[tlocoh-info] WG: nsv and mnlv

Andy Lyons lyons.andy at gmail.com
Fri Sep 12 05:25:18 CEST 2014

Hi Julia,

That's a good question, and probably very common as many GPS devices are 
programmed to go to sleep during certain intervals to save battery 
power. I don't think the omission of night time locations would cause 
much of a problem in terms of generating a space use model with T-LoCoH 
per say, but it would affect what you can claim about your space use 
model (including the 'homerange' which is a subset or product of a space 
use model).

First thing to note is that when there is no sampling at night, the 
estimated utilization distribution (isopleths) should be interpreted as 
the UD of the sampled data, and not necessarily the individual as a 
whole. Take for example a dataset where the sampling is once an hour 
during the day, but the GPS unit goes to sleep from 6pm to 6am. Now 
consider a nest, where the individual was recorded at 6pm, and again at 
6am, because it never moved during the night. If the goal is to 
construct a utilization distribution that represents the overall 
relative intensity of habitat use, then that nest should really be 
represented by 13 locations, not 2. So we couldn't claim a space-use 
model generated from those data represent that, but what we can say more 
confidently is that the isopleths generated from our data represent how 
space is used during the day, and that based on our knowledge of the 
species, the overall pattern of space use will be encompassed in the day 
time space use (although that may not be true for all species). Whether 
or not that more conservative claim about our analysis is an issue for 
the study as a whole depends on the research question. If our research 
question only requires an outline of the core area (50% isopleth), or 
the 'homerange' (95% isopleth), and the gradient of use within the core 
or homerange doesn't really matter, then this is probably not that big 
of a deal. On the other hand if we're going to feed our UD into another 
level of analysis where the gradient of the intensity of use matters, 
for example a parameter estimation for a resource selection function or 
volume intersection with another UD, then the omission of night time 
points might be more of a deal breaker.

Secondly, if you are generating time-use metrics (nsv and mnlv), you 
certainly wouldn't want the intervisit gap period to be shorter than the 
period the device was programmed to go to sleep, otherwise it would 
appear as though a stationary individual (in the extreme case, dead) was 
making multiple visits to the nest, when in fact it hadn't moved at all. 
Does that make sense?

If the omission of night time points is a deal-breaker for your 
analysis, you could potentially model the missing data (i.e., insert 
fake nightime points) based upon the assumption that the individual 
didn't move during the night. T-LoCoH doesn't have a function to do 
this, but it wouldn't be hard to make one. You could also test whether 
the insertion of fake points is reasonable or not by computing the 
distance between the last location of each day and the first location of 
the following day, and see if indeed the distances are actually close to 

Hope this helps. I invite others to chime in, as these are issues that 
affect not just T-LoCoH but any kind of space-use modeling method.


On 9/10/2014 10:13 AM, Julia Krejci wrote:
> Hi, thank you for your quick answer!
> I have another question, not really related to the one below: My 
> transmitters were switched off during the night to save energy and 
> because the birds I investigate are only active during the day. This 
> creates a gap in the data, which is also visible in the 
> lxy.plot.freq(my.lxy, deltat.by.date=T) function. I've attached an 
> example. Does this in any way affect the analysis? What I want is 
> basically home range and core area, nsv and mnlv. Do I have to account 
> for that in any way?
> Thank you,
> Best wishes,
> Julia
> *Von:*Andy Lyons [mailto:lyons.andy at gmail.com]
> *Gesendet:* Mittwoch, 10. September 2014 11:56
> *An:* Julia Krejci
> *Cc:* Tlocoh-info at lists.r-forge.r-project.org
> *Betreff:* Re: [tlocoh-info] WG: nsv and mnlv
> Hi Julia,
> Good questions. See some comments below. Also take note:
> 1) Version 1.17 of the T-LoCoH package has a bug. If you updated to 
> that version, *please update to v1.18* (which was posted today)
> update.packages(oldPkgs="tlocoh", repos="http://R-Forge.R-project.org" 
> <http://R-Forge.R-project.org>)
> or
> install.packages("tlocoh", repos = "http://R-Forge.R-project.org" 
> <http://R-Forge.R-project.org>)
> 2) There's a new tip sheet about time-use analysis on the website that 
> you might find useful, see 
> http://tlocoh.r-forge.r-project.org/tips_faqs.html.
> Other comments below:
> On 9/9/2014 6:33 AM, Julia Krejci wrote:
>     Dear tlocoh-list,
>     I've calculated revisitation rate and mean duration of visit for
>     some birds I put GPS-transmitters on.  I chose an inter-visit-gap
>     of 12 hours. Maybe I'm already work-blind, but I can't seem to
>     understand the intervals the output gives me.
>     If I display the nsv data, it shows me all points which are
>     considered as consecutive visits to a hull, right? And the colour
>     code shows if the individual was there rarely or often. The
>     intervals of my output are:
>     1 -- 11.6
>     11.6 -- 22.2
>     22.2 -- 32.8 ... and so on.
>     So, this means, the individual revisited this hull once or 22
>     times during one inter-visit-gap? That doesn't seem right. I'm
>     quite sure I'm missing something.
> nsv stands for number of separate visits, where a visit is defined as 
> not being away from the hull for 12 hours or more. So the hull where 
> nsv=22 doesn't mean the individual visited 22 times during one 
> intervisit gap period, but rather it was there and left for more than 
> 12 hours and then came back, 22 times.
> nsv values will of course be integer values. Those ranges you show I 
> presume are from the plot legend, which R computes by taking the range 
> of values and chopping it up into equal intervals. But the nsv values 
> themselves should be all integers
>  It is the same for the mean duration of visit. This means the mean 
> number of records taken of an individual during one visit to the hull, 
> right? But the output gives me
> 1.30 -- 11.56
> 11.56 -- 21.82 and so on up to 52.60.
> This cannot mean the bird stayed in this hull for 52 records. My GPS 
> interval is one hour and the transmitters are shut down during the 
> night to save energy, so they don't record over night. Maybe I have to 
> keep that in mind?
> A hull where the mnlv=52 means the animal was within the hull for 52 
> locations during at least one visit, where a visit again is defined by 
> a period of separation. Hence that "one visit" could theoretically go 
> on for several weeks, if for example the individual left and returned 
> every 11 hours like clockwork, it would all be considered one visit 
> because your inter-visit period is 12 hours. That of course is very 
> unlikely, more probably the hull where mnlv=52 could also contain a 
> bunch of closely spaced locations, perhaps a site where it stayed for 
> a long time or returned at intervals shorter than your ivg value, etc. 
> The tip sheet on the website illustrates how you can investigate the 
> time use metrics of individual hulls.
>  I tried to send you a sample image for illustrationbut it seems to be 
> too big to be sent.
> I hope my explanation is understandable. I'd be very grateful for some 
> advice.
> Thank you and best wishes,
> Julia
> Hope this helps. Let me know what other questions you come across.
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