Mark-Resight Input Files

questions concerning anlysis/theory using program DENSITY and R package secr. Focus on spatially-explicit analysis.

Mark-Resight Input Files

Postby mjgould » Fri Feb 12, 2016 5:59 pm

Hi Murray,

I’m analyzing some data that seems to be appropriate for a mark-resight analysis, but I have a few clarifying questions about the input files. The goal is to estimate the density of badgers using camera traps at water tanks with individual ID based on variation in dorsal head stripes. The cameras were stationed at a tank for 21 consecutive days, which will be split into sampling occasions. Looking at the mark-resign vignette, the data best fits model 1a, which is a mark-resight model with incomplete identification of marked animals.

In relation to markocc, can there be multiple mark occasions? If so, can marking occasions be mixed throughout the sighting occasions or only at the beginning? For example, let's say there are 6 total sampling occasions. With a mixed design, occasion 1 and 3 are coded as marking, and with an un-mixed design only occasion 1 and 2 are marking. If the marking occasions are unmixed, i.e., adjacent to each other, should they be truncated into 1 large occasion? A truncated session doesn’t seem appropriate because you would lose information on the initial detection of marked individuals. However, I want to double check that assumption. Last, when creating the Tu and Tm files, the vignette describes the format as, “session”, “marking”, “sighting(s)” with “marking” coded as binary and “sighting” coded as a count. Yet, I don’t see any mention for a Trap ID. Should there be a Trap ID or does secr assume that the order of the rows is identical to the order of the rows in the trap file?

Thanks for the clarification,

Matt
mjgould
 
Posts: 18
Joined: Fri Apr 18, 2014 2:07 pm

Re: Mark-Resight Input Files

Postby murray.efford » Fri Feb 12, 2016 6:12 pm

Hi Matt

Quickly answering (what I think is) your core question: Yes, there may be multiple marking occasions, but No these cannot at present be interspersed (the jargon I'm using). The theory works fine with interspersed occasions, I have just been lazy about coding for that, waiting for someone to say they really need it and to find the time. Search the pdf for 'interspersed'.

But aren't your badgers pre-marked?

I think you're right that I am assuming the row order of the Tu data is the same as the order in the trap layout file. It's worth checking that it is not expecting them in the (alphabetically) sorted order of trapID. Until you or I do that, maybe just make sure your trap layout file is pre-sorted.

Murray
murray.efford
 
Posts: 686
Joined: Mon Sep 29, 2008 7:11 pm
Location: Dunedin, New Zealand

Re: Mark-Resight Input Files

Postby mjgould » Fri Feb 12, 2016 7:07 pm

Perfect. Thanks for the clarification, Murray.

Yes, they are pre-marked since their head stripes are permanent, but perhaps I'm not as sure about marking and sighting occasions as I thought. The badgers are only "marked" once we have identified an individual in the picture. Yet, if these individuals are not identified in the marking occasion then they will be considered unidentified during the sighting occasions, right? What I'm trying to determine is how many marking occasions should I have and where should they be located in the markocc vector? If the number of individuals identified receives a large bump in the middle of sampling, would it be advantageous to conduct another marking period during that timeframe? I would guess that identifying more individuals would help with parameter precision, but since I'm new to mark-resight the arbitrary decision to include another sighting occasion worries me.
mjgould
 
Posts: 18
Joined: Fri Apr 18, 2014 2:07 pm

Re: Mark-Resight Input Files

Postby murray.efford » Fri Feb 12, 2016 7:19 pm

If all badgers can be identified then you have a capture-recapture dataset, not a mark-resight dataset. If the natural marks on some are inadequate for them ever to be identified then you have a pre-marked mark-resight study with unknown fraction marked (model 3 or 3a in that scheme) (see Rich, L. N., Kelly, M. J., Sollmann, R., Noss, A. J., Maffei, L., Arispe, R. L., Paviolo, A., De Angelo, C. D., Di Blanco, Y. E., and Di Bitetti, M. S. (2014). Comparing capture-recapture, mark-resight, and spatial mark-resight models for estimating puma densities via camera traps. Journal of Mammalogy 95, 382-391).

The capture-recapture models in 'secr' don't allow for the category 'marked, but mark not identified' (pID<1), which may be your problem.

Murray
murray.efford
 
Posts: 686
Joined: Mon Sep 29, 2008 7:11 pm
Location: Dunedin, New Zealand

Re: Mark-Resight Input Files

Postby mjgould » Mon Feb 15, 2016 1:24 pm

Thanks, Murray. Obviously, I misunderstood when the marking process occurred.
mjgould
 
Posts: 18
Joined: Fri Apr 18, 2014 2:07 pm


Return to analysis help

Who is online

Users browsing this forum: No registered users and 14 guests