On Mon, Aug 2, 2010 at 12:40 PM, Corrie Curtice <[email protected]> wrote: > 2010/7/28 Damiano G. Preatoni <[email protected]>: >> In un messaggio del Wednesday 28 July 2010, Corrie Curtice ha scritto: >>> On Wed, Jul 28, 2010 at 2:35 AM, Anne Ghisla <[email protected]> wrote: >>> > On Tue, 2010-07-27 at 15:27 -0400, Corrie Curtice wrote: >>> >> Hello, >>> >> >>> >> I am trying to export the home range for a single individual animal. >>> >> I'm getting the error "Error in re[[i]] : subscript out of bounds" -- >>> >> I looked on the archive and found my own posting of this question for >>> >> the 100% isopleth. :) So now I'm wondering, why does the error occur >>> >> at lower isopleth levels? Ideally I would like the 95% KHRE to show >>> >> the "home range" of each animal, and this works with all other >>> >> individuals. The answer to my last posting noted that the isopleth >>> >> went beyond the grid limits. I'm not passing in an underlying grid. >>> >> Here's my call: >>> >> >>> >> ud <- kernelUD(xy, grid=100, h="href") >>> >> kvtmp <- getverticeshr(ud, lev = 95) >>> >> >>> >> Levels up to 85 work fine. Is there anything I can do to fix this, if >>> >> not what is the proper way to report the result for this animal? If >>> >> you need more code or output I can send. >>> > >>> > Hi Corrie, >>> > >>> > it sounds like the issue reported here: >>> > >>> > https://trac.faunalia.it/animove/ticket/13 >>> > >>> > does your dataset show anisotropy? The one attached to the ticket is a >>> > narrow cloud of points along a horizontal line. The default grid created >>> > by kernelUD is likely not able to encompass the whole UD. If the case, I >>> > would try creating a wider grid and providing it to kernelUD. >>> > >>> > hope this helps! >>> >>> Yes, that's exactly it. I tried increasing the value passed into the >>> grid parameter -- is this right? Is there some way to determine what >>> the correct value would be? >> >> There is no "correct" value for the grid parameter. >> It it a known "feature" of adehabitat. >> >> That is, passing "grid=<some integer value>" means that kernel calculations >> (see e.g. Worton classical text) start with superimposing your point >> locations >> a mesh with <integer value> x <integer value> _cells_. Worton's default is >> 40x40. >> >> Problem is that is more meaningful having the possibility to supply the _cell >> size_ insteda of the _number of cells_. >> >> This means that if your points cloud covers a _wide_ extent, say, half a >> state, you will have in your case a 100x100 cells mesh, and a single cell >> side >> will be some tenths of kilometers! >> >> To overcome this problem, one should use "grid=<a kasc object>" (look into >> kernelUD source...). >> >> I normally do like this: >> - using my favorite GIS package, I create a raster with the cell size I want, >> making it so that covers my study area. This way I'll have for instance a >> raster with 100 m cells, with a size of such and such rows and columns (I say >> 'such and such' since we're not interested in how many squares we have, but >> in >> how long is a square side!). >> - I export that raster in ASCII GRID format. >> - back into R I use read.asc function and create a kasc object that then I >> will use as my "reference grid" in home range calculations, like this: >> >> my.reference.grid <- read.asc('refgrid.asc') >> ud <- kernelUD(xy, grid=my.reference.grid, h="href") > > Thanks Damiano, this is helpful information. I have a follow up question. > > It sounds like from what you say, that the smaller cell size is > better. ie: 100m vs 1000m or greater. I've read quite a bit of > background lit, but until I try this on my own I don't fully > understand all the implications. I am not able to find much that > discusses the impact of cell size during kernel calculation. More > focus is on the smoothing parameter. > > I created a grid of 100m cells, and re-ran the kernelUD for one set of > animals in my study (at one island). The UDs in this home range are a > bit smaller and more detailed than the ones created with 100x100 grid, > pretty close but I do like it a little better. > > So, is there a process to decide on the best cell size, related to the > data? Would I be safe to pick 100m for each of my sites and > individuals? These are marine mammals that range over wide areas, > some as far as almost 300km, but mostly w/in 100km.
I retract that comment: the UDs created are exactly the same -- I was looking at a wrong image when comparing the first time, apologies. Thanks for the guidance. _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
