## Occupancy rate of 1, CI [0,1]

questions concerning analysis/theory using program PRESENCE

### Occupancy rate of 1, CI [0,1]

Hi,

I have encountered a problem with my occupancy analysis that I am hoping to get some guidance on. I am doing an occupancy analysis of five small mammal species across five plots. I am performing this analysis in R using the unmarked package and the AICcmodavg package.

The issue I am encountering is in regards to the occupancy estimate confidence intervals. This issue only applies to one species. For this species, I get reasonable occupancy estimates across the five plots. Plot was included as a site covariate in the top competing models so the predicted occupancy rate varies across the plots. For two plots (Sand_sheet_east & Sand_sheet_west), this species was detected very often. The detection histories for these two plots are almost all 1's, with only a few 0's. So the occupancy probability is basically one, with a very small standard error. This seems to make sense. What I do not understand is why the confidence interval goes from 0 to 1, and not ~ 0.98 to 1. I posted the predicted occupancy output below.

mod.avg.pred uncond.se lower.CL upper.CL. Plot
1 0.726145 0.083266 0.538517 0.857657 Cottonwood
2 0.550194 0.089675 0.375419 0.713412 Acacia
3 0.768903 0.077462 0.586047 0.886617 Heather
4 0.999989 0.000780 0.000000 1.000000 Sand_sheet_east
5 0.999993 0.000685 0.000000 1.000000 Sand_sheet_west

Thanks in advance for any help,

Jaran
Jaranlanae

Posts: 4
Joined: Tue Mar 29, 2022 3:16 pm

### Re: Occupancy rate of 1, CI [0,1]

I'm guessing that unmarked is calculating confidence intervals on the logit-scale, then back transforming to the real scale. This tends to work fine, except when you have real estimates that are very close to 0 or 1 because on the logit-scale, the SE tends to be really, really big, which leads to really wide intervals on the logit-scale and how you end up with real-scale CI or 0-1.

It's a case where you have to ignore the output, and/or try other CI methods (eg bootstrapping, profile likelihoods, etc) if you're not satisfied by saying it's a range that is very close to 1 (in this case)

Cheers
Darryl
darryl

Posts: 493
Joined: Thu Jun 12, 2003 3:04 pm
Location: Dunedin, New Zealand

### Re: Occupancy rate of 1, CI [0,1]

Jaranlanae wrote:Hi,
I am performing this analysis in R using the unmarked package and the AICcmodavg package...

The group is very active, and there are any number of unmarked users (including most of the developers) who routinely reply to posted questions.
egc

Posts: 201
Joined: Thu May 15, 2003 3:25 pm

### Re: Occupancy rate of 1, CI [0,1]

Darryl,

Thank you so much for your response. Your knowledge and work is inspiring.

Egc,

I apologize for posting on the wrong group. I am new to these group threads and getting help through them. I did not realize there was a more appropriate option. Thank you for passing on that info.

-Jaran
Jaranlanae

Posts: 4
Joined: Tue Mar 29, 2022 3:16 pm

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