[R-sig-eco] combing UDs in homerange analysis

[Clement Calenge]

Dear Louise,

I already replied to your question on R-sig-Geo [1]. Please avoid
cross-posting.
Best regards,

Clément Calenge
[1] https://stat.ethz.ch/pipermail/r-sig-geo/2012-July/015557.html


On 07/04/2012 02:18 PM, Soanes, Louise wrote:
> Hello all
> I am trying to use the kernelbb method to estimate home range of several birds that I have GPS tracked, however I do not want to include time spent on land between trips, so I have performed the analysis on individual trips and then have tried to combine the UD's as has previously been suggested in other posts on this forum, however I am having trouble combining the UD's of the different trips, and does anybody know what the error message below means when I try to work out the 50% homerange area?
>
>> data<-read.csv("three.csv")
>> library(adehabitatHR)
>> gmt<-(data$gmt)
>> data$gmt<-as.POSIXct(strptime(gmt, "%d/%m/%Y%H:%M:%S"))
>> tr=as.ltraj(xy, data$gmt, id, burst = data$Burst, typeII = TRUE, slsp ="remove")
>> lik<-liker(tr, sig2=1, rangesig1=c(10, 100))
>> hrBB<- kernelbb(tr, sig1 =  6, sig2 = 1, grid = 100, byburst=TRUE)
>> hrBB
>> image(hrBB)
>> plot(getverticeshr(hrBB, 95), add=TRUE, lwd=2)
>> plot(getverticeshr(hrBB, 50), add=TRUE, lwd=2)
> Error in plot(getverticeshr(hrBB, 50), add = TRUE, lwd = 2) :
>    error in evaluating the argument 'x' in selecting a method for function 'plot': Error in re[[i]] : subscript out of bounds
>> j<-kernel.area(hrBB, unout=c("km2"))
>> j
>           X1       X2       X3       X4
> 20 0.000000 0.000000 0.000000 0.000000
> 25 0.000000 0.000000 0.000000 0.000000
> 30 0.000000 0.000000 0.000000 0.000000
> 35 0.000000 0.000000 0.000000 0.000000
> 40 0.000000 0.000000 0.000000 0.000000
> 45 0.000000 0.000000 1.403292 0.000000
> 50 0.000000 0.000000 1.403292 0.000000
> 55 0.000000 0.000000 1.403292 0.000000
> 60 0.000000 0.000000 1.403292 0.000000
> 65 0.000000 0.000000 1.403292 0.000000
> 70 0.000000 0.000000 1.403292 0.000000
> 75 0.000000 0.000000 1.403292 0.000000
> 80 0.000000 0.000000 1.403292 0.000000
> 85 1.403292 0.000000 1.403292 1.403292
> 90 1.403292 0.000000 2.806585 1.403292
> 95 2.806585 1.403292 2.806585 2.806585
>
> # I then try to combine these 4 individual UD's using the following code
>
> UDs<- lapply(1:length(hrBB), function(i) hrBB[[i]]$UD)
> UDend<- liUD[[1]]
> for (i in 2:length(liUD))
> UDend<- UDend + liUD[[i]]
> nlocs<- unlist(lapply(1:length(tr), function(i) nrow(tr[[i]])))
> wi<- nlocs/sum(nlocs)
> UDt<- UDs[[1]]
> for (i in 2:length(UDs))
> UDt<- UDt+wi[i]*UDs[[i]]
>
> # And also tried:
>
> liUD<- lapply(1:length(tr), function(i) {
> hrBB[[i]]$UD * (nrow(tr[[i]]) / sum(sapply(tr, nrow)))
> })
> UDend<- liUD[[1]]
> for (i in 2:length(liUD))
> UDend<- UDend + liUD[[i]]
>
> But get this error message:
>
> Error in image.default(UDend) : argument must be matrix-like
>
> Any help would be appreciated
> Many thanks
> Louise Soanes
>
>
>
>
> School of Environmental Sciences
> University of Liverpool
> Brownlow Hill
> L69 3GP
>
> www.puffinisland.org.uk
>
>
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>
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-- 
Clément CALENGE
Cellule d'appui à l'analyse de données
Direction des Etudes et de la Recherche
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14