm.edu/rsenr/vtcfwru/spread ... upancy.htm
The single species, single season models are covered in chapter 3.

Tim

[ReneeLorica]

Hi Tim,

Thank you so much for all your help! I really appreciate it!

Renee

[darryl]

Hi There,
A few quick points:
1. The design matrix Tim has suggested says that the effect of rain is different in each year (so in one year more rain might be better, but another year more rain could be worse). If you think the effect of rain is the same each year (so more rain is always better) then you could have the different rain covariate stacked in a single column. If you split the data up into 3 separate analyses you're unable to consider models that share information across years in some manner.
2. Why wouldn't you be interested in colonization and extinction? To me, that's like saying you're interested in abundance but not survival or recruitment. Sure there's going to be cases where that's reasonable, but understanding processes of change (I think) is a much more interesting question than just comparing patterns.
3. You can think of colonization and persistence (ie 1-extinction) as occupancy probabilities. They are just occupancy probabilities that we're going to allow to be different depending on whether the species was absent or present at a site in the previous year. For many species that exhibit some sort of site fidelity you would expect the probability of them occupying an area to be higher if they'd been there the previous year.
4. You mentioned that you had 3 observers but in an earlier post you had just a single observer covariate in your design matrix. If you've just coded your observers 1, 2, 3, then with a single covariate you're saying there's a consistence difference between them and that observer 2 is always in the middle. More generally you might want to consider using indicator variables for the observer effect. See the weta example in the Presence exercises and worked examples from the help menu.

Cheers
Darryl

[ReneeLorica]

Hi Darryl,

Many thanks for the response.

1. I think the effect is different so I'm trying Tim's suggestion.
2. Only because the initial results of my analysis is showing that there isn't any colonization or extinction that is happening but it could be that I made a mistake inputting my data (very new to PRESENCE so I'm just trying out what has been suggested by others). What I'm more interested in is extinction since I'd like to know if my leopard cats leave the area when harvest of cane is on-going. But right now, my results isn't showing changes in occupancy.
3. Hmm... I didn't think of it as occupancy probabilities too, thanks for that!
4. That probably explains why I'm getting the results I'm getting. I may have coded that wrong. Thanks for pointing it out.