Hi Stef, Thanks so much for your answer and insights. I agree, the kernelbb should be more suitable to explore the behaviour of such species. I was not able to plot the results in a realistic manner (I was getting big squares of different colours and could not manage to get anything realistic but I have not had that much time to play with it yet). I'll try again and see how I go. Kind regards, Elodie
Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email: [email protected] Website: http://hors-des-sentiers-battus.e-monsite.com/ Mobile: (+61) 049 794 0793 -----Original Message----- From: AniMov [mailto:[email protected]] On Behalf Of [email protected] Sent: Tuesday, 19 August 2014 8:00 PM To: [email protected] Subject: AniMov Digest, Vol 102, Issue 9 Send AniMov mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: 1. Re: AniMov Digest, Vol 102, Issue 8 (stefano anile) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Aug 2014 11:33:18 +0100 From: stefano anile <[email protected]> To: "[email protected]" <[email protected]> Subject: Re: [AniMov] AniMov Digest, Vol 102, Issue 8 Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi Elodie, ? glad to see that you move to explore also the BB approach.? However, I am sorry but I don't see the point of comparing the "traditional" kernel estimation with the BB approach, because the BB approach lies on a quite different assumption (time spent in an area) so comparison with "traditional" kernel could make no sense, although as stated in some papers, usually the Kernel estimation and the BB estimation are quite comparable. I ?would guess that the problem here is with the different methods used to calculate the overlap, e.g. BA and UDOI. Might be useful to carefully go further into the details of such methods as they are quite different in their outputs. Additionally, according to what I can figure out from the behaviour of your species (penguin), I personally think that the BB approach should be more "realistic" than the kernel as "foraging" movements from one patch of food (schools of fish) to another should be probably better "described" by the former approach.? >From the code you posted, it seems like everything is fine. One additional tip, what happened if you plot the two approach (traditional kernel vs BB)? A visual inspection of what the models do can drive you into the topic better than numbers. ? All the best Stef Il Luned? 18 Agosto 2014 12:00, "[email protected]" <[email protected]> ha scritto: Send AniMov mailing list submissions to ??? [email protected] To subscribe or unsubscribe via the World Wide Web, visit ??? http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to ??? [email protected] You can reach the person managing the list at ??? [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: ? 1. interpretation of kerneloverlap and kerneloverlaphr ? ? ? (Elodie Camprasse) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Aug 2014 14:34:07 +1000 From: "Elodie Camprasse" <[email protected]> To: <[email protected]> Subject: [AniMov] interpretation of kerneloverlap and kerneloverlaphr Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" G'day everyone, I am working on tracking data from penguins and would like to determine the consistency of space use from each of my individuals from one trip to the next. I calculated kerneloverlap between consecutive trips (standard kernel) and wanted to compare the results of the kerneloverlaphr after using the Brownian bridge model. I am not understanding the results I am getting, however, and I was hoping someone could help me understand them. I pretty much get opposite results (in the case of kerneloverlap, the individuals are consistent from one trip to the next, and in the case of kerneloverlaphr, they are not). I have created a reproducible example (csv attached) where an individual has GPS coordinates for two consecutive trips. I used the following code: test2_kernel<-read.csv("reproducible_example_kerneloverlap2.csv", header=T) # Try the kerneloverlap approach test2_kernel_df<-SpatialPointsDataFrame(coords=test2_kernel[, c(2,3)], data=test2_kernel[, c(1,4)], proj4string = CRS("+proj=utm +zone=55 +south +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs"), bbox = NULL) test2_kernel_BA<-kerneloverlap(test2_kernel_df[,1], grid=200, meth="BA") test2_kernel_BA test2_kernel_UDOI<-kerneloverlap(test2_kernel_df[,1], grid=200, meth="UDOI") test2_kernel_UDOI # Try the kernelbb and then kerneloverlaphr approach test2_kernel$timestamp <-as.POSIXct(strptime(as.character(test2_kernel$timestamp),"%d/%m/%Y %H:%M"), "GMT") test2_coords<-test2_kernel[, c(2,3)] test2_coords_meters<-project(as.matrix(test2_coords), "+proj=utm +zone=55 +south +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs") test2_coords_meters<-as.data.frame(test2_coords_meters) colnames(test2_coords_meters)<-c("Longitude_meters", "Latitude_meters") test2_kernel$Longitude_meters<-test2_coords_meters$Longitude_meters test2_kernel$Latitude_meters<-test2_coords_meters$Latitude_meters test2_ltraj<-as.ltraj(xy = test2_kernel[,c("Longitude_meters","Latitude_meters")], date = test2_kernel$timestamp, id=test2_kernel$id) lik <- liker(test2_ltraj, sig2 = 4, rangesig1 = c(0, 10)) test2_kernelbb<-kernelbb(test2_ltraj, sig1=5, sig2=4, grid = 200) test2_kernelbb_BA<-kerneloverlaphr(test2_kernelbb, grid=200, meth="BA") test2_kernelbb_BA test2_kernelbb_UDOI<-kerneloverlaphr(test2_kernelbb, grid=200, meth="UDOI") test2_kernelbb_UDOI. In the kerneloverlap approach, I am getting high indices, like this: test2_kernel_BA ? ? ? ? ? 1st_trip? 2nd_trip 1st_trip 0.9998753 0.8604860 2nd_trip 0.8604860 0.9998635 > test2_kernel_UDOI ? ? ? ? ? 1st_trip? 2nd_trip 1st_trip 1.4040774 0.7812684 2nd_trip 0.7812684 1.3015604 In the kerneloverlap approach, I am getting low indices, like this: test2_kernelbb_BA ? ? ? ? ? 1st_trip? 2nd_trip 1st_trip 1.0000000 0.1375754 2nd_trip 0.1375754 1.0000000 > test2_kernelbb_UDOI ? ? ? ? ? 1st_trip? 2nd_trip 1st_trip 6.46508189 0.02059335 2nd_trip 0.02059335 2.75579098 Could anyone tell me what I'm missing please? Your help would be greatly appreciated! Kind regards, Elodie Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email:? <mailto:[email protected]> [email protected] Website:? <http://hors-des-sentiers-battus.e-monsite.com/> http://hors-des-sentiers-battus.e-monsite.com/ Mobile:? <tel:%28%2B61%29%20049%20794%200793> (+61) 049 794 0793 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.faunalia.it/pipermail/animov/attachments/20140818/ba58755b/att achment-0001.html> ------------------------------ Subject: Digest Footer _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov ------------------------------ End of AniMov Digest, Vol 102, Issue 8 ************************************** -------------- next part -------------- An HTML attachment was scrubbed... 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