NA lines and survey effort for multiple visits.

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Stephanie Nefas

Jun 9, 2021, 3:44:13 PMJun 9
to distance-sampling
I have been finding this group very helpful but had a my own questions on a few things I was not confident with. I am a PhD student working with point count data from bird surveys for the first time.

I am using the R package Distance for the first time and just wanted to make sure I was setting everything up correctly. I couldn't find an example to check if the flat file for when you visit a point to conduct point counts more than once. In some of the data I am working with we have two visits to a set of points each summer for two years.

For a point with no detections do I just need one line of data with an NA or does the Distance package require a NA line for each visit where there was no detections?

For effort I think 4 is correct but if I look at each year separately I would have to make a new effort value of 2 correct? 

When using dht2() stratification = "replicate" for multiple visits, is that the only setting that needs to be adjusted for multiple visits?

Thank you,

Eric Rexstad

Jun 10, 2021, 5:03:02 AMJun 10
to Stephanie Nefas, distance-sampling


Have a look at the `wren_snapshot` data set available in the Distance package.  It is data for winter wrens taken from the study carried out by Prof Buckland for his 2006 Auk paper:

Buckland, S. T. (2006). Point transect surveys for songbirds: Robust methodologies. The Auk, 123(2), 345–357.
It is an example of a point transect survey consisting of two visits to each station.  You will note that all stations, with the exception of Station 15, had detections.  There is the single line with distance=NA for Station 15.  Effort is set to "2" for all stations.  This is identical to the way you would handle your multiple-visit per year situation.
With respect to your `dht2` question, you need not make use of `dht2` if you wish to produce a single estimate of density for the year, combining data across visits.  You would only bring `dht2` into action if you treat each visit as a "stratum" to produce visit-specific density estimates and then wish to produce an overall estimate.  I can't speak to your situation, whether the repeat visits were to address a question of interest, or rather to increase the number of detections to strengthen the inference from the detection function fitting.

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Eric Rexstad
Centre for Ecological and Environmental Modelling
University of St Andrews
St Andrews is a charity registered in Scotland SC013532
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