Which software for trapping simulation?

[Kim]

G'day all,
with a simple simulation I want to explore the influence of habitat shape on trapping success.
The specific case I want to investigate:
- standardised trapping protocoll (line transect, even distances between traps)
- two different habitat shapes (long and very narrow, i.e. essentially one-dimensional and larger habitat patches - both are surrounded by unsuitable habitat, whid the animals don't use)
- animals occupy home ranges of a certain surface area but these aren't exclusive

In the long and narrow habitat, the line transect will intersect with fewer home ranges than in the habitat patches (because the home ranges will be long and narrow, too).
With this simulation I want to explore the effect this has on trap success. Hence I'd need a software in which at the minimum I can specify the habitat shape, home range size and my trapping protocoll (ie length of the transec and spacing of traps).

I would be very grateful for any hints towards which software(s) might be suitable for this application!
Cheers,
Kim

[murray.efford]

Kim
The Windows software Density (PowerAnalysis module) and the R package 'secr' simulate many sorts of trapping data. 'secr' is more flexible and complete, but requires some facility with R. See the Density | secr subforum for details.
Here is a brief example, simulating a population within 100 m of a long trap line (40 m would do, as that is the maximum detection radius in this example). You would want to put this in a loop and summarise the results (Density does this for you).
Murray

Code: Select all

library(secr)
mygrid <- make.grid(nx = 100, ny = 1)
mypop <- sim.popn(core = mygrid, buffer = 100, D = 10)
summary(sim.capthist(mygrid, mypop, detectpar =
    list(g0 = 0.2, sigma = 40), detectfn = 'uniform'))


Typical result:
Object class capthist
Detector type multi
Detector number 100
Average spacing 20 m
x-range 0 1980 m
y-range 0 0 m
Counts by occasion
1 2 3 4 5 Total
n 84 86 81 85 79 415
u 84 33 15 10 6 148
f 23 36 45 35 9 148
M(t+1) 84 117 132 142 148 148
losses 0 0 0 0 0 0
detections 84 86 81 85 79 415
detectors visited 58 55 51 57 55 276
detectors used 100 100 100 100 100 500

[murray.efford]

Kim
BTW simulations in Density and secr assume circular home ranges. I don't know of any easy way to simulate highly elongated ranges, but then that wasn't one of your minimum requirements! It may also be a bit fanciful, biologically.
Murray

[Kim]

Thanks for your advice and the sample script, Murray.
I'll have a play with Density and secr. The circular home ranges might be a problem since the long and narrow habitat strips in my system force animals to occupy elongated ranges. But certainly a good starting point and I'll see how I go with these two models.
Thanks again. Kim

[murray.efford]

Do you just want to simulate elliptical ranges with their main axis parallel to the trap line? I would guess this can be done by scaling x: e.g., simulate ellipses with (maj/min axis = 2; density = D; trap spacing s) by circles (radius=minor axis; density = D*2; trap spacing s/2). Check this before you use it!
Murray

[bacollier]

Kim,
You might also want to look at the R package WiSP as I think it will do several of the things you have listed.

http://www.ruwpa.st-and.ac.uk/estimatin ... ance/WiSP/

Bret

[Kim]

Thanks again, Murray and Bret.
I'll see how I go with these options and will post my results here in case you are interested.
Since I just got my thesis-reviews back, I don't know when I'll get around to, though.
Cheers Kim