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. Thanks for the guidance. Corrie _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
