[R-sig-eco] Re : problem with kernel UD estimation using adehabitatHR

[Mathieu Basille]

Hey Lindsey,

Just a blind guess here, did you try using a SpatialPixels instead of the default number for the 'grid' parameter in 'kernelUD'? It might solve your problem, in addition to give you more flexibility on the format of the output.

Mathieu.


---- Le mar., 03 juin 2014 17:03:46 -0400 lnmessinger<lindsey.messinger at huskers.unl.edu> a écrit ---- 

 > I have data containing locations of 100+ pheasants during 3 seasons. I am 
 > looking to estimate kernel home ranges for each of the seasons for each 
 > individual. I run the kernelUD() function with no errors or warnings, but am 
 > receiving an error message when I attempt to use the getverticeshr() and 
 > kernel.area() functions to extract 95% polygons and area estimates from the 
 > kernel UD's. 
 >  
 > Here is the structure of the input data set: 
 >  
 > Formal class 'SpatialPointsDataFrame' [package "sp"] with 5 slots 
 >   ..@ data       :'data.frame':    2376 obs. of  1 variable: 
 >   .. ..$ ID: Factor w/ 122 levels "150.002_2013_KOR",..: 1 1 1 1 1 1 2 2 2 2 
 > ... 
 >   ..@ coords.nrs : num(0)  
 >   ..@ coords     : num [1:2376, 1:2] 347887 347862 347948 347964 348200 ... 
 >   .. ..- attr(*, "dimnames")=List of 2 
 >   .. .. ..$ : NULL 
 >   .. .. ..$ : chr [1:2] "X_Estimate" "Y_Estimate" 
 >   ..@ bbox       : num [1:2, 1:2] 315869 4442294 349590 4472129 
 >   .. ..- attr(*, "dimnames")=List of 2 
 >   .. .. ..$ : chr [1:2] "X_Estimate" "Y_Estimate" 
 >   .. .. ..$ : chr [1:2] "min" "max" 
 >   ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots 
 >   .. .. ..@ projargs: chr NA 
 >  
 > The following code works without errors or warnings for my "pre" season 
 > data: 
 >  
 > kud.pre<-kernelUD(pre.hr.id[,1],h="href",extent=1) 
 > pre.hr.poly<-getverticeshr(kud.pre, percent=95) 
 > pre.kud.area<-kernel.area(kud.pre,percent=95) 
 >  
 > However, when I repeat my other 2 seasons, kernelUD() runs with no errors or 
 > warnings: 
 >  
 > kud.early<-kernelUD(early.hr.id[,1],h="href",extent=1) 
 >  
 > but I get the following error when running the getverticeshr() function: 
 >  
 > early.hr.poly<-getverticeshr(kud.early, percent=95) 
 >  
 > Error in getverticeshr.estUD(x[[i]], percent, ida = names(x)[i], unin,  :  
 >   The grid is too small to allow the estimation of home-range. 
 > You should rerun kernelUD with a larger extent parameter 
 >  
 > I have adjusted the extent parameter as requested, using values of 
 > 0.5,1,5,10,25,100 and all produce the same error. I am able to generate 
 > mcp's using the same data without a problem and like I said, kernelUD() 
 > works with no errors or warnings for all 3 seasons and I am able to see each 
 > UD when I look at the image. 
 >  
 > What I find particularly strange is that I am able to run kernel.area() and 
 > even with warnings that say: 
 >  
 > 1: In kernel.area(j, percent, unin, unout) : 
 >   The grid is too small to allow the estimation of home-range 
 > for the following value of percent: 95. You should rerun kernelUD with a 
 > larger extent parameter 
 >  
 > I still get a data frame with area values for each individual. It seems as 
 > if an area is estimated regardless of the error warning of small extent 
 > size. 
 >  
 > Has anyone experienced a similar issue or have a suggestion as to how I 
 > should proceed? 
 >  
 > Thanks, 
 > Lindsey 
 >  
 >  
 >  
 >  
 >  
 >  
 > -- 
 > View this message in context: http://r-sig-ecology.471788.n2.nabble.com/problem-with-kernel-UD-estimation-using-adehabitatHR-tp7578930.html 
 > Sent from the r-sig-ecology mailing list archive at Nabble.com. 
 >  
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 > 


--

~$ whoami 
Mathieu Basille, PhD 
 
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University of Florida \\ 
Fort Lauderdale Research and Education Center 
(+1) 954-577-6314 
http://ase-research.org/basille 
 
~$ fortune 
« Le tout est de tout dire, et je manque de mots 
Et je manque de temps, et je manque d'audace. » 
  -- Paul Éluard