Many thanks Josh.

 

This makes it much clearer now. I do rely on time intervals as I do the
tracking based on an “1-image-per-second” basis as calibration for further
modelling where I also plan to work with fixed time steps.

 

Now I know how I will handle ltraj. :-)

 

Thanks again,

 

Jacqueline

 

From: Josh Nowak [mailto:Joshnwk@yahoo.com] 
Sent: vrijdag 26 augustus 2011 16:18
To: J. Augusiak
Subject: Re: [R-sig-eco] bursts in adehabitat

 

Jacqueline, 

In my experience it really only matters if the statistics you are doing
require that the fixes be separated by regular time intervals.  This is why
bursts are useful to me, a GPS collar will often take fixes at regular
intervals, but sometimes it misses a fix and so the fix interval is made
irregular.  If my goal is some sort of movement analysis that requires
regular intervals then I will use bursts so as not to throw out data or rely
on interpolating the missed fixes.  This approach is a nice fix, but the
regular interval requirement can likely be overcome too.   

 

Josh Nowak
Département des sciences du bois et de la foręt
Université Laval
Québec, QC G1K 7P4
(418) 656-2131 Ext.6110

 

 

  _____  

From: J. Augusiak <jaugusiak@googlemail.com>
To: r-sig-ecology@r-project.org
Sent: Fri, August 26, 2011 9:36:50 AM
Subject: Re: [R-sig-eco] bursts in adehabitat

Hi Roman,



I use cameras which are fixed centered above an aquarium which is 1m2 of
size. I record the movement for, say, one hour. Then I take the video file,
dissect it into its single frames which I then import as image sequence in
ImageJ, an open source image processing software. A custom made plugin for
this software then analyzes frame by frame the position of my animal in the
aquarium, so basically I get a set of plain x and y coordinates.



Due to some setup restrictions on some images in the sequence the animal
can't be detected by the software and it interrupts the current track. E.g.
On images 1-300 the animal can be seen, I get a coherent track. On images
301 to 367 the animal cannot be seen but is visible again on image 368 to
400. This would give me track 1 (1-300) and track 2 (368-400).



Adehabitat's definition of a burst is as follows:

For a given individual, trajectories are often sampled as "bursts" of
relocations. For example, when

an animal is monitored using radio-tracking, the data may consist of several
circuits of activity (two

successive relocations on one circuit are often highly autocorrelated, but
the data from two circuits

may be sampled at long intervals in time). These bursts are indicated by the
attribute burst. Note

that the bursts should be unique: do not use the same burst id for bursts
collected on different animals.



I already had lengthy discussions with my colleagues about it.
Theoretically, one could say that I have one "circuit of activity" with one
movie (=one burst). On the other hand, I get those track fragments as
described above. Those fragments themselves could be interpreted as bursts
also.



So what do I need to do when setting up my ltraj objects? Define burst as
"1", because it's one movie, or say burst = 1, 2, 3,... depending on the
number of track fragments for one movie?



Many thanks for your reply and time!



Jacqueline 



From: romunov@gmail.com [mailto:romunov@gmail.com] On Behalf Of Roman
Luątrik
Sent: vrijdag 26 augustus 2011 14:49
To: J. Augusiak
Subject: Re: [R-sig-eco] bursts in adehabitat



Hi Jacqueline,



what software/hardware are you using for tracking your animals?



Cheers,

Roman





On Fri, Aug 26, 2011 at 2:09 PM, J. Augusiak <jaugusiak@googlemail.com>
wrote:

Dear list,



I have a question concerning the definition of a "burst" in the adehabitat
package. Somehow I 'm not able to wrap my mind around it and to adopt it
appropriately for my data set.



I want to analyze the movement behavior of aquatic invertebrates and how it
may be impacted by different environmental influences. In order to study
this I have set up an arena where I let the animals walk around and video
tape their locomotion over time.



However, my image quality is bad at times, or an animal hides under an
object that I placed in the arena, which causes the tracking software to
loose a track but it may pick it up again after some time when the
individual is visible again. Those separate tracks get different numbers by
default.



My problem of understanding is now, are the different track ID's that I get
from the tracking software "bursts" or not. It's only one animal per movie I
look at and it's only one movie of, say, one hour that I record and for
which I get track no.1, 2, 3. etc.



According to my current understanding I am dealing with only one burst in a
situation as described above and I would get several bursts, if I would
record one animal for 10 minutes, have a break of 10 minutes, record again
for 10 minutes, etc.



I'm sorry if this is a trivial question. But the longer I think about it or
the more often I read about it the more I get confused and unsure.



Many thanks for your time!



Jacqueline








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