single-season, spatial replicates

[PaulS]

Hello all,
   I am assisting a scat-detection dog survey, which will use mark-recap methods of uniquely identified individuals (genetic id of a threatened carnivore), to help them gather additional data to estimate occupancy and/or abundance of co-occurring species.  The basic study design will consist of a team of 3-4 people and a dog walking transects.  Each transect will only be walked once during the study to cover as large of an areas as poossible, but the tranects will likely be grouped within a larger grid, perhaps 4km x 4 km.  Thus, the study will have spatial replicates rather than temporal replicates.  Because this survey will be expensive and large-scale, the team would like to gather additional data on ungulates and other carnivores in the area to assist management.  I plan to suggest distance sampling for estimating ungulate densities along these walking transects using the distsamp function in unmarked.  I would also like to add occupancy modeling for tracks and scat/dung as well, which they will certainly encounter while walking transects.  I am familiar with the occupancy model with spatial replicates from Hines et al 2010, which was analyzed in program Presence.  Is it currently possible to analyze occupancy data with spatial replicates (and no temporal replicates) in the unmarked package?   In addition, I was wondering if some type of double-observer approach for abundance estimation of ungulate herds or carnivore groups (since individual identity won't be possible) might be possible with tracking or scat/dung collection data.  I would appreciate any insights the forum might have.
  
Thanks,
Paul

[Andy Royle]

hi Paul,

 unmarked does _not_ have the Hines et al. type of models implemented. If anyone has an interest in writing code for that, it would be a good addition.

 People do use ordinary occupancy models with spatial subsamples as replicates. Ignoring the dependence structure in this way is not always so bad.

 

 unmarked does have double observer modeling capabilities although I don't understand the specific context that you envision.

 

regards

andy

 

J. Andy Royle
Research Statistician
USGS Patuxent Wildlife Research Center
12100 Beech Forest Rd.
Laurel, MD 20708
http://profile.usgs.gov/professional/mypage.php?name=aroyle
andy_...@usgs.gov
phone: 301-497-5846
fax: 301-497-5545

Book: "Hierarchical Modeling and Inference in Ecology: The Analysis of Data from Populations, Metapopulations and Communities" by J. A. Royle and R.M. Dorazio.  

unmarked: A very useful R package for fitting certain hierarchical models using likelihood methods. Available from: http://cran.case.edu/web/packages/unmarked/index.html

A 5 hour "introduction to unmarked" Webinar can be found here: http://www.pwrc.usgs.gov/Royalvideo.cfm

-----unma...@googlegroups.com wrote: -----

To: unma...@googlegroups.com
From: PaulS <pasch...@gmail.com>
Sent by: unma...@googlegroups.com
Date: 07/22/2012 07:47AM
Subject: [unmarked] single-season, spatial replicates

[Jeffrey Royle]

Dear Anais,

 at this point we don't have plans to do this.

regards

andy

 

On Thu, Dec 6, 2012 at 8:18 AM, Anaïs Charbo <charbonn...@gmail.com> wrote:

Dear Mr Royle,

Do you project to implement the Hines et al. type of models in the unmarked package ?
Thanks,
Anaïs