[R-sig-Geo] adehabitatHR kernalBB batch processing

[SheilaD]

Has anyone been able to batch process the kernelbb function from adehabitatHR
with individual sig1 values?

p.s. im running
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
adehabitatHR_0.4.7 adehabitatLT_0.3.11?

Sheila


Phil H wrote
> I am attempting to use the kernalBB function from adehabitatHR. Now it  
> works just fine with just one fish, however I have quite a number of  
> fish and would like to run the analysis on all the fish in one  
> go-while maintaining individual sig 1 estimates. See below for example  
> coding...
> 
> library(adehabitatHR)
> library(adehabitatLT)
> data(puechabonsp)
> 
> loc$DT <-as.POSIXct(strptime(loc$Date, format='%y%m%d' ))
> ltraj <- as.ltraj(coordinates(loc), loc$DT, id = loc$Name, burst =
> loc$Name,
> + typeII = TRUE)
> 
> sig255<-liker(ltraj, sig2 = 255, rangesig1 = c(0, 1000))
> 
> *****************************************
> 
> Maximization of the log-likelihood for parameter
> sig1 of brownian bridge
> 
> Brock : Sig1 = 2.002 Sig2 = 255
> Calou : Sig1 = 0 Sig2 = 255
> Chou : Sig1 = 1.001 Sig2 = 255
> Jean : Sig1 = 2.002 Sig2 = 255
> 
> ##so now I would like to run the kernalBB on all 4 fish individually.
> ##so i tried...
> 
>> tataall <- kernelbb(ltraj, sig1 = sig255, sig2 = 255, grid =
>> 100,byburst=T)
> 
> #Error in sig1^2 : non-numeric argument to binary operator
> 
> ##I dont have a great deal of experience working with list formats-  
> can anyone ##assist me in calling the relevent sig 1 for each fish?
> 
> 
> 
> #now if I know I can used a fixed sig 1 for all fine ie
>> tataall <- kernelbb(ltraj, sig1 = 1, sig2 = 255, grid = 100,byburst=T)
> 
> 
> ##I am sure it is something stupid and easy....
> 
> ##I see that when you do a similar thing for the D function in the BRB  
> function it seems to work fine  (I assume that this is using differing  
> D levels for each fish..)
> 
> vv2<- BRB.likD(ltraj, Dr=c(1,50000), Tmax = 5*(24*60*60) + 1, Lmin = 0.1)
> testud <-BRB(ltraj, D =vv2, Tmax =5*(24*60*60) + 1, Lmin =0.1, hmin = 100)
> 
> 
> finally, I notice that we get some zero sig 1 values both in my  
> dataset and in the example of Calou. Is this an issue?
> 
> Thanks for any help
> 
> Phil H.
> 
> p.s. im running
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> adehabitatHR_0.4.2 adehabitatLT_0.3.6
> 
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