Decide on consistent units and arg names

[timcdlucas]

I think I agreed to switch to match yours.

tm, v

I think "radial distance to the detected animal" and "a priori maximum radial distance" should be given different but related names. Same goes for angle of detection.

I'll make a more thorough glossary in this thread at some point.

2f74527 Changes rem (from remBoot).

Still accepts the same units (r in meters, v in km per day and tm in hours Convert to r in km, tm in days (v remains in km per day) for actual calculation. 28396fd Changes gREM.

Now only accepts units to match rem (r in meters, v in km per day and tm in hours Convert to r in km, tm in days (v remains in km per day) for actual calculation. b63df6a Tests and confirms that rem and gREM give the same results. Though I note that in my emails I forgot that you cannot just put theta = 2*pi into the REM model.

d2b3e31 My changes to rem have broken your regression test. But this has also made me think that the data in hDat is in kilometers for r, not meters as requested in the docs. So I just want to check whether you prefer meters or kilometers for r. But that can be discussed in the "what units should we use" wiki.

So let me know what you think. I haven't carefully checked through other functions to see if anything else needs changing.

Not sure where to keep discussions. Maybe here is best.

The wiki is now up to date. https://github.com/timcdlucas/RandEM/wiki/Glossary

However, I am wondering whether we should use different names for 1) a known or estimated value, typically a property of the sensor (e.g. the detection distance of a sensor) vs 2) a realisation of a related property such as the distance between a specific animal and the sensor.

Actually the only place I can see the latter is in hDat and it's called dist there. However, in hDat, the observed angle of animals is called theta while in gREM the known detection angle of the sensor is called theta. As usual I'm perfectly happy to change gREM arg names.

I think it would make sense to have different names for each value. Perhaps the value in hDat (and, hence, distance-to-target) should be changed to d. One of the theta arguments could be changed to phi. Like theta, phi is often associated with plane angles in mathematics.

Yup those both sound like good plans to me.

[tundraboyce]

Hi all, thanks for this package! Am just getting to testing now.

I'm hoping for some clarity on the distance unit that should be used in data files? As you mentioned here and in the readme and help files in R, the function asks for radial distance in meters but I can only assume the hDat text file has r in km. Just wondering which the model calls for specifically?

Also, I'm not getting anything in the link to the glossary here, just a blank github page so I will ask a couple quick questions here.

1) Is "a priori maximum radial distance" a different argument called for in the function, or more specifically a term addressing for ex-situ parameterization of distance?

2) Is gREM a different function that can be used? Specific to animal group size maybe? Am reaching here but just curious as I would like to use this if it were incorporating group size.

Thanks in advance

[timcdlucas]

Sorry, the glossary is here: https://github.com/timcdlucas/RandEM/wiki/Glossary

rem now takes radial distance in metres. Animal movement is in km per day. r gets converted from m to km within the function so that the two match. The actual model doesn't care as long as they match.

gREM is for acoustic detectors mostly. i.e. if the animal can only be detected when facing the acoustic detector. The reference is: Lucas, T. C. D., Moorcroft, E. A., Freeman, R., Rowcliffe, J. M., Jones, K. E. (2015), A generalised random encounter model for estimating animal density with remote sensor data. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12346

"a priori maximum radial distance" is what is referred to here as r. The distance a sensor can detect animals i.e. you do a field test of your camera before deployment and find that animals 10 metres away don't get detected.

The rem function and some other methods instead say, "at what distance did we detect animals". The first animal walked 1m from the camera, the 2nd 4m, etc. They then take the max of those (I think) and use that as r.

Hope that helps.

[tundraboyce]

@timcdlucas thanks a bunch for the explanation! that clears it up.