[tlocoh-info] auto.a() function suggests much too high a-values
lyons.andy at gmail.com
Tue May 19 09:27:00 CEST 2015
Good questions. Your diagnosis shows that you understand what's going
on. You're quite right that selecting a value for 'a' is not intuitive,
in part because it represents a cumulative distance of each point to
several of its nearest neighbors, and in the case where time is
incorporated in the selection of nearest neighbors (s>0), the distance
is not a physical distance.
The auto.a() function provides a starting point that has proven useful
for many datasets, but it really is just that - a starting point to
narrow down the range of 'a' values that provide a reasonable balance
between over-estimation and under-estimation. The ultimate selection of
'a' should be based on your (admittedly subjective) assessment of
minimizing spurious holes in the utilization distribution, and spurious
cross-overs. Part of the subjectivity in selecting a parameter value
(for any home range estimation method really) involves reflecting upon
whether your research question requires better fidelity to the core area
or overall 'home range'. In other words, there is no recommended 'a'
value. There are only recommended principles for selecting 'a' or 'k'
(see appendix I of Lyons et al 2013), along with some tools (plots) to
help you select a value. All of which is less convenient to be sure than
a one-click solution, but hopefully keeps you close to your data and
pushes you to think about what you want from your space use model.
As to why the upper and lower ranges returned by the 'auto.a()' function
did a poor job for your dataset is hard to say, but it could be related
to the geometry of the points or the sampling frequency. Remember that
auto.a(ptp = 0.98, nnn = 2) returns the value of 'a' such that 98% of
points have at least two nearest neighbors. If the distribution of
points is wide ranging, this could result in a large "lower bound" that
blows up the core areas. The suggestion to let k = sqrt(numberOfPoints)
is likewise a a starting point and not meant to be a recommended value.
There is alternative function called lxy.amin.add() to help identify
upper and lower bounds for 'a'. But it is more of a convenience function
and it operates on similar principles as auto.a(). There is also a
relatively new function in tlocoh.dev that opens a GUI (Shinyapp) which
is designed to help select parameter values. It isn't documented yet but
see some sample code below.
Hope this helps.
if (!require(tlocoh.dev)) stop("Please install tlocoh.dev")
## Loading required package: tlocoh.dev
if (packageVersion("tlocoh.dev") < "1.2.02") stop("Please update your
## Load suggested packages
pkgs <- c("rgdal", "raster", "shiny", "dismo")
not.installed <- pkgs[!sapply(pkgs, function(p) require(p,
## Create a hullset with evenly spaced parameter values (in this case
## (could also be evenly spaced 'a' values, use something like
a=seq(from=1000, to=15000, by=1000)
raccoon.lhs <- lxy.lhs(raccoon.lxy, s=0.05, k=4:20, iso.add=TRUE,
## Download a background imagefor display
raccoon.gmap <- lhs.gmap(raccoon.lhs, gmap="hybrid")
## Graphically select one of the parameter values by examining the
isopleths, EAR plot, and ISO area plot
raccoon.sel <- lhs.selection(raccoon.lhs)
raccoon.sel <- lhs.shiny.select(raccoon.lhs, selection=raccoon.sel,
## Apply selection
raccoon.lhs <- lhs.select(racoon.lhs, selection=raccoon.sel)
On 5/18/2015 10:38 AM, André Zehnder wrote:
> Hi all,
> I am performing a home range analysis with GPS data of some leopards
> and lions. The input data has a highly variable point density and
> result in quite large areas (roughly a magnitude of 500 to 1’000 km2
> for the 95% isopleth). In agreement with the tutorial, I begin with
> selecting the value for the temporal parameter s and then select
> suitable k values. As an orientation for that I use the rule of thumb
> ( k = sqrt(numberOfPoints)) and the plots. When a k-value has been
> chosen, the tutorial recommends to use the auto.a() function
> (lxy.nn.add(toni.lxy, s=0.003, a=auto.a(nnn=15, ptp=0.98))).
> However, the recommended a-value is massively too high and results in
> a oversmoothed home range that lacks any details. The higher the
> s-value, the more severe is this issue. While the result of the
> suggested a-value still shows a few weak spatial details for s=0,
> almost circular home ranges result for all isopleths with s>0. I
> checked whether this issue occurs only for one dataset, but it is the
> same for all 5 datasets I have checked. I attached two images that
> present the result when using the recommended a-value (auto_) and one
> that presents a manually selected a-value (manually_). For example,
> for s=0.005, I would rather take an a-value between 150’000 and
> 190’000 than the recommended value of 1’150’000. The auto.a() function
> should thereby include at least k points for 90% of all hulls.
> Therefore the question: Has anyone experienced the same issue or is it
> even a known technical problem with the package? My datasets contain
> 5’000 to 30’000 fixes, have some gaps and includes sometimes different
> sampling intervals. May the auto.a() function have severe problems due
> to that? The choice of an a-value is rather subjective and not really
> intuitive, especially when s>0. But when the auto.a() function can’t
> be used to get an approximate reference, what other measures are
> available to be able to justify your choice of the a-value?
> PS: I use T-LoCoH version 1.34.00 with RStudio 0.98.1103.
> Best regards,
> André Zehnder
> Tlocoh-info mailing list
> Tlocoh-info at lists.r-forge.r-project.org
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