Thanks a lot for pointing me in the direction Mathieu! It makes more sense now! Kind regards, Elodie
Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email: elodie.campra...@gmail.com Website: http://hors-des-sentiers-battus.e-monsite.com/ Mobile: (+61) 049 794 0793 -----Original Message----- From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of animov-requ...@faunalia.it Sent: Wednesday, 13 August 2014 8:00 PM To: animov@faunalia.it Subject: AniMov Digest, Vol 102, Issue 6 Send AniMov mailing list submissions to animov@faunalia.it 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 animov-requ...@faunalia.it You can reach the person managing the list at animov-ow...@faunalia.it When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: 1. Re: Problem with kerneloverlap output when method=HR (Mathieu Basille) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Aug 2014 09:16:52 -0400 From: Mathieu Basille <basille....@ase-research.org> To: Animal Movement <animov@faunalia.it> Cc: elodie.campra...@gmail.com Subject: Re: [AniMov] Problem with kerneloverlap output when method=HR Message-ID: <53ea13c4.3050...@ase-research.org> Content-Type: text/plain; charset=windows-1252; format=flowed Dear Elodie, Who said that overlaps had to be symmetrical? Based on your data, this should make it clearer: library(adehabitatHS) locs <- read.csv("reproducible_example_kerneloverlap.csv") coordinates(locs) <- ~Longitude+Latitude mcp1 <- mcp(locs[, 1]) plot(mcp1) As you can see, the MCP of the first trip is (almost) entirely included in the MCP of the second trip. But the reverse is not true. Also please check the ref from the doc [1], where you will find why, and which is the best overlap estimate that suits your needs (hint: MCP is generally not). Last but not least, not sure that lat/long degrees makes sense when it comes to overlap... You might want to project your data in some local coordinate system. Best, Mathieu. [1] Fieberg, J. and Kochanny, C.O. (2005) Quantifying home-range overlap: the importance of the utilization distribution. Journal of Wildlife Management, 69:1346-1359. Le 11/08/2014 02:40, Elodie Camprasse a ?crit : > G?day folks, > > I am encountering a problem when working with the function kerneloverlap in > the package adehabitatHR. I am trying to calculate the overlap in home > ranges within consecutive trips of the same animal. In order to use the > function, I first created the spatialPointsDataFrame object called example > from a dataframe that has in order, a column with the ID (trip number), one > column with Longitude, one column with Latitude and a column with a > timestamp (see attached csv) like this: > > example_df<-SpatialPointsDataFrame(coords=example[, c(2,3)], data=example[, > c(1,4)], proj4string = CRS("+proj=longlat +ellps=WGS84")). > > From the output I get (below), I deduce that creating this new object has > worked. > > class : SpatialPointsDataFrame > > features : 130 > > coord. ref. : +proj=longlat +ellps=WGS84 > > variables : 2 > > names : id, timestamp > > min values : 1st_trip, 15/10/2013 18:18 > > max values : 2nd_trip, 18/10/2013 6:54 > > When I try to use the kerneloverlap function however, I get an output that > I don?t understand. > > > > kerneloverlap(example_df[,1], meth="HR") > > 1st_trip 2nd_trip > > 1st_trip 1.0000000 1 > > 2nd_trip 0.4895288 1 > > I am not sure why the results are not symmetrical (in one instance the overlap between trip 1 and 2 is 1, in the other it is 0.4895288?). Trying the first calculate the UD distribution with kernelUD and using the function kerneloverlaphr to calculate the overlap yielded the same result. I thought that would have fixed the problem as I read on the forums that inconsistent output could come from the grid size changing from individual to individual (or in my case trip to trip) but using the parameter same4all=TRUE and conditional=TRUE for kerneloverlaphr did not provide a different result. > > Could someone let me know if I have made a mistake and how to fix it > please? Thanks in advance! > > Kind regards, > > Elodie > > Elodie Camprasse > > 6/187 Auburn Road > > Hawthorn, VIC 3122 > > Australia > > Email: elodie.campra...@gmail.com <mailto:elodie.campra...@gmail.com> > > Website: http://hors-des-sentiers-battus.e-monsite.com/ > > Mobile: (+61) 049 794 0793 <tel:%28%2B61%29%20049%20794%200793> > > > > _______________________________________________ > AniMov mailing list > AniMov@faunalia.it > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > -- ~$ whoami Mathieu Basille, PhD ~$ locate --details 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 ?luard ------------------------------ Subject: Digest Footer _______________________________________________ AniMov mailing list AniMov@faunalia.it http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov ------------------------------ End of AniMov Digest, Vol 102, Issue 6 ************************************** _______________________________________________ AniMov mailing list AniMov@faunalia.it http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
