From irene.weinberger at uzh.ch Wed Jun 11 18:43:35 2014 From: irene.weinberger at uzh.ch (Irene Weinberger) Date: Wed, 11 Jun 2014 18:43:35 +0200 Subject: [tlocoh-info] Parameter selection in a linear moving species Message-ID: <53988737.9060204@uzh.ch> Dear tlocoh-Group I have followed the discussion with Anna and Thomas and it has clarified some questions. Unfortunately not all. I am working with otters that move along rivers and I think that LocoH's are a fine approach to estimate home range size as they are built nicely along the linear features. However, I am facing few problems and I wonder what you think about it: a) I have data of only few animals but from them, I have a time span of radiotracking of 6 months to about 28 months. Following your advices to Thomas, I used an individuell varying s for each individual for the timespan of 6 months (as this is the shortest tracking period) using the "sfinder". So far, I did not subsample my data (I do have busts of locations of 2-16 hours every 15 min followed by days when the animal has not been tracked or just single locations within those days and all varies among the individuals). I was wondering if I need to subsample of if I account for this when using s > 0. b) My animals belong to a linear moving species that keeps to rivers and streams. I understand that I should be using the same k for all individuals for the estimation of the home range. However, while most of the LocoH's converge at around k=38, I have two individuals where the locoH's converge only at high ks (85 and 190, respectively) and if I use the highest k for all of the individuals, then I get much too large home ranges. I am here at a loss how to proceed and would like to hear if you have any suggestions. Best wishes Irene From julia.krejci at chello.at Thu Jun 12 14:25:06 2014 From: julia.krejci at chello.at (Julia Krejci) Date: Thu, 12 Jun 2014 14:25:06 +0200 Subject: [tlocoh-info] Overlapping Home Ranges Message-ID: <000001cf8639$58114b60$0833e220$@chello.at> Dear t-locoh group, my name is Julia. I work on home ranges of Northern Bald Ibis and chose t-locoh to analyse them. I have 11 individuals for which I already calculated individual home ranges. Now I wonder if it is possible to "overlap" these home ranges/isopleths to see how similar they are in size but also geographically. Is there a way to do see to which percentage they are similar? I would like to investigate for example if the core areas of the individuals have the same geographical position and similar size. Thank you very much for your help, Best wishes, Julia -------------- next part -------------- An HTML attachment was scrubbed... URL: From lyons.andy at gmail.com Thu Jun 12 16:16:01 2014 From: lyons.andy at gmail.com (Andy Lyons) Date: Thu, 12 Jun 2014 07:16:01 -0700 Subject: [tlocoh-info] Overlapping Home Ranges In-Reply-To: <000001cf8639$58114b60$0833e220$@chello.at> References: <000001cf8639$58114b60$0833e220$@chello.at> Message-ID: <5399B621.3040509@gmail.com> Hi Julia, Good question. The R script below illustrates how to find the area of overlap between isopleths for two individuals. This is relatively easy because T-LoCoH saves isopleths (and hulls) as SpatialPolygonDataFrames, which is a pretty common format for spatial objects in R so there are a lot of packages and functions that can manipulate polygons in this format. http://tlocoh.r-forge.r-project.org/isopleth_overlap_exericse.txt Check that out and let me know if you have any other questions. Andy On 6/12/2014 8:25 AM, Julia Krejci wrote: > > Dear t-locoh group, > > my name is Julia. I work on home ranges of Northern Bald Ibis and > chose t-locoh to analyse them. I have 11 individuals for which I > already calculated individual home ranges. Now I wonder if it is > possible to "overlap" these home ranges/isopleths to see how similar > they are in size but also geographically. Is there a way to do see to > which percentage they are similar? I would like to investigate for > example if the core areas of the individuals have the same > geographical position and similar size. > > Thank you very much for your help, > > Best wishes, > > Julia > > > > _______________________________________________ > Tlocoh-info mailing list > Tlocoh-info at lists.r-forge.r-project.org > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/tlocoh-info -------------- next part -------------- An HTML attachment was scrubbed... URL: From lyons.andy at gmail.com Sun Jun 15 00:05:49 2014 From: lyons.andy at gmail.com (Andy Lyons) Date: Sat, 14 Jun 2014 15:05:49 -0700 Subject: [tlocoh-info] Parameter selection in a linear moving species In-Reply-To: <53988737.9060204@uzh.ch> References: <53988737.9060204@uzh.ch> Message-ID: <539CC73D.4010507@gmail.com> Hi Irene, Sounds like an interesting study. A few comments below: On 6/11/2014 9:43 AM, Irene Weinberger wrote: > Dear tlocoh-Group > > I have followed the discussion with Anna and Thomas and it has clarified > some questions. Unfortunately not all. I am working with otters that > move along rivers and I think that LocoH's are a fine approach to > estimate home range size as they are built nicely along the linear > features. However, I am facing few problems and I wonder what you think > about it: > > a) I have data of only few animals but from them, I have a time span of > radiotracking of 6 months to about 28 months. Following your advices to > Thomas, I used an individuell varying s for each individual for the > timespan of 6 months (as this is the shortest tracking period) using the > "sfinder". So far, I did not subsample my data (I do have busts of > locations of 2-16 hours every 15 min followed by days when the animal > has not been tracked or just single locations within those days and all > varies among the individuals). > I was wondering if I need to subsample of if I account for this when > using s > 0. In general, incorporating time into nearest neighbor selection (s>0) will have the effect of treating bursts of locations separately. Two points that are close together in space will nevertheless be considered very far apart (for determining nearest neighbors) if they are widely separated in time (relative to other observations). So presuming you want each burst of locations to be treated separately, if you use s>0 there shouldn't be a need to subsample your data. That being said, it is also worth noting that if you select nearest neighbors using the k-method, and you have one or more 'burst' of points with fewer than k locations, then by necessity those hulls will be constructed by locations taken from other bursts as well (which may be undesirable). For example if you have a burst of 10 locations (& no other locations for days before / after), and you are using a k=15, then constructing those hulls will necessarily require using points that were days apart. If that's undesirable, you could use a smaller value of k or the 'a' method (preferable). Another issue to keep in mind when you have irregular data sampling is that the density isopleths (which essentially mirror the density of points) could in fact be a reflection of the sampling as opposed to how the individual used space. In other words, an area where the individual was located during a period of heavy sampling may appear as a 'core' area (lower isopleth level) relative to an area the animal happened to be when sampling was light, due purely to the sampling. Whether this is an issue or not will depend on your data, your questions, and the animal. Subsetting data in different individuals to a achieve a comparable sampling interval is most essential when you are computing hull-based association metrics, but that doesn't seem to be the case in what you are doing. > b) My animals belong to a linear moving species that keeps to rivers and > streams. I understand that I should be using the same k for all > individuals for the estimation of the home range. However, while most of > the LocoH's converge at around k=38, I have two individuals where the > locoH's converge only at high ks (85 and 190, respectively) and if I use > the highest k for all of the individuals, then I get much too large home > ranges. I am here at a loss how to proceed and would like to hear if you > have any suggestions. For exactly the reasons you state, I don't fully subscribe to the principal that one should always use the same value of 'k' (or 'a') for different individuals (or the same individual during different time periods). Using the same value of k makes sense for different individuals when the movement data are comparable, i.e. similar sampling rate, similar proportions of time spent in different movement modes, etc. To illustrate this point with a theoretical counter-example, if you have one individual who is territorial (protecting a nest for example), and another individual who wonders around a lot, there would be no reason to expect the same value of k would best represent space use for both individuals. Another fabricated example would be if you have one individual tracked with the sampling rate of 15 minutes, and a second individual with 1 hour sampling, you would almost definitely need different values of 'k' to achieve a comparable balance between Type I and Type II errors (or what I call 'Swiss cheese' territories and spurious cross-overs). I would argue that the best value of k should be the one which produces the most authentic model of space use, which for most studies includes 1) differentiating the gradient of intensity of space-use (or another hull metric depending on the question), 2) delineating spatial boundaries (hard edges) in movement, and potentially 3) delineating temporal partitions of space use. I recognize however that selecting parameter values for each individual separately, based on a common set of principles, can be more work, and for large numbers of individuals may not even be feasible. I invite other comments. I don't know if that helps or makes your choices more confusing. I also might have misconstrued your question - are you seeking to construct home ranges for each individual separately, or perhaps estimate a single UD for all individuals combined? Andy > Best wishes > Irene > > _______________________________________________ > Tlocoh-info mailing list > Tlocoh-info at lists.r-forge.r-project.org > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/tlocoh-info >